Liquid Crystal Biosensors

Transcription

1 Liquid Crystal Biosensors A thesis submitted to the University of Manchester for the degree of Doctor of Engineering in the faculty of Engineering and Physical Sciences 011 Thomas Cronin School of Physics and Astronomy 1

2 Contents Chapter 1 Introduction (31) 1.1 Biosensors and liquid crystals (31) 1. Sharp Laboratories of Europe (34) 1.3 Sociological drivers for the research project (35) 1.4 Commercial drivers for the research project (36) 1.5 Position of the project within SLE's corporate strategy (37) 1.6 Progression of the project (38) 1.7 Commercial value of the current state of the project and further development needed for commercialisation (40) 1.8 Potential markets for the project (41) 1.9 Structure of the thesis (41) Chapter Existing Work in the Field of Liquid Crystal Biosensors, a Literature Review (43).1 Surface bound analytes (44).1.1 Oblique gold (44).1. Detection of gaseous analytes (46).1.3 Detection of DNA (46).1.4 Substrates without a gold layer (46).1.5 Investigations into the system parameters important for analyte detection (47).1.6 Quantification of analyte binding (51).1.7 Modelling the effects of surface bound analytes on LC alignment (5). LC-aqueous interfaces (54)..1 LC films supported by copper and gold grids (54).. DNA detection at LC-aqueous interfaces (57)..3 Modelling of the effect of analytes bound at the LCaqueous interface on LC alignment (57).3 Detection of analytes in the liquid crystal bulk (57).4 Non-optical detection (58)

3 .5 Wearable sensors (59).6 Summary (59) Chapter 3 Liquid Crystal Theory (63) 3.1 Introduction to liquid crystals (63) 3. Liquid crystal phases (65) 3.3 Chirality (67) 3.4 The nematic order parameter (69) 3.5 The birefringence of liquid crystals (71) 3.6 Dielectric anisotropy (73) 3.7 Liquid crystal alignment (75) 3.8 Liquid crystal textures (77) 3.9 Elastic Constants (81) 3.10 Measuring the elastic constants of nematic liquid crystals (8) 3.11 Anchoring energy (87) Surface chemistry (87) Surface topography: grooved surfaces (89) 3.1 Particles in liquid crystals (93) 3.13 Summary (95) Chapter 4 Modelling a Biological Analyte with Latex Beads (98) 4.1 Introduction (98) 4. Materials used (99) 4..1 Biotin coated beads and streptavidin coated surfaces (99) 4.. Liquid crystals (101) 4.3 Cell construction (101) Measurements of cell thickness (103) 4.4 Optical polarized microscopy (104) Conoscopy (106) 4.5 Results (107) Testing alignment layers (108) 4.5. Imaging beads with 5CB (109) Sensitivity of 5CB to UV illumination (111) 3

4 4.5.4 Imaging beads with ZLI 1695 (11) 4.6 Investigation into bead-surface binding patterns (115) 4.7 Summary (116) Chapter 5 Modelling a Biological Analyte Using Gold Microdots (119) 5.1 Introduction (119) 5. Introduction to liquid crystals used (11) 5.3 Refractive index measurements (13) 5.4 Capacitance measurements using commercial cells (15) Elastic constants calculated from capacitance measurements (16) 5.5 Substrate construction (130) 5.6 SAM construction (13) 5.7 Cell fabrication (134) 5.8 Optical polarising microscopy (135) 5.9 Summary (139) Chapter 6 Ancillary Results Physical Properties of Liquid Crystals (140) 6.1 Refractive index measurements (140) 6. Elastic constants measurements (149) 6.3 Summary (157) Chapter 7 The Effect of Controlling Surface Chemistry Using Thiols (159) 7.1 Images of the behaviour of the 5CB on the surfaces (160) Plain Au (161) 7.1. Alcohol thiol: 3-mercapto-1-propanol (165) Acid thiol: 3-mercaptopropionic acid (166) 7. Reflection of monochromatic light as a function of temperature (168) 7..1 Plain Au (166) 4

5 7.. Alcohol thiol: 3-mercapto-1-propanol (173) 7..3 Acid thiol: 3-mercaptopropionic acid (175) 7.3 Discussion (178) 7.4 Summary (179) Chapter 8 The Effect of Cell Thickness (181) 8.1 Nominal 7.5µm thickness (183) 8. Nominal 10.0µm thickness (187) 8.3 Nominal 1.7µm thickness (191) 8.4 Nominal 40.0µm thickness (194) 8.6 Discussion (197) Intensity vs. thickness (198) 8.7 Summary (01) Chapter 9 The Effects of Different Liquid Crystals (03) 9.1 5CB (04) 9. E7 (08) 9.3 ZLI 1695 (14) 9.4 ZLI 113 (19) 9.5 MDA (5) 9.6 Discussion (31) Optical textures in the nematic phase (3) 9.6. Optical textures on heating and cooling (34) The relationship between peak height and birefringence (35) The relationship between peak height and elasticity (37) 9.7 Summary (41) Chapter 10 The Effects of Spot Size and Separation, Array Properties (43) 10.1 µm spot diameter, 5µm array pitch (44) 10. 4µm spot diameter, 7µm array pitch (46) µm spot diameter, 10µm array pitch (48) 5

6 10.4 4µm spot diameter, 0µm array pitch (50) µm spot diameter, 40µm array pitch (5) µm spot diameter, 0µm array pitch (54) µm spot diameter, 40µ array pitch (56) 10.8 Reflected intensities (58) µm spot diameter, 5µm array pitch (58) µm spot diameter, 7µm array pitch (59) µm spot diameter, 10µm array pitch (59) µm spot diameter, 0µm array pitch (61) µm spot diameter, 40µm array pitch (6) µm spot diameter, 0µm array pitch (6) µm spot diameter, 40µm array pitch (63) 10.9 Discussion (64) The effect of spot size (64) The effect of spot separation (68) Summary (71) Chapter 11 Conclusions (7) 11.1 Measurements taken and effects observed (74) 11. Summary of results (73) 11.3 Implications for biosensor design (74) 11.4 Future work (74) Appendix A Calculating the Elastic Constants (77) A.1 Modelling the permittivity curve (77) A. Permittivity calculations and the elastic constants (79) Appendix B Fitting Using MATLAB (9) B.1 Fredhybridpre (93) B. Fredhybridpreepsfit (96) 6

7 List of Figures Figure 3.1 A model of the chemical structure of the liquid crystal 5CB as a rigid rod. The length of the rod in the z axis is longer than in the x and y axes. The dotted line represents the prolate spheroid shape of a usual mesogen model. (65) Figure 3. Orientation of calamitic mesogens in a nematic liquid crystal. (66) Figure 3.3 (a) Schematic of the layered structure of the Smectic A phase. (b) Schematic of the layered structure of the smectic C phase. (67) Figure 3.4 The helical orientation of mesogens in a cholesteric liquid crystal. Note, this does not indicate a layered structure, as in the case of smectic phases. (68) Figure 3.5 Azimuthal rotation of mesogen tilt between the layers of the SmC* phase. (69) Figure 3.6 Orientational order parameter, S, as a function of T/T NI for a typical nematic. [Redrawn from reference 10, pg 133]. (71) Figure 3.7 Indicatrix of optically positive and optically negative uniaxial mediums. [Figure redrawn from reference 11, pg 36.] (7) Figure 3.8 Diagram showing how the indicatrix interacts with light propagating in direction k, to give n e. [Figure redrawn from reference 13, pg 87.] (73) 7

8 Figure 3.9 Different alignments of liquid crystal mesogens on glass substrates in the x, y plane. (a) Random planar orientation of mesogens lying in the plane of the substrate. (b) Aligned, homogeneous planar orientation. (c) Homeotropic orientation with mesogens orientated at 90 to the x, y plane. [Figure redrawn from reference 11, pg.] (75) Figure 3.10 Surfactant induced homeotropic alignment. (a) Sufficient concentration of amphiphiles allows steric interdigitation with LC mesogens. (b) Too high a concentration of amphiphiles prevents alignment. [Figure redrawn from reference 1, pg 8.] (76) Figure 3.11 Strength, molecular alignment and Schlieren brushes of the four defect types seen in nematic liquid crystals. [Figure redrawn from references1, pg 138] (79) Figure 3.1 (a) Vertical cross-section of a pair of Dupin cyclides. (b) Smectic A focal-conic domain. [Figures from reference 1, pg 184 and reference 4, pg 3 respectively] (80) Figure 3.13 Arrangement of tangential focal conics building up polygonal domains. [From reference 14, pg 468.] (80) Figure 3.14 Schematics of the three fundamental elastic deformations of nematic liquid crystals 9 showing the change in n with respect to x, y and x for each deformation. 6 [Figure redrawn from reference 9, pg 60, and reference 6, pg 1.] (81) Figure 3.15 A planar aligned nematic liquid crystal cell. (a) With no electric field. (b) With an electric field perpendicular to the plane of the substrates with V>V 0. [Figure redrawn from reference 1, pg 09.] (83) Figure 3.16 The behaviour of the permittivity of a planar nematic liquid aligned cell in response to a potential difference across the cell. (84) 8

9 Figure 3.17 Schematic of a pure twist cell. [Figure redrawn from reference 1, pg 14.] (88) Figure 3.18 The director of a nematic liquid crystal on a grooved glass substrate. (a) With the director aligned perpendicular to the grooved direction. (b) With the director aligned parallel to the grooves, out of the page. [Figure redrawn from reference 39, pg 13.] (90) Figure 3.19 A Schematic one of the planar micro textured surface used by Batalioto et al. [Figure redrawn from reference 40, pg 1.] (9) Figure 3.0 Schematic of a possible director distortion about a spherical particle with homeotropic anchoring producing a quadrupole deformation with a disclination loop. [Figure redrawn from reference 41, pg 959] (93) Figure 3.1 Three different director configurations around a particle with homeotropic anchoring. (a) Dipole deformation with hedgehog defect. (b) Quadrupole with Saturn ring disclination loop (represented by the dotted line). (c) Quadrupole without disclination loop (weak anchoring). [Figure from redrawn from reference 4, pg 168.] (94) Figure 3. The director profile around a particle with planar anchoring. The two surface defects or boojums are generated to meet the surface boundary conditions. [Figure from reference 43, pg 66.] (95) Figure 4.1 The chemical structure of Biotin. (100) Figure 4. Chemical structure of 5CB. (101) Figure 4.3 Schematic of cell construction. (10) 9

10 Figure 4.4 Schematic of optical observation by polarising microscopy. The addition of the ultra violet arm is specific to this investigation. (105) Figure 4.5 Schematic diagram of the light paths that form a conoscopic image. [Figure redrawn from reference 0.] (106) Figure 4.6 Characteristic Maltese cross and concentric dark circles of a uniaxial, homeotropic liquid crystal under conoscopic observation. [Figure redrawn from reference 3, pg 16.] (107) Figure 4.7 Polarized microscopic images of cells with: (a) Plain glass coverslip, at an angle of minimal optical transmission relative to the polariser directions. (b) PVA coated coverslip, rubbed left to right, at an angle of optical extinction. (c) Lecithin coated coverslip; the circular defect is the result of a water mark on the glass and is included as a reference for the dark appearance. (108) Figure 4.8 Microscopic images of the edge of the circular bead stain for cells filled with 5CB. (a, d, g and j) White light transmission without polarisers. (b, e, h and k) UV illumination in reflection without polarisers. (c, f, i and l) White light transmission through crossed polarisers. The bead concentrations in suspension prior to deposition are: (a-c) 1% (d-f) 0.5%, (g-i) 0.05%, (j-l) 0.01%; the images were taken at 5 C (nematic phase). (110) Figure 4.9 Images of an air bubble in 5CB. (a) White light illumination in transmission through uncrossed polarisers. (b) White light transmission through crossed polarisers after minutes UV exposure. (11) Figure 4.10 Microscopic images of the edge of the circular bead stain for cells filled with ZLI (a, c, e, g and i) White light transmission without polarisers (b, d, f, h and j) White light transmission through crossed polarisers. The bead concentrations in suspension prior to deposition are: (a+b) 0.01%, (c+d) 0.005%, (e+f) 0.005%, (g+h) %, (i+j) %. Bead concentrations below this did not cause a visible alignment change. (113) 10

11 Figure 4.11 Fluorescence image from Amersham Biosciences, Typhoon Trio + Variable Mode Imager. The image was taken with illumination from a 633 nm laser and 670nm BP30nm filter. Extremely low contrast imaging shows initial binding of biotin beads to substrate post rinsing. (116) Figure 5.1 Polarised optical micrographs of the behaviour of 5CB on a silicon substrate with raised gold dots as the liquid crystal is heated through the nematic to isotropic transition. (a) 30 C. (b) 35.3 C (=T NI ). (c) 36 C. (The images were taken in reflection with a homeotropically aligned coverslip.) (10) Figure 5. Schematic diagrams of the chemical structures of the liquid crystals and their components. (a) 5CB, (b) 7CB, (c) 8OCB, (d) 5CT, (e) cyano-cyclohexylcyclohexane, (f) cyano-phenylcyclohexane. 3 R represents the different alkyl chains of the molecules. (1) Figure 5.3 Schematic of the prisms of an Abbé Refractometer. (14) Figure 5.4 Schematic of the director profile of a planar aligned cell filled with nematic liquid crystal. (a) with no applied voltage (b) with a voltage greater than the Freedericksz threshold applied between the surfaces of the cell. (17) Figure 5.5 A side profile of the photolithographic process used to manufacture the Au-Si substrates. (In reality the mask is much closer to the top layer of photo-resist than it appears here and diffraction of the incident radiation has been exaggerated for clarity.) (a) Ultraviolet light passing through the mask softens and breaks down the top layer, the imaging resist. Developer is then used to remove the patterned imaging resist along with a slightly larger area of liftoff resist. (b) An Au film is then deposited, by vapour deposition, over the whole area of the wafer. The bi-layer, under-cut resist profile promotes discontinuous deposition between the top and bottom layers of gold. All remaining resist is then removed leaving just the bottom island of gold. (130) Figure 5.6 Schematic of the layout of the arrays on each substrate. Array Series 1 and are duplicates. (13) 11

12 Figure 5.7 Schematic diagram of a thiol SAM on a gold surface, the hydrocarbon chain length and functional R group differs between thiols. (133) Figure 5.8 Chemical structures of the two thiols used: (a) 3-Mercapto-1-propanol, (b) 3-Mercaptopropionic Acid. Figures from Sigma-Aldrich product data sheets. (134) Figure 5.9 Schematic of a liquid crystal cell constructed with a patterned gold-silicon substrate. (135) Figure 5.10 Schematic of optical polarised microscope set up for measuring the effect of Au-Si patterned substrates on liquid crystal alignment. (136) Figure 5.11 Polarised optical images of the behaviour of 5CB in the nematic phase on an array of 3x6µm Au spots. The tilted planar alignment of the liquid crystal on the spots can be seen as the sample is rotated. (The images were taken in reflection with a homeotropically aligning coverslip and a 0x objective. There is a 0 rotation between frames. The large defect on the clean area of the substrate is included as a reference point.) (137) Figure 5.1 The reflected light intensity from homeotropically aligned MDA on an array of circular plain gold microdots 8µm in diameter, separated by 0µm. The sample was cooled at a rate of 1 C.min -1. (138) Figure 6.1 Variation of refractive index with temperature for E7, including a comparison with results from reference 3. (14) Figure 6. Birefringence of E7, measured values compared with those from reference 3. (143) Figure 6.3 Variation of refractive index with temperature for 5CB. (144) 1

13 Figure 6.4 Variation of refractive index with temperature for ZLI (145) Figure 6.5 Variation of refractive index with temperature for ZLI 113. (146) Figure 6.6 Variation of refractive index with temperature for MDA (147) Figure 6.7 Comparison of the birefringence of the liquid crystals as a function of reduced temperature as they are heated towards the isotropic phase. (148) Figure 6.8 Comparison of fitted values of K 11 for E7 as a function of reduced temperature with results obtained by others (see references 3, 11 and 1). (150) Figure 6.9 Comparison of fitted values of K 33 for E7 with results obtained by others (see references 3 and 1). (151) Figure 6.10 Comparison of fitted values of K 11 for 5CB with values obtained by others (see references 11 and 14). (15) Figure 6.11 Calculated values of K 33 for 5CB as a function of reduced temperature. (153) Figure 6.1 Fitted values of K 11 and K 33 for ZLI 1695 as a function of reduced temperature. (153) Figure 6.13 Fitted values of K 11 and K 33 for ZLI 113 as a function of reduced temperature. (155) 13

14 Figure 6.14 Fitted values of K 11 and K 33 for MDA as a function of reduced temperature. (155) Figure 6.15 Comparison of fitted values of K 11 for the five LCs investigated as a function of reduced temperature. (155) Figure 6.16 Comparison of fitted values of K 33 for the five LCs investigated. (156) Figure 6.17 Comparison of the fitted values of K 33 /K 11 for the five LCs investigated. (157) Figure 7.1 Microscopic images of a ~10µm thick 5CB cell in the nematic phase. a) With no polarisers. b) With crossed polarisers. The left half of the bottom substrate is coated in a layer of gold ~500nm thick. T-T NI =-4.8K. (161) Figure 7. Polarised microscopy images of the edge of the Au layer as the substrate is rotated between the polarisers. T-T NI =-0.8 C (16) Figure 7.3 Microscopic images of the gold-glass border of a ~10µm thick 5CB cell as it is heated through the nematic-isotropic transition at 1 C.min -1. (a) No polarisers. (b-d) Crossed polarisers for sequential heating. (163) Figure 7.4 Microscopic images of the gold-glass border of a ~10µm thick 5CB cell as it is cooled through the nematic-isotropic transition at -1 C.min -1. (a) No polarisers. (b-d) Crossed polarisers for sequential cooling. (164) 14

15 Figure 7.5 Microscopic images of the gold-glass border of a 5CB cell ~10µm thick. The cell has an alcohol terminated SAM on the gold surfaced substrate. (a) No polarisers. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers for heating through the nematic-isotropic transition at 1 C.min -1. (d) Crossed polarisers for cooling through the isotropic-nematic transition at -1 C.min -1. (165) Figure 7.6 Microscopic images of the gold-glass border of a 5CB cell ~10µm thick. The cell has an acid terminated SAM on the gold surfaced substrate. (a) No polarisers. (b) Crossed polarisers in the nematic phase. (c-d) Crossed polarisers for sequential heating through the nematic-isotropic transition at 1 C.min -1. (e-f) Crossed polarisers for sequential cooling through the isotropic-nematic transition at - 1 C.min -1. (167) Figure 7.7 Reflected intensity of 5CB on a plain gold substrate as it is heated through the nematic-isotropic transition. The cell is 7.9µm thick. The dotted line represents the nematic to isotropic transition. (169) Figure 7.8 Reflected intensity of 5CB on a plain gold substrate as it is cooled from the isotropic to the nematic phase at a rate of -1 C.min -1. The area of measurement is 7.9µm thick. (170) Figure 7.9 Reflected intensity of 5CB on a plain gold coated substrate as it is rotated between crossed polarisers. The spread of data at a single point is shown at 0 rotation. The area of measurement is 7.9µm thick. (171) Figure 7.10 Reflected intensity of 5CB on a plain gold coated substrate as it is rotated between crossed polarisers. The area of the cell analysed is different from that in Figure 7.9. The spread of data at a single point is shown at 0 rotation. The area of measurement is 7.7µm thick (17) Figure 7.11 Reflected intensity of 5CB on a plain gold coated substrate at the angle of maximum intensity. Measurements are taken for the same area over a long period of time. The area of measurement is 7.9µm thick. (173) Figure 7.1 Reflected intensity of 5CB on a gold substrate with an alcohol terminated SAM as it is (a) heated and (b) cooled through the nematic-isotropic transition. The area of measurement is 6.0µm thick. (The dotted line marks the nematic to isotropic transition temperature on heating.) (174) 15

16 Figure 7.13 Reflected intensity of 5CB on a gold substrate with an alcohol terminated SAM as it is cooled from the isotropic to the nematic phase. The substrate is rotated between crossed polarised. (a) First area, day one, 6.0µm thick. (b) Second area, two days later, 7.7µm thick. (175) Figure 7.14 Reflected intensity of 5CB on a gold substrate with an acid terminated SAM as it is (a) cooled and (b) heated through the nematic-isotropic transition. Measurements are shown at the angle of maximum intensity. The area of measurement is 1.5µm thick. (176) Figure 7.15 Reflected intensity of 5CB on a gold substrate with an acid terminated SAM as it is cooled through the isotropic-nematic transition. (a) First area, 1.5µm thick. (b) Second area, 1.5µm thick. Data were taken on the same day, approximately 30 minutes apart. (176) Figure 7.16 Reflected intensity of 5CB on a gold substrate with an acid terminated SAM as it is cooled through the isotropic-nematic transition. Data was taken from the same area over a two day period. The variation between days is within the difference in a single day. The cell is 1.5µm thick. (177) Figure 8.1 A schematic of the silicon substrates showing the relative position of the arrays of interest and the positions of the thickness measurements. (18) Figure 8. Microscopic images of a cell filled with 5CB and an acid terminated SAM. The nominal thickness is 7.5µm. Images show Array 1 with spot diameter 8µm and array pitch 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. Images were taken with white light. (184) Figure 8.3 Polarising microscopy images of a cell with a nominal thickness of 7.5µm filled with 5CB and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1, 7.7µm thick. (b) Array, 7.7µm thick. (c) Array 3, 7.4µm thick. (d) Array 4, 7.4µm thick. Images were taken with white light. (185) 16

17 Figure 8.4 Reflected intensity of monochromatic light from a cell filled with 5CB on cooling. (a) Array 1, 7.7µm thick. (b) Array, 7.7µm thick. (c) Array 3, 7.4µm thick. (d) Array 4, 7.4µm thick. (186) Figure 8.5 Microscopic images of a cell filled with 5CB and an acid terminated SAM. The nominal cell thickness is 10.0µm. Images show Array 1 with spot diameter 8µm and array pitch 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. Images were taken with white light. (187) Figure 8.6 Polarising microscopy images of a cell with a nominal thickness of 10.0µm, filled with 5CB and an acid terminated SAM. Four different arrays of 8µm gold spots separated by 0µm are observed. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1, 9.4µm thick. (b) Array, 9.4µm thick. (c) Array 3, 8.5µm thick. (d) Array 4, 8.5µm thick. Images were taken with white light. (188) Figure 8.7 Reflected intensity from of monochromatic light from a cell filled with 5CB on cooling. (a) Array 1, 9.4µm thick. (b) Array, 9.4µm thick. (c) Array 3, 8.5µm thick. (d) Array 4, 8.5µm thick. (189) Figure 8.8 Microscopic images of a cell filled with 5CB and an acid terminated SAM. The nominal thickness is 1.7µm. Images show Array 1 with spot diameter 8µm and array pitch 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. Images were taken with white light. (191) Figure 8.9 Polarising microscopy images of a cell with a nominal thickness of 1.7µm, filled with 5CB and an acid terminated SAM. Four different arrays of 8µm gold spots separated by 0µm are observed. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1, 13.0µm thick. (b) Array, 13.0µm thick. (c) Array 3, 1.7µm thick. (d) Array 4, 1.7µm thick. Images were taken with white light. (19) Figure 8.10 Reflected intensity of monochromatic light from a cell filled with from 5CB on cooling. (a) Array 1, 13.0µm thick. (b) Array, 13.0µm thick. (c) Array 3, 1.7µm thick. (d) Array 4, 1.7µm thick. (193) 17

18 Figure 8.11 Microscopic images of a cell filled with 5CB and an acid terminated SAM. The nominal thickness is 40.0µm. Images show Array 1 with spot diameter 8µm and array pitch 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. Images were taken with white light. (194) Figure 8.1 Polarising microscopy images of a cell with a nominal thickness of 40.0µm filled with 5CB and an acid terminated SAM. Four different arrays of 8µm gold spots separated by 0µm are observed. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1, 40.0µm thick. (b) Array, 40.0µm thick. (c) Array 3, 36.5µm thick. (d) Array 4, 36.5µm thick. Images were taken with white light. (195) Figure 8.13 Reflected intensity of monochromatic light from a cell filled with from 5CB on cooling. (a) Array 1, 40.0µm thick. (b) Array, 40.0µm thick. (c) Array 3, 36.5µm thick. (d) Array 4, 36.5µm thick. (196) Figure 8.14 Monochromatic reflected intensity peak height plotted against sin (πd. n/λ 0 ). (00) Figure 9.1 Polarising microscopy images of a cell ~9µm thick filled with 5CB and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (05) Figure 9. Reflected intensity from a cell filled with 5CB on heating through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (06) Figure 9.3 Reflected intensity from a cell filled with 5CB on cooling through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (07) Figure 9.4 Optical microscopy images of a cell ~9µm thick filled with E7 and an acid terminated SAM over an array of 8µm gold spots separated by 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. (08) 18

19 Figure 9.5 Polarising microscopy images of a cell ~9µm thick filled with E7 and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (09) Figure 9.6 Reflected intensity from a cell filled with E7 on heating through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (10) Figure 9.7 Polarising microscopy images of a cell ~9µm thick filled with E7 and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (11) Figure 9.8 Reflected intensity from a cell filled with E7 on cooling through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The dotted lines represent the width of the biphasic temperature range. (1) Figure 9.9 Optical microscopy images of a cell ~9µm thick filled with ZLI 1695 and an acid terminated SAM over Array 3 of 8µm gold spots separated by 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. (15) Figure 9.10 Polarising microscopy images of a cell ~9µm thick filled with ZLI 1695 and an acid terminated SAM over three different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array. (b) Array 3. (c) Array 4. (16) Figure 9.11 Polarising microscopy images of a cell ~9µm thick filled with ZLI 1695 and an acid terminated SAM over three different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array. (b) Array 3. (c) Array 4. (17) Figure 9.1 Reflected intensity from a cell filled with ZLI 1695 on cooling through the nematic to isotropic phase transition. (a) Array. (b) Array 3. (c) Array 4. The dotted lines represent the width of the biphasic temperature range. (18) 19

20 Figure 9.13 Optical microscopy images of a cell ~10µm thick filled with ZLI 113 and an acid terminated SAM over Array 1 of 8µm gold spots separated by 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. (19) Figure 9.14 Polarising microscopy images of a cell ~10µm thick filled with ZLI 113 and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (1) Figure 9.15 Reflected intensity from a cell filled with ZLI 113 on heating through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. () Figure 9.16 Polarising microscopy images of a cell ~10µm thick filled with ZLI 113 and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (3) Figure 9.17 Reflected intensity from a cell filled with ZLI 113 on cooling through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The dotted lines represent the width of the biphasic temperature range. (4) Figure 9.18 Optical microscopy images of a cell ~8µm thick filled with MDA and an acid terminated SAM over Array 1 of 8µm gold spots separated by 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. (6) Figure 9.19 Polarising microscopy images of a cell ~8µm thick filled with MDA and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (7) 0

21 Figure 9.0 Reflected intensity from a cell filled with MDA on heating through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (8) Figure 9.1 Polarising microscopy images of a cell ~8µm thick filled with MDA and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. (9) Figure 9. Reflected intensity from a cell filled with MDA on cooling through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The dotted lines represent the width of the biphasic temperature range. (30) Figure 9.3 Graphs of peak height on (a) heating and (b) cooling plotted against the retardance of the liquid crystals at the phase transition. (36) Figure 9.4 Graphs of peak height on (a) heating and (b) cooling plotted against the birefringence of the liquid crystals at the phase transition. (37) Figure 9.5 Graphs of peak height on (a) heating and (b) cooling plotted against the elastic constant K 11 of the liquid crystals at the phase transition. (38) Figure 9.6 Graphs of peak height on (a) heating and (b) cooling plotted against the elastic constant K 33 of the liquid crystals at the phase transition. (39) Figure 9.7 Peak height on (a) heating and (b) cooling plotted against the ratio of the elastic constants of the liquid crystals at the phase transition K 33 / K 11. (40) 1

22 Figure 10.1 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. µm diameter spots, 5µm array pitch (s5p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. (45) Figure 10. Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 4µm diameter spots, 7µm array pitch (4s7p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. (47) Figure 10.3 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 4µm diameter spots, 10µm array pitch (4s10p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. (49) Figure 10.4 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 4µm diameter spots, 0µm array pitch (4s0p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. (51) Figure 10.5 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 4µm diameter spots, 40µm array pitch (4s40p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. (53) Figure 10.6 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 8µm diameter spots, 0µm array pitch (8s0p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1, Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1, Array Series 1 and. (55)

23 Figure 10.7 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 16µm diameter spots, 40µm array pitch (16s40p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1, Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1, Array Series 1 and. (57) Figure 10.8 Reflected intensity on cooling of 5CB on acid SAM and s5p array. (a) Array Series 1. (b) Array Series. (58) Figure 10.9 Reflected intensity on cooling of 5CB on an acid SAM and a 4s7p array. (a) Array Series 1. (b) Array Series. (59) Figure Reflected intensity on of 5CB on an acid SAM and a 4s10p array. (a) Heating Array Series 1. (b) Heating Array Series. (c) Cooling Array Series 1. (d) Cooling Array Series. (60) Figure Reflected intensity on cooling of 5CB on an acid SAM and a 4s0p array. (a) Array Series 1. (b) Array Series. (61) Figure 10.1 Reflected intensity on cooling of 5CB on acid SAM, 4s40p. (a) Array Series 1. (b) Array Series. (6) Figure Reflected intensity of 5CB on acid SAM, 16s40p. (a) Cooling Array Series 1. (b) Cooling Array Series. (63) Figure Schematic of the layout of the cell with reference to the thickness at certain points. Array Series 1 and are duplicates. (65) 3

24 Figure Reflected intensity of monochromatic light from arrays with different spot diameters on (a) heating and (b) cooling, plotted against spot size. (67) Figure Reflected intensity of monochromatic light from arrays with 4µm spot diameter on (a) heating and (b) cooling, plotted against spot separation. (69) Figure Images of sequentially clearer defect formation on patterned substrates, numbers refer to the height of the peaks in reflected intensity as the cell is cooled through the isotropic to nematic transition. Array properties are: (a) 4s7p, (b) 4s10p, (c) 4s0p, (d) 16s40p. (70) Figure A.1 The behaviour of the permittivity of a planar aligned nematic liquid crystal in response to a potential across the cell. (78) Figure A. A schematic of the distribution of θ in a planar liquid crystal cell under the influence of an electric field in the z direction. The substrates are in the x-y plane and the liquid crustal has a positive dielectric anisotropy. (80) 4

25 List of Tables Table 0.1 TRLs in the Medical Materiel Regulatory Process. (GLP: Good Laboratory Practice, GCP: Good Clinical Practice, cgmp: current Good Manufacturing Practice, IDE: Investigational Device Exemption, IND: Investigational New Drug, NDA: New Drug Application, BLA: Biologics License Application, PMA: Premarket Approval). (39) Table 5.1. Previously known physical properties of the nematic liquid crystals used. The values are from Merck data sheets. The elastic constants data are from reference 3. Other values for MDA are from reference 4. (13) Table 8.1 A summary of the optical response observed on heating and cooling through the nematic to isotropic phase transition at different cell thicknesses. (197) Table 9.1 A summary of the optical response observed on heating and cooling through the nematic to isotropic phase transition of the different liquid crystals. *Intensity profiles with a distinct peak at the isotropic to nematic phase transition. (31) Table 10.1 A summary of the optical responses observed on heating and cooling through the nematic to isotropic phase transition of 5CB on arrays with different spot diameters. (64) Table 10. A summary of the optical response observed on heating and cooling through the nematic to isotropic phase transition of 5CB for different spot separations. (68) 5

26 Abstract This thesis, Liquid Crystal Biosensors, is submitted by Thomas Cronin for the degree of Doctor of Engineering (EngD) at The University of Manchester on 8 June 011. The aim of the thesis was to identify and hence investigate the physical properties of liquid crystals that influence their potential as components of biosensor devices. Silicon surfaces presenting photolithographically fabricated arrays of 50nm thick gold spots were used as the model for a biosensor that detects the surface binding of a biological analyte. The spots ranged in diameter from µm to 16µm and their spatial separation varied between 5µm to 40µm. A Self Assembled Monolayer (SAM) of the thiol 3-mercaoptopropionic acid was used to control the surface chemistry of the gold. The responses of the nematic liquid crystals 5CB, E7, ZLI 1695, ZLI 113 and MDA to were measured by optical microscopy. The spots were seen to induce a tilted planar alignment in the liquid crystals in their nematic phase for spot diameters down to 4µm and for all separations. Anchoring transitions between different tilt angles were observed between spots for some arrays. This was linked to a change in anchoring energy at the gold, possibly stemming from the angle of gold deposition. When heated through the nematic to isotropic phase transition cross defects were observed to nucleate on the gold spots for all spot sizes above 4µm. On cooling through the transition grid patterns of defects were observed to nucleate pinned between the spots for arrays of spots with length scales between 10µm and 0µm. The birefringence and elastic constants K 11 and K 33 of the liquid crystals were measured for temperatures up to their nematic to isotropic transition points. The birefringences of the liquid crystals at the transition were found to range between and The device thickness was varied between 7µm and 40µm.Values for the elastic constants were found to range between 1pN and 4pN. The intensity of monochromatic light (670nm) reflected from the arrays as the liquid crystals were cooled through the phase transition was found to increase for smaller values of the elastic constants and found to be highest where the grid of defects on the array was observed most clearly. The effect on the intensity of the birefringence and cell thickness was shown to be small compared to the effect of elasticity. Two possible biosensor designs are proposed. The first would identify the presence of a biological analyte at a surface by the change in alignment of a liquid crystal. This type of sensor would be optimised by carefully controlling the anchoring energy of the liquid crystal at the surface to minimise the quantity of surface binding required to induce an anchoring transition. The second would detect the presence at a patterned surface of an analyte by the defects that form over the pattern as the liquid crystal changes between the nematic to isotropic phases. This type of sensor would be optimised by choosing a liquid crystal with small elastic constants at the phase transition and by designing a patterned surface with length scales between 10µm and 0µm. 6

27 Declaration No portion of the work referred to in this thesis has been submitted in support of an application for another degree or qualification of this or any other university of institute of learning. 7

28 Copyright Statement i. The author of this thesis (including any appendices and/or schedules to this thesis) owns certain copyright or related rights in it (the Copyright ) and s/he has given The University of Manchester certain rights to use such Copyright, including for administrative purposes. ii. Copies of this thesis, either in full or in extracts and whether in hard or electronic copy, may be made only in accordance with the Copyright, Designs and Patents Act 1988 (as amended) and regulations issued under it or, where appropriate, in accordance with licensing agreements which the University has from time to time. This page must form part of any such copies made. iii. The ownership of certain Copyright, patents, designs, trade marks and other intellectual property (the Intellectual Property ) and any reproductions of copyright works in the thesis, for example graphs and tables ( Reproductions ), which may be described in this thesis, may not be owned by the author and may be owned by third parties. Such Intellectual Property and Reproductions cannot and must not be made available for use without the prior written permission of the owner(s) of the relevant Intellectual Property and/or Reproductions. iv. Further information on the conditions under which disclosure, publication and commercialisation of this thesis, the Copyright and any Intellectual Property and/or Reproductions described in it may take place is available in the University IP Policy (see in any relevant Thesis restriction declarations deposited in the University Library, The University Library s regulations (see and in The University s policy on presentation of Theses 8

29 The Author Thomas Cronin was born on 7 th April He completed an MPhys in physics at the University of Manchester and graduated first class with honours in 005 before starting this EngD. 9

30 Acknowledgements I would like to thank my academic supervisors Professor Helen Gleeson and Dr Ingo Dierking and my industrial supervisors Dr Harry Walton, Dr Antony Glauser, Dr Pamela Dothie and Dr Martin Tillin for all their help and guidance. I would also like to thank all the members of the Liquid Crystals Physics Group for their moral support. Special mention should go to Dr Paul Brimicombe for acting as a role model and for his clarity of perspective. Finally I would like to thank my parents for their support during the trying times and my girlfriend Kristin for her love and understanding and for putting up with me during my writing up period. 30

31 Chapter 1 Introduction This thesis presents an investigation into the physical parameters of liquid crystal cells with respect to their potential as components of biosensor devices. This work was carried out as part of an Engineering Doctorate degree (EngD). The EngD program is run by the Engineering and Physical Sciences Research Council (EPSRC) and combines academic PhD-level research with commercial project management. EngD students carry out a project with joint supervision from an academic university and an industrial sponsor. The technical research is complimented with a number of taught courses that comprise a Diploma of Management Science. The intention is to inform the student of the commercial and industrial implications of the project and prepare them for work in industrial research. 1 This project was performed as a collaboration between the University of Manchester and Sharp Laboratories OF Europe (SLE). This introduction will briefly explain the essential nature of a biosensor and of the liquid crystalline state of matter. The properties of liquid crystal materials that make them potentially useful as components of a biosensor are also detailed. The company SLE will be introduced along with the industrial motivation behind the project. The current status of the project is assessed with respect to its Technology Readiness Level (TRL) and the steps SLE might take to implement the findings of this thesis into saleable products are outlined. The structure of the thesis will then be explained. 1.1 Biosensors and liquid crystals For the purpose of this thesis a biosensor is defined as a device that quantitatively measures the presence or action of a biological analyte. Biosensors of this type currently find use in the defence forces (for the detection of bio-warfare agents), 3 in hospitals and clinics, and more recently in the home. Typical analytes of sensors in the latter two cases are glucose or insulin, mainly for the control of diabetes. This investigation into the potential use of liquid crystals as components of biosensors was prompted by a research paper by Abbott et al. 4 He showed that a liquid crystal film supported on chemically functionalised substrates could be used to optically 31

32 detect the presence of microscopic quantities of certain biological molecules bound to the surfaces. The liquid crystal (LC) phase is a lesser known state of matter that exists between the well established solid and liquid phases. A defining characteristic of a crystalline solid material is that its molecules have a high degree of order, both in their positioning within the crystalline matrix and in their orientation relative to each other. In a liquid, while molecules may be as densely packed as in a solid, the molecules move around each other with no positional restrictions beyond the liquid s container and the molecular axes have no defined direction. Liquid crystals are materials that have a distinct phase or phases that have properties of both the solid and liquid states. Liquid crystal molecules have well defined anisotropy and are often modelled as small rods or discs. The molecules in a liquid crystal phase have some degree of orientational order and, depending on the type of phase, may also have some degree of positional order whilst still being able to move and flow similar to molecules in a liquid. 5 The use of liquid crystals in displays (LCDs) has long been established. The same properties that make liquid crystals useful in displays also make them potentially useful as biosensors. A critical property of these displays is the flatness and cleanliness of the glass with which they are built. This is because when liquid crystals are confined between glass plates intermolecular interactions cause the liquid crystal molecules to align in certain directions, dependent on the topography of the glass and the chemistry of any surface coating. This surface alignment is determined by the surface anchoring (W, measured in J.m - ) of the liquid crystal molecules to the molecules at the surface. It is this alignment that is crucial for the display to function. As such changes in surface chemistry and nanoscopic perturbations to a glass surface can cause an adjacent liquid crystal to align significantly differently 6 and may have a much greater effect on the functionality of the display than their physical size might suggest. Another crucial property of liquid crystals is that the forced alignment of molecules at a surface will influence the alignment of the molecules some distance away into the liquid crystal material. This is due to weak intermolecular forces that act between the liquid crystal molecules, these forces are comprise the elasticity of the material and in a simple LC phase are often summarised by three elastic constants (K 11, K and K 33, measured in pn) that correspond to three fundamental distortions in 3

33 liquid crystal molecular alignment. 7 Liquid crystals are used in displays because they are birefringent. Light of different polarisation will experience different refractive indices when passing through a liquid crystal sample dependent on the alignment of the liquid crystal molecules relative to the direction of the light. 8 The maximum birefringence of a material is termed n. In a biosensor, these three physical properties: surface anchoring, elasticity and birefringence allow the potential visual detection of biological molecules. Changes in surface chemistry and shape from small quantities of an analyte can change the surface anchoring of the liquid crystal, the alignment of the molecules propagates into the liquid crystal sample due to its elasticity and this alignment can be detected optically due to the material's birefringence. These three properties of liquid crystals are also identified in the literature as being important in determining the response of liquid crystals to changes in surfaces (see Chapter ). This project is concerned with measuring and analysing the effect of surface perturbations in a class of liquid crystals known as thermotropic (their properties change with temperature). Liquid crystal samples are confined between a flat silicon oxide substrate and a glass coverslip separated and held parallel at distances of 7-40µm. The action of biological molecules on a surface are first modelled by nano sized polystyrene beads bound to the silicon and subsequently by an array of microscopic gold circles raised from the silicon surface by 50nm. The effect of these surface changes on the confined liquid crystal film are measured by polarising optical microscopic inspection of the liquid crystal textures, and by measurements of the intensity of light reflected from the sample as it is heated and cooled. Surface chemistry is controlled by the use of Self Assembled Monolayers (SAMs) of thiols on the gold surfaces. Liquid crystals with different values of birefringence and elasticity are used to investigate the effects of these properties on the visualisation of the surfaces. The size and separation of the gold circles is varied to determine the potential spatial resolution detection limits for the size and concentration of biological molecules for this type of system. 33

34 1. Sharp Laboratories of Europe The parent company of our industrial partner, Sharp was founded in Japan in 191 by Tokuji Hayakawa. In 1915 he invented the "Ever-Ready Sharp Pencil" a that would eventually give the company its present name in In 1990, Sharp Laboratories of Europe was set up as a wholly owned subsidiary of Sharp. It was created to develop ideas and technologies for Sharp of Japan and for other Sharp subsidiaries in Europe. SLE was deliberately located in Europe to facilitate access to and collaboration with leading European research institutions that would be harder to reach from Japan. SLE has two major focuses of research, to solve specific problems for the manufacture of Sharp products (particularly in Japan) and "blank sheet" research where the goal is to create a new technology that can be implemented in a family of products. Because SLE's customers are all internal, there is an overall philosophy of teamwork. This enables both customer and supplier to communicate more easily than in is allowed in a more traditional (and sometimes adversarial) relationship. Greater co-operation and teamwork enables SLE to concentrate on adding value to Sharp products and the Sharp brand. SLE moved to its current laboratories in Oxford in 199. It currently includes a European Design Centre which has the specific task of helping Sharp branches in Europe to design new products based around existing Sharp technology with an emphasis on Liquid Crystal Displays (LCD technology). More recently the Design Centre has expanded its purview to include solar energy and lighting products and is ready to take advantage of new technological developments from the other major research areas. SLE has four main research groups: Optoelectronics, Information Technology, Revolutionary Displays and Health and Energy Technology. Optoelectronics is largely focused on Light Emitting Diode (LED) technology, developing and finding novel uses for LEDs in multiple existing and new technologies. Their other focus is on high efficiency photovoltaic technology. Information Technology (IT) researches and develops the hardware and software to run Sharp's products. Due to SLE's a This is often confused with the "Eversharp" pencil invented by the American Charles R. Keeran around the same time. 34

35 position of being Japanese owned but based in Britain the IT group also develops a large number of language and translation programs. Lastly the IT group works on developing new networking tools to integrate multiple systems to better facilitate communication at work and at home. It also designs the security systems and devices necessary for this to work safely. Sharp has always been closely connected to the development of LCD technology. In 1973 Sharp developed the world's first COS electronic calculator incorporating an LCD. The Revolutionary Displays group is largely focused on liquid crystals for display devices, particularly 3D displays, displays with changeable viewing angles and displays that incorporate their operating hardware into the glass of the display itself. The Health and Energy Technology Group (HETG) is invested in a relatively new area of research and production for Sharp. The reasons for setting up this research group are closely linked to the reasons for investing in this project and are outlined below. One of the principal research interests of the Health and Energy group are sensors and devices to measure the health of individuals both at home and at the "point of care" (POC). A POC product is one that performs its action in the immediate proximity of the patient; typical examples are within a GP's surgery or in an operating theatre. They are especially useful because they provide quick results without the need for expensive and time consuming transport to offsite laboratories. Other research interests of the HETG are the system aspects of photovoltaic technology, energy management systems for the home, improved methods of energy storage and new heating and cooling technologies. 1.3 Sociological drivers for the research project In general life spans are extending. A child born in the United Kingdom now will on average live approximately 8% longer than a child born in 1981 (based on principal projections of Period expectation of life). 10 Initially this may seem a small amount but it is important to note that for the child born now, the percentage of life lived over the age of 65, traditionally old-age and retirement is 30-40% higher than the percentage for the child born in This trend is more pronounced when looking at developed countries as a whole and it is even more so when looking at less developed ones 35

36 where there is a significant migration towards urban living and a corresponding increases in education and life expectancy. 11 It is also known that even in developed countries older people require more medical care and are more susceptible to illness, disease and disability than younger people. 1 Lastly people are becoming more health conscious in general. 13 All these factors contribute to an increasing demand for health care and health related products. 1.4 Commercial drivers for the research project Predicting the cost of health care both to individuals and to governments is complex enough to have spawned its own branch of economics, "health economics". There are many conflicting theories on how to model the links between population trends and health costs. There are even arguments that in specific areas, sufficiently high levels of health in a population may cause the cost of care per person to decrease. 14 However, there is a general belief that the overall costs of health care will increase for individuals, for insurers and for states and governments. This belief has been influenced by a number of reports from influential consulting and research organisations over a number of years 15,16 and it has a large effect on the markets for health and health technology. Biosensors have long been recognised as a health product. In % of the biosensor market's revenue came from the home diagnostic and POC sectors. This dominance is predicted to continue through to Glucose sensing is by far the largest single application as a percentage of the market and this is because glucose sensing products are positioned in both of these market sectors. A report on the global biosensor market performed by Global Industry Analysts, Inc., the world's largest market research company, predicts that the market will grow to US $1Billion by In addition to this, it can be seen that the marketing of biosensor products has lagged behind the development of the technology by researchers. 19 As a result of these factors, there is significant opportunity to exploit a potential gap in the market. Developing cheap and reliable commercial biosensor products, particularly those aimed at the home diagnostics and POC sectors would be a very positive achievement for a corporation. 36

37 1.5 Position of the project within SLE's corporate strategy SLE's corporate strategy directly mirrors that of its parent company Sharp. Sharp corporation's business interests are focused in three main areas. The first is the production and development of products in well established markets. These include displays, device components and printers and currently generate the majority of Sharp's income. Improvement and development of the technologies behind these products tends to be small and incremental. The second business area is the development of the immature technologies and markets that have not yet reached their potential. Examples of this are the crystalline solar cell and thin film solar cell technologies that Sharp are developing. These are focused because it is believed that they will comprise the mainstay of the company's operations in the future. Lastly there is the research and development of new technologies that have not yet been fully commercialised into products and of technologies whose markets have not matured to a fully commercially viable stage. Positioned below these three interest areas are a number of revenue generating business groups that generally service only one of the areas. Sharp also operates a number of cost centres. One of the major cost centres is the Corporate Research and Development Group (CRDG) of which SLE is an overseas laboratory. Increasingly Sharp wants the CRDG to produce new technologies to develop the Health and Energy section of the business's interests. Any new technologies utilising the findings of this project would likely be commercialised by the Health and Environmental Systems Group (HESG), a business group operating in the future products business interest area. The HESG is a growing concern within Sharp; the operating income of the group is predicted to rise by 1.5% as a percentage of the operating income of the whole business between the financial years of 010 and Sharp has a strategy of aggressive, wide-spectrum marketing for products based around new technologies. An example of this is the Plasmacluster Ion air purifier line of products from the HESG. These air purifiers denature airborne pathogens and are designed to operate in homes and in industry. 1 Information on the line was circulated on Facebook and prizes were given to individuals who spread product awareness most 37

38 effectively. Specific case studies and focused examples of the benefit of the technology to disadvantaged children were coupled with an educational drive to explain the working principles of the purifier devices. In addition to this, sponsorship of the Hong Kong movie "Shaolin" was secured. As an emerging market without dominant product positioning, potential biosensor products might receive a similarly strong marketing drive. 1.6 Progression of the project The project to investigate and develop the suitability of liquid crystals as a biosensor technology is one of Sharp's "blank sheet" exercises. This type of research is more commonly known as "blue sky" because of its open ended nature. As a result, the success of the project is difficult to judge. However, a Technology Readiness Assessment (TRA) is a tool designed for precisely this situation. Technology Readiness is a method of assessing and categorising a new technology with respect to its nearness to commercial application. In other words it aims to give an objective measure of how ready a technology is to be sold or implemented in a saleable product. TRAs are used by many large organisations and companies, notably the United States of America Department of Defense (DoD), the National Aeronautics and Space Administration (NASA) 3 and the European Space Agency (ESA) 4. Each of these has slightly different definitions of and approaches to carrying out TRA. However, in all cases a Technology Readiness Level (TRL) between one and nine is assigned, where one is an idea or concept and nine is a fully developed and implemented technology. The TRLs were originally written by NASA and were closely linked to concepts of "mission readiness" and "flight tested". The definitions of the TRLs must be appropriate to the technology they describe and to the markets in which that technology will operate. As a result, for the purposes of a biosensor, the definitions written by the United States Army Medical Research and Materiel Command (USAMRMC) are more suitable; these may be seen in Table

39 Technology Readiness Level Chart Novel Concepts and Emerging Technologies Generate/test hypotheses and experimental designs Synthesize candidate countermeasures Identify sites and mechanisms of action Device components and design identified Initial proof of concept Translation of Research to Solutions of Military Problems Technological assessment requirements identified Non-GLP formulation, dose, and pharmacokinetic studies Non-GLP safety and efficacy studies Assays/procedures for GLP/GCP studies identified Device design history file/review initiated cgmp pilot lot production GLP safety and efficacy studies Endpoints of clinical or surrogate efficacy Stability studies initiated Pre-IDE meeting and IDE prepared and submitted for Class III device 510(k) preliminary data suggest substantial equivalency to predicate device Prototype Maturation and Demonstration Pre-IND meeting IND prepared and submitted Phase 1 clinical trials Investigation of Class III device in clinical trials Safety demonstrated Production technology demonstrated 510(k) data demonstrate substantial equivalency to predicate device Phase clinical trials Investigation of Class III prototype in clinical trials Safety and evidence of efficacy demonstrated Final dose, dose range, and schedule established Pre-Phase 3 meeting Phase 3 clinical study plan or surrogate test plan approved Class III device design validated and final prototypes produced 510(k) final prototype produced and tested Phase 3 clinical trials Investigation of final Class III prototype in clinical trials Safety and efficacy demonstrated Process validation completed Facility PAI completed Pre- NDA/BLA/PMA meeting NDA/BLA/PMA/ 510(k) prepared, submitted, and approved Product and Distribution Marketing and distribution Post marketing studies Post marketing surveillance TRL 1-3 TRL 4 TRL 5 TRL 6 TRL 7 TRL 8 TRL 9 Table 1.1 TRLs in the Medical Materiel Regulatory Process. (GLP: Good Laboratory Practice, GCP: Good Clinical Practice, cgmp: current Good Manufacturing Practice, IDE: Investigational Device Exemption, IND: Investigational New Drug, NDA: New Drug Application, BLA: Biologics License Application, PMA: Premarket Approval). It is notable that the first three levels are merged in this table. In general this is because at this stage a gestating technology should consume very little resource and consequently should be a low risk for an organisation. A more discrete, generalised description is can be summarised as: TRL 1. Basic principles observed and reported. (The "idea" stage) TRL. Technology concept and/or application formulated. TRL 3. Analytical and experimental critical function and/or characteristic proof of concept. There are several benefits of this system. It gives an objective, formulaic way of assessing the progress of a technology or project. Furthermore, in large projects with 39

40 multiple technologies it allows for the identification of potential development bottlenecks. It also allows for the commercial valuation of a project based on the known probabilities of a technology at that level succeeding. There is an often quoted statistic that for every 3000 ideas there is only one commercial success. 5 This project was started when the use of liquid crystals as biosensors could be categorised as TRL1. The basic principle of liquid crystals changing alignment on chemically patterned surfaces was reported by Abbot et al. in Since then there have been many variations on the theme. This work improves the TRL of the project to TRL 3 by providing analytical evidence for the physical function of liquid crystals changing orientation on arrays of chemicals and anisotropic topographies. 1.7 Commercial value of the current state of the project and further development needed for commercialisation Given the commercially underdeveloped nature of the work in this thesis, it is difficult to gauge its current commercial value. However, the steps required to develop a technology to saleable product form by SLE and Sharp are well defined. It is typical for SLE to develop new technologies through TRLs 1-3 without significant external input. Beyond this stage, test devices and demonstrations are designed in order to generate interest from one of Sharp's business groups. In the case of this work, the HESG would likely be approached. The aim of this is to secure additional funding to develop the product through TRLs 4 and 5 and confirm some aspects of product design. b In some cases, advanced demonstration of a nascent product may be given to the target market of the research group as part of market research. Favourable reception is important for the success of the technology. Final product development (TRLs 6-8) would be carried out by the HESG in Japan in collaboration with engineers from SLE. Three sequential levels of development are performed with three distinct testing stages. Test samples, engineering samples and customer samples are used to measure the success of these stages respectively. b SLE's funding comprises 70% from the CRDG and 30% from specific business groups interested in developing products. 40

41 From the point of view of this work, the next crucial step would be incorporating the findings of this report into a biosensor device. It must be sufficiently sensitive to low levels of biological contamination to be useful in the home environment and rugged enough to operate outside of the laboratory. 1.8 Potential markets for the project The biosensors market is currently in a state of rapid growth. As a consequence, the results of market research into possible trends and profitability performed by research groups such as Frost and Sullivan and Global Industry Analysts, Inc. (referred to in references 17 and 18) remain proprietary knowledge. The costs of acquiring these data are beyond the scope of this project. However, it is known that Sharp intends to enter the home testing and point of care markets and it is likely that any products developed from the findings of this report would be targeted there. 1.9 Structure of the thesis This thesis will first summarise the current state of research into the potential use of liquid crystals as biosensors, this puts the work done in this project into a wider context and explains some of the decisions behind the directions the research took. The physics relevant to the use of liquid crystals in this manner is explained in more detail than is given above. The results and limitations of initial experiments carried out at the beginning of the project are reported and this informs the decision to conduct the investigation into the effect of regularly patterned surfaces on liquid crystal alignment. The techniques and apparatus used to take measurements of these liquid crystal systems are then described. The ancillary results of measurements of the birefringence and elastic constants of the liquid crystals used are presented. These are followed by the effects of surface chemistry and cell thickness on the optical responses of the liquid crystal cells. The responses of the different liquid crystals are reported and these are analysed with respect to the measurements of their birefringence and elasticity. Lastly the effects of the topography of the gold patterned silicon substrates are detailed as spot size and spot separation are varied. These results are summarised and conclusions drawn with reference to the implications of this research into future biosensor design. 41

42 1 Engineering and Physical Sciences Research Council, Swindon. (Information available online at (accessed ). Maizlish, B. and Handler, R. (005), IT Portfolio Management Step by Step: Unlocking the Business Value of Technology, John Wiley & Sons, Inc., Hoboken, New Jersey. 3 Sabelnikov, A., Shukov, V. and Kempf, R. (006), Biosens. Bioelectron. 1, Gupta, V.K., Skaife, J.S., Dubrovsky, T.B and Abbott, N.L. (1998), Science 79, Collings, P. J. and Hird, M. (1997), Introduction to Liquid Crystals Chemistry and Physics, Taylor and Francis, London. 6 Skaife, J.J. and Abbott, N.L. (1999), Chem. Mater. 11, Frank, C.F. (1958), Discuss. Faraday Society 5, Dierking, I. (003), Textures of Liquid Crystals, Wiley-VCH, Weinheim Office for National Statistics (ONS), Biennially, Online edition, Period and cohort life expectancy tables (Available online at: (accessed )). 11 Yaukey, D. and Anderton, D.L. (001), Demography: The Study of Human Population, Waveland Press, Prospect Heights, IL. 1 Gist, Y.J. and Hetzel, L.I. (004), We the People: Aging in the United States (Census 000 Special Reports), U.S. Census Beaureau. (Available online at: (accessed )). 13 Niknian, M., Lefebvre, R. C. and Carleton, R.A. (1991), American Journal of Public Health, 81, no., Gray, A. (005), Aging Horizons, no., Sager, A. and Socolar, F. (006), Durable Health Care for All Will Require Cost Control, Boston University of Public Health, Boston. (Available online at: (accessed )). 16 Hewitt Report (010), The Road Ahead: Under Construction With Increasing Tolls, Hewitt Associates LLC. (Available online at: US/KnowledgeCenter/ArticlesReports/Articles.aspx (accessed )). 17 Thusu, R. (010), Strong Growth Predicted for Biosensors Market, Frost and Sullivan/ (available online at: (accessed )). 18 Press release (011), PRWeb, Vocus, San Jose. (Available online at: (accessed )). 19 Luong, J.H.T., Male, K.B. and Glennon, J.D. (008), Biotechnology Advances, 6, Katayama, M. (Sharp Corporation President) (011), Sharp Business Strategy for FY011, Sharp Corporation, Japan. (Available online at: (accessed on )). 1 Sharp Publication (011), Sharp Eye 117, Sharp, Japan. Department of Defense, Director, Research Directorate, Defense Research and Engineering (009), Technology Readiness Assessment (TRA) Deskbook. (Available online at: (accessed: )). 3 Mankins, J.C. (1995), Technology Readiness Levels: A White Paper, NASA, Office of Space Access and Technology Advanced Concepts Office. (Available online at: (accessed )). 4 Giménez, A. (005), 'The life cycle of an ESA science mission and how to get involved', in V.M. Pillet, A. Aparicio, and F. Sánchez (eds), Payload and Mission Definition in Space Sciences, Cambridge University Press, Cambridge, Stevens, G. A. & Burley, J. (1997), Research Technology Management, 40, no. 3, Gupta, V.K., Skaife, J.S., Dubrovsky, T.B and Abbott, N.L. (1998), Science 79,

43 Chapter Existing Work in the Field of Liquid Crystal Biosensors, a Literature Review In reviewing the literature available on the investigation of liquid crystals as biosensors, two potential device configurations are used multiple times. Much of the initial work in the use of LCs for biosensors has been carried out by the Abbott group. Their first work in demonstrated that thin films of nematic liquid crystal could respond to the binding of a very small amount of ligands to the supporting substrate with a subsequent change in the LC alignment. This alignment change is detectable by optical polarising microscopy when the substrates are combined with glass cover-slips to construct viewing holders (commonly referred to as cells) for the liquid crystal films. This is possible because of the birefringent properties of LCs. The work showed that LCs could potentially be used as a mechanism for the sensing of microscopic amounts of biological analytes and be used as a biosensor. This is one of the two configurations reviewed. In addition to this, it was found that an alignment change could be detected at the interface between a liquid crystal film and an aqueous phase when analytes adsorb at the phase boundary. This comprises the second possible sensor device configuration reviewed. Most of the liquid crystals used have been thermotropic nematics. Though in some cases cholesteric, smectic and lyotropic liquid crystals have been used. For more information on liquid crystal phases see Chapter 3. This review presents summaries of the work in both of these detection geometries. Investigations and modelling of the critical physical parameters of the systems in order to tune potential sensors sensitivity are also detailed. Details of innovative non-optical detection of analytes by liquid crystals and steps towards wearable LC based biosensors are also outlined. The ways in which these reports inform many of the decisions made during the work submitted in this thesis are then explained. 43

44 .1 Surface bound analytes A large majority of the work in this area has been carried out with the liquid crystal material 4-cyano-4 pentylbiphenyl (5CB) and with surfaces comprising gold films on silicon. The first work was concerned with proof of the principle of alignment change. Subsequently systems were modified to investigate crucial system parameters that would affect analyte detection..1.1 Oblique gold In the method described by Abbott et al., 1 substrates are formed by the oblique deposition of a gold film onto a glass slide. This gives a grooved structure that encourages planar alignment in the liquid crystal 5CB through steric interactions (see Chapter 3). A self assembled monolayer (SAM) of biotin deposited on the surface was shown not to significantly- alter the surface roughness or LC alignment. Substrates were then dipped in avidin, which binds to the biotin. Control samples without avidin were shown to induce good homogeneous alignment in 1-0µm thick films of the liquid crystal. However, samples that had avidin bound produced either random planar or homeotropic alignment, where the underlying surface anisotropy of the gold-biotin layer was masked by the avidin. Biotinylated substrates dipped in avidin solution, premixed with an excess of biotin exhibited no binding and induced homogenous planar alignment. The antibody goat anti-biotin immunoglobulin, which also binds to biotin, was also shown to smooth the surface roughness. This first report showed the ability of liquid crystals to optically amplify the binding of ligands to surfaces and opened the gates to more research. Similar work was performed in 1999 that showed that submillimetre sized droplets of 5CB could be used in instead of films. 3 In addition Abbott showed that the alignment of 5CB could be influenced by obliquely deposited gold film surfaces which have anisotropy too small to be seen by visual inspection of AFM images. 4 Later it was shown that rubbed SAMs of bovine serum albumin (BSA) induced homogeneous orientation in 5CB cells but that the specific binding of Anti-BSA immunoglobulin G (IgG) to the surfaces prevented the uniform orientation. Binding of non-specific proteins did not affect the alignment. 5 Further work showed that it is possible to determine the concentration of an immunoglobulin used to mask an anisotropic substrate by measuring the gray scale brightness of a supported LC film. 6 44

45 Also, the BSA films may be functionalized to promote the binding of other specific IgGs. 7 The response of LCs to the binding of the IgGs has been shown to be affected by the type of SAM to which the IgG binds. However, the effect of the nanometre scale surface anisotropy dominates over the molecular interactions with the SAM in these cases. 8,9 A similar system using biotin functionalized alkanethiol SAMs and an anti-biotin immunoglobulin analyte showed that the same behaviour can be observed with lyotropic liquid crystals. 10 Other experiments showed that some lyotropic LCs can act as both solvent and detector for binding of antibodies to surface bound antigens. Properties of the LCs such as viscosity, birefringence and whether or not the LC blocks the binding sites all affect the suitability of different LC materials. 11 It is interesting to note that it has also been shown that in certain cases specific SAMs can cause liquid crystals to orientate in the plane of the substrate but perpendicular to the direction of maximum surface roughness, 1 which is normally energetically unfavourable (see Chapter ). It has also been reported that proteins printed onto gold film substrates change alignment of 5CB from homeotropic to planar. 13 It has been shown that the orientation of proteins bound to a surface can influence the binding of additional proteins. 14 Additionally, affinity microcontact printing of the epidermal growth factor receptor, EGFR, was shown to cause a planar to patterned texture change. 15 Peptide-peptide binding with a SAM on a gold film can also be imaged with 5CB. 16 The packing density of immobilised peptides has been shown to affect the time for a liquid crystal to relax from an initially disordered orientation to a more ordered one. Increasing peptide density increases the time for liquid crystal to form a uniform planar alignment. 5CB was also used to image the orientation of bound proteins on gold films with SAMs incorporating the protein of interest. Uniform protein alignment corresponds to near uniform liquid crystal alignment while randomly anchored proteins produce less uniform textures. 17 Poly (ε-caprolactone) (PCL) brushes (groups of hydrocarbon chains grown up from the surface of a SAM) were also shown to affect LC surface anchoring on obliquely deposited gold

46 .1. Detection of gaseous analytes The liquid crystal 8CB was also used to demonstrate the viability of detecting gaseous analytes in its smectic phase. 19 A thin film of the liquid crystal was supported on a SAM which presented surface immobilised Cu + ions. Gaseous organophosphonate (dimethyl methyl phosphonate, DMMP) was then blown across the film. This produced an alignment change through competitive binding between the nitrile group of the liquid crystal and the DMMP to the surface ions. A homeotropic to planar transition was observed for concentrations of DMMP of down to 10 parts per billion by volume (ppbv) in N..1.3 Detection of DNA Jae-Hoon Kim et al. 0 have extended Abbot s work to the binding of DNA. Single stranded biotin-conjugated DNA immobilised to a Biotin Chip TM was shown to induce homeotropic alignment in a 10µm thick 5CB cell. Hybridization by its complementary partner DNA forms double strands that effectively increase the packing density of DNA on the surface. This has the effect of reducing the interdigitation of the liquid crystal mesogens with the DNA strands and generates planar alignment. Similar results were shown by Park and Jang using DNA immobilised on a SAM with planar anchoring Substrates without a gold layer The use of substrates without a gold film has also been investigated. Hoogboom et al. have conducted work related to Abbott's using anisotropically grafted organosiloxane on rubbed glass to align 5CB. Exposure to a lipase (CALB) hydrolysed the alignment layer, changing its end groups from benzene groups to acid groups and thus changing the polarity. This was seen to change the orientation of surface mesogens from planar to homeotropic. In other work they showed that the directional drying of a droplet of low-salt Tris-EDTA (TE)-buffer is capable of forming a planar alignment layer without mechanical contact with the surface. 3 This is potentially very useful in bio-sensing applications where disrupting surface immobilised particles with mechanical rubbing is undesirable. 46

47 Choi et al. 4 also showed that biotin receptors spin coated onto microscope slides without any underlying metallic film would reorient the liquid crystal ZLI-93 when binding avidin ligands to the surface..1.5 Investigations into the system parameters important for analyte detection In an investigation into the cause of these changes in alignment, functionalised amine terminated monolayers, were shown to induce an anchoring transition in 5CB due to the electrical double layer that forms at the interface between the amine terminated surface and the liquid crystal after incubation of the samples. 5 Areas of the substrates that were affinity microcontact printed with anti-biotin IgG do not induce the transition. Furthermore, 5CB was observed to reorient on anionic and cationic gold film substrates when they were treated with solutions containing negatively charged vesicular stomatitis viruses. This occurred over a period of days, consistent with a dipolar coupling between 5CB and electrical double layers formed at the ionic interface. Non-ionic substrates showed no alignment change, suggesting that this reflects the electrostatic binding of the virus to the surface. 6 More recent work with viruses has shown that the structure of the virus can play a role in determining LC orientation. Jang et al. 7 reported that of four similarly shaped viruses, the factor that determined LC orientation appeared to be the presence of a lipid bilayer enveloping the virus structure. Those with a bilayer promote homeotropic anchoring, whilst the virus without induced a largely planar texture. In some cases it can be shown that hydrogen bonding of 5CB to an acid terminated thiol can dominate over the underlying surface anisotropy. In a system of competitive binding between LC mesogens and targeted analytes to a specific binding site on a SAM, Abbott et al. showed that once the binding sites were occupied by the analyte the LC adopted an alignment induced by the surface grooves. 8,9 This was also shown to allow the detection of low concentrations (~0ppbv) of a gaseous analyte as it diffused through a liquid crystal film over a time period of seconds. This makes this system a very promising basis for a liquid crystal based biosensor. The action of hydrogen bonds in LC orientation was explored further where the orientation of 10 liquid crystals on COOH terminated SAMs was shown to be dependent on the nature of the H bond acceptors of the mesogens. This was shown not to be the case for methyl terminated SAMs. It was also shown that liquid crystals containing nitrogen 47

48 atoms disrupt interfacial H bonds in SAMs. 30 The liquid crystals used included 5CB, a 8CB, b TL05, b PCH7, E7 a and MBBA. The separate influence of hydrogen bonding and an electrical double layer, both of which can induce homeotropic anchoring in 5CB, was shown by Park et al. 31 when they performed experiments attempting to tune 5CB to perform better as a detector of microcontact printed proteins. 5CB was mixed with 4-cyano-4 -biphenylcarboxylic acid and/or irradiated with U.V. light. In both cases the LC produced homeotropic orientation on hydroxyl and ammonium terminated surfaces. But it was concluded that in the former case this was due to the formation of hydrogen bonds between the acid and the hydroxyl groups and in the latter it was due to the formation of an electrical double layer at the ammonium surface. Further investigations of the anchoring interactions of LCs in these systems by Clare et al. 3,33 report that a torque balance method is capable of measuring the azimuthal anchoring energy of a liquid crystal and the effect that increasing concentrations of a peptide at the surface have on this energy. The method involves measuring the angle between the supposed easy axis of a twist cell with a SAM at one substrate and a reference plate providing strong orthogonal alignment at the other. The difference between the observed equilibrium position of the director and the anisotropy of the SAM can give a measure of the torque within the bulk of the LC and hence the energy of the system. Additional work has demonstrated that concentrations of antibodies down to 10pM may be detected by their effect on anchoring energy 34 and that multiple arrays of printed antibodies may be analysed in the same liquid crystal cell using image analysis techniques that allow for spatial resolution of <10µm. 35 Much work has also been done by outside of the Abbott group. Evans et al. 36 have shown that surface plasmon resonance (SPR) microscopy can be used to determine the anchoring orientation of 8CB on surfaces presenting differently functionalised SAMs. It was also possible to show that on melting from the crystalline phase, the nematic phase forms first on the surface, before in the LC bulk. Later Alkhairalla et al. 37 used a From Merk, Germany. b From EM Industries, Hawthorne, NY. 48

49 a Brewster-angle evanescent wave ellipsometric technique to study the orientational order of xcb LCS (x=5-9) at the substrate-lc interface. It was determined that the more hydrophobic a SAM is the more likely a likely a given liquid crystal is to form a homeotropic alignment. Furthermore, longer LC mesogens require a less hydrophobic surface to be homeotropically aligned. Cheng et al. 38 used microcontact printing of alkanethiols onto smooth gold films to produce substrates chemically patterned in arrays of differing properties. These were shown to produce differing alignment in the supported LC films of 7CB and 9CB in both their nematic and smectic phases to a spatial resolution of ~4µm. This was expanded upon by Bramble et al. 39 exploring differing geometries of SAMs, improving resolution to <µm and showing the focal conics that form on these SAMs in smectic phases. 40 The Abbott group showed that the manner of gold deposition has an effect on the surface anchoring. By using vapour deposition to deposit the gold from a shorter distance between the source and the substrate (15cm compared with 50cm) a gradient in the nano-scale anisotropy can be produced. This has the effect of allowing easier optimization of surface topography for investigating LC binding effects. 41 Alkhairalla et al. 4 investigated the interaction of competing anchoring energies between gold substrates and surface SAMs by using smooth gold substrates with fluorinated SAMs of varying hydrocarbon chain length. The different lengths corresponded to changing distances between the substrates gold surface and the terminal groups of the SAMs (and hence the LC interfaces). An anchoring transition from planar to homeotropic alignment was detected by measurements of the Brewster angle at a certain chain length for 5CB and it was hypothesised that this occurs for low surface energy, particularly when it is below the liquid-vapor surface tension of the LC. This anchoring transition was supported by further work that used surface plasmon polariton (SPP) Raman scattering to measure the orientation of the nematic director for 6CB films supported on different SAMs. 43 On SAMs with dipoles orientated normal to the surface, homeotropic anchoring was observed. Where the dipole was in the plane of the substrate planar anchoring was seen. 49

50 Atherton et al. 44 showed that twisted nematic (TN) devices (where the azimuthal angle of LC alignment is different at the different surfaces of the cell) are also very susceptible to surface chemistry. SAMs were printed in long stripe patterns that aligned the liquid crystal despite not having a rubbing direction. They showed that in such cells some areas form optically uniform textures when the energy of the bulk twist is comparable to the weak surface anchoring. This is not seen in conventional TN cells where the surface anchoring is much stronger. Similar substrates were used to successfully align columnar discotic liquid crystals. 45 In a different technique Prompinit et al. 46 constructed SAMs from cyano-biphenyl based thiols. Normally these induce homeotropic alignment in liquid crystals but they are cleaved by exposure to UV to leave a surface decorated with carboxylic acid groups. These promote planar alignment. Because of the relative ease of UV exposure this allows substrates to be tailored to help position focal conic domain defects in smectic phases. The Kim research group have also conducted investigations into the effect of nano imprinted surface topographies on nematic alignment. 47 They have showed that it is possible to tune the surface anchoring of an alignment layer by altering the degree of mechanical brushing to which it is exposed. This is balanced by an underlying pattern of sub micron sized stripes of nano scale alignment pattern. The alignment direction on the stripes is orthogonal to the direction of the rubbing. When the anchoring energies are matched appropriately alternating alignment directions may be seen on and off the stripes producing a discreet bi stable alignment at the surface. In related work using a planar and homeotropic alignment layer one on top of the other it was shown to be possible to control the pre-tilt of an adjacent LC film from 5-89 by altering the thickness of the uppermost homeotropic layer. 48 This has the effect of masking the underlying planar layer s effect on the LC to a greater or lesser degree. Zhang et al. 49 showed that this technique of a double alignment layer could be used to tune the sensitivity of an LC based sensor to the presence of lecithin dissolved in the nematic bulk. By effectively reducing the surface anchoring energy the response of the system to the analyte became both more sensitive and more abrupt, something greatly desired in a potential sensor where a clear cut yes/no signal is required. 50

51 Other work on tuning anchoring energies was performed by Yeung et al. 50 They used a polyimide alignment layer that was a mixture of two different polymers, one with strong anchoring and another with weak to no anchoring. By altering the relative concentrations varying polar and azimuthal anchoring can be obtained. The Yang research group in Singapore have performed related experiments using silicon wafers without the presence of a nano-structured gold film. In Bi et al. 51,5 they created hybrid aligned nematic (HAN) LC cells (where the top substrate had homeotropic alignment and the bottom substrate had planar alignment). The presence of multiple glycerine oligomers was detected when they formed monolayers on the surface of the bottom substrate, disrupting the LC alignment when the thickness of the monolayer increased above 0.5±0.1nm. Two homeotropically aligned substrates were also shown to demonstrate the sensitivity of 3-15µm thick films of 5CB to surface immobilised proteins above a certain critical concentration. 53 The Yang group also demonstrated that a similar system is capable of distinguishing between the reaction of dialdehydes and monoaldehydes at a surface decorated with amine groups. 54 Dialdehydes react to produce a surface that is covered in aldehyde groups which induce an alignment change in supported films of 5CB. The same reaction with monoaldehydes produces a surface covered in hydrocarbons which do not induce the alignment change. In a similar experiment the orientation of 5CB was shown to be sensitive to different strains of the bacteria E. Coli. A strain with an extracellular polymeric substance (EPS) was shown to induce homeotropic orientation, whilst two strains without the EPS did not. 55 The same system was modified to respond to gaseous glutaraldehyde as it diffuses through a film of 5CB. 56 An optimised system of a 0µm thick film was shown to be sensitive to 07ppmv of glutaraldehyde within 0s..1.6 Quantification of analyte binding The Yang group s technique was also reported to allow the imaging of oligonucleotides immobilised on DNA microarrays and that interference colours from the change in LC alignment could be used to give information on the concentration of the oligonucleotide. 57 Later this was improved to allow for the quantification of amounts of DNA on a similar surface. 58 Quantification was achieved by using an 51

52 array of sequentially diluted DNA solutions on the substrates. Those above a critical concentration caused an alignment change, those below did not. Diluting these solutions further and measuring the alignment again provides an estimate of the degree to which the solutions are in excess of the critical concentration. An optical bar chart technique was also demonstrated recently by Bi et al. 59 A printed assay of immobilised oligopeptides was exposed to the protease trypsin with a graduated immersion time across the length of the assay. The trypsin acts to cleave and reorganise the oligopeptides, decreasing their length. At a critical time of immersion (and hence critical length) this change in configuration induces an ordering transition in a supported liquid crystal film. This produces a clear difference between immersion times of the assays and gives rise to a line of bright spots leading up to the critical time..1.7 Modelling the effects of surface bound analytes on LC alignment By using a two-dimensional model of a liquid crystal cell, de Pablo et al. 60 showed a number of effects that back up and expand upon currently observed experimental phenomena. The model uses the tensor order parameter of the system and assumes the one elastic constant approximation. They showed that in a simulation of a cell with two identical boundary walls there is a critical concentration of nano particles adsorbed at these walls that will disrupt the surface induced alignment. Below this concentration the particles have the effect of slowing the growth of the ordered nematic phase when cooling from the isotropic. It was also shown that randomly distributed nano particles have a different effect from those arranged periodically and that the critical concentration is different for different arrangements. 61 If particles are clumped into clusters they may have less effect than if dispersed individually. Fang et al. 6 showed that homeotropically aligned LC cells were able to visually amplify individual immobilised fat, muscle and neuron cells. They also used an elastic continuum model in the one constant approximation and produced theoretical images that matched the observed optical textures for homeotropic anchoring at the cell surfaces. They calculated the spatial limit of detection for their technique to be 1.5µm using 5CB and a 500nm light source. In contrast Zhao et al. 63 did not use the one 5

53 constant approximation but used finite-element method to model the director orientation of 5CB around self assembled lipid tubules Hwang and Rey 64 also used a finite difference time domain (FDTD) model to show that in a system with proteins adsorbed to a solid substrate, optical detection is more sensitive to low percentage coverage if low wavelengths ( 500nm) and thinner LC films are used. In systems with high percentage protein coverage (generally a better situation), higher wavelengths and thicker LC films are found to be more sensitive. Wincure and Rey 65 also used computational analysis to calculate that in a system of a liquid crystal supported on a patterned substrate with strong anchoring, there is a coupling between the surface anchoring and interfacial dynamics as the nematic phase nucleates from the isotropic. This can cause the growth of defects at the interface that may persist in the nematic bulk. 66 Anquetil-Deck and Cleaver 67 performed molecular simulations on a similar system. They showed that for substrates patterned with alternating stripes of homeotropic and homogeneous anchoring it is possible to achieve a continuous variation in polar anchoring angle from completely homeotropic to completely planar. The competition between molecular interaction anchoring and nano-scale topography steric anchoring was investigated theoretically by Hamaneh and Taylor. 68 They performed molecular dynamic simulations on 5CB molecules adjacent to polyvinyl alcohol (PVA) surfaces patterned with nano-scale grooves perpendicular to the orientation of the polymer chains. They showed that only the deepest grooves overcame the inclination of the LC mesogens to align with the polymer chain direction. Similar results have been seen by Yi et al. 69 using substrates patterned with nano-scale square wells. The interaction between molecular and steric anchoring was used by Barbero et al. 70 to explain the unusual behaviour (non-monotonic) of the surface tilt angle of certain nematics as a function of temperature. It was also used to explain the inverse link between the anchoring strength of the LC MBBA on monolayers of fatty acids and the acid molecular chain length. 71 The model shows that for longer chain lengths the LC actually causes the monolayer to deform as a result of a bend distortion in the bulk of the LC. 53

54 Atherton and Sambles used an elastic continuum, free energy model to calculate that the bulk energy of a nematic liquid crystal in contact with alternating homeotropic and planar anchoring is dependent on the elastic constants of the liquid crystal. 7 They also showed that there exists a critical anchoring energy about which alignment in either state can be observed. The influence of these modelled findings on the work performed in this thesis is discussed below.. LC-aqueous interfaces Other forms of LC biosensor might be used to detect the presence of an analyte at a liquid-liquid interface. A comprehensive review of aqueous-lc interfaces and their potential as for biosensors was written in 005 by Lockwood and Abbott LC films supported by copper and gold grids In 00 Brake and Abbott demonstrated that a LC-aqueous interface could be used to optically image the adsorption of the amphiphile sodium dodecyl sulphate (SDS). The LC was supported in a copper grid which stabilised the LC phase against the presence of the aqueous phase through capillary forces between the LC and the copper. In 003 Abbott et al. showed that the self assembly of phospholipids at a 5CB-aqueous interface induces a change of orientation in films of the liquid crystal supported by gold grids on octadecyltrichlorosilane (OTS) coated glass. 74 Later, concentrations as low as 100nM of PLA (a substance found in snake venom) were shown to change the alignment of 5CB by reacting with an aqueous interface laden with the lipid D-DPPC (D-α-dipalmitoyl phosphatidycholine). 75 Fluorescently labelled lipids were used to correlate changes in optical texture with lipid concentrations. Simulations carried out by Kim et al. suggested that the interactions between different thermotropic LCs and a phospholipid bilayer may in part be influenced by the solubility of the LC in water. 76 Gold specimen grids have also been used to investigate the influence of surfactant tail branching on the orientation of the nematic liquid crystal TL Linear surfactants promoted planar alignment up to a threshold surfactant concentration, beyond which homeotropic alignment was observed. In contrast, branched surfactants gave planar 54

55 alignment for all concentrations up to the critical micelle concentration, C c =0. c TL05 was also used to image the reorganisation of Matrigel extra cellular matrices under the influence of human embryonic stem cells. 78 The interaction between polyelectrolytes and liquid crystal-aqueous interfaces laden with amphiphilic polymers has also been shown to couple strongly to the orientation of the liquid crystal mesogens. 79 Oligopeptide-based amphiphiles were later reported to have a similar effect, 80 with the significant advantage that they can be covalently bonded to a lipid monolayer producing an orientation change and subsequently enzymatically cleaved from the layer to change the orientation again. In addition to this, the orientation of 5CB at a LC-aqueous interfaces was shown to be influenced by the continuous increase in concentration of ganglioside GM 1 (a lipid that occurs in the brain) as a SAM is formed from solution in the aqueous phase. 81 In a modification to the systems described above Gupta et al. 8 showed that a monodisperse suspension of LC droplets in an aqueous phase is sensitive to the concentration and adsorption of an amphiphile (sodium dodecylsulfate, SDS) in the suspension. Six distinct stable topological configurations of mesogens within the droplets were identified for increasing concentrations of the amphiphile. In addition to this the system has shown itself to be sensitive to the difference between encapsulated and non-encapsulated bacteria (bacteria with and without a surrounding lipid envelope) and to respond to the presence of low (10 4 pfu/ml) d concentrations of a virus. 83 Furthermore, Kinsinger et al. showed that certain amphiphilic polyamines could not only cause ordering transitions within the droplets but immobilise the droplets on planar surfaces. 84 In other work with LC-aqueous interfaces supported by copper grids the Yang group developed a ph sensor where the alignment of 5CB doped with 4'-pentyl-biphenyl-4- carboxylic acid (PBA) changes orientation reversibly as the ph of the aqueous solution changes. 85 PBA has a ph sensitive functional group that promotes an alignment change when the local ph of the interface changes. It was also shown to be c C c = Log [concentration / critical micelle concentration]. At the critical micelle concentration a surfactant has completely loaded the surface or interface and additional surfactant molecules form micelles. d pfu = plaque forming units. This is a measure of the number of infective virus particles present in a sample. 55

56 capable of responding to the change in ph from the hydrolysis of penicillin G (used as an antibiotic) by the enzyme penicillinase (produced by penicillin-resistant bacteria) immobilised on the copper. This technique is considerably faster and more sensitive to ph changes than earlier work performed by Kinsinger et al. 86 Gold grids were used in a similar manner to produce a system sensitive to phospholipase-like toxins through their hydrolysis 87 and again to show the sensitivity of phospholipid monolayers at LCaqueous interfaces to the presence of 0nm gold particles coated in proteins. 88 In a more advanced experiment the gold support grids were used to perform real time detection of protein binding at an LC-aqueous interface (something not done before). 89 The protein ubiquitin with a histidine tag was immobilised on the LC surface by a SAM of nitrilotriacetic acid terminated amphiphiles. When exposed to the protein antibody anti-ubiquitin, an alignment change in 5CB was observed. More recently a model antibody, anti-flag M was shown to have a similar effect. 90 Phospholipid vesicles immobilised on a surface by specific binding events have also been reported to alter the orientation of adjacent films of 5CB. It is hypothesised that the ordering may be influenced by the presence of aliphatic side chains on the phospholipids. 91 An alternative to the gold and copper grids used above is an array of nickel micropillars on a glass substrate that stabilise a liquid crystal film through the capillary forces that act between the pillars. This has shown to be a robust system for the detection of both vapour and aqueous phase analytes. 9 McCamley et al. have developed another alternative to the gold and copper grids for stabilising thermotropic LC films in the presence of an aqueous interface. 93 They used selective exposure of UV photoresist to create square "wells" of polymer on glass substrates. The properties of sensors developed from these can be altered by tuning the size (50-50µm) and depth (5-5µm) of the wells. Modelling of the device was performed using a Landau-de Gennes model and good agreement was seen between simulations and experiments. 56

57 .. DNA detection at LC-aqueous interfaces Price and Schwartz 94 have also shown that DNA hybridisation induces an orientational transition when it occurs at an aqueous-lc interface. Tan et al. 95 made modifications to the above systems, by including silver ions in the LC solution. Ascorbic acid (a by product of the hydrolysis of bound DNA by the chemical DNA probe) reduces the silver ions which then form a layer of metallic silver on the substrate surface, altering the adjacent LC alignment...3 Modelling of the effect of analytes bound at the LC-aqueous interface on LC alignment Rey 96 applied the Gibbs adsorption isotherm to a LC-aqueous interface with a solution of anionic surfactants. The model showed that as the concentration of the surfactant increases, the orientation of the adjacent LC changes sequentially from planar, to homeotropic (as the surfactant chains provide steric interactions), to random (as the surfactant packing becomes too dense for interdigitation). This behaviour agrees qualitatively with the experimental work performed by Brake and Abbott. Other models have also been developed to deal with surfactant laden LC-aqueous interfaces. A static, force-torque balance model with interfacial curvature constitutive equations 97 and a linear thermal fluctuation model that allowed anchoring energies to be calculated from experimental data 98 were both reported in the same year..3 Detection of analytes in the liquid crystal bulk It is possible that a desirable detector would function without the binding of an analyte to a surface of phase interface. The detection of particles suspended in the liquid crystal bulk has also been investigated. Qi and Hegmann 99 showed that the alignment behaviour of nematic LCs can be influenced by the concentration of alkyl thiolate-capped gold nano particles dispersed in the LC bulk. For certain conditions, it was possible to generate a reversible switch between homeotropic and planar alignment with a change in temperature. Chambers et al. report that cholesteric liquid crystals (CLCs) can also be used to detect the presence of biological analytes. 100 The binding of barbiturates to receptors 57

58 incorporated into the CLCs was seen to shift the selective reflection wavelength of LC cells by as much as 70nm, a change clearly visible to the human eye. In contrast, work by Lavrentrovich et al. has focused on director distortions in lyotropic chromonic liquid crystals. Particularly around spherical particles in the bulk of a sample. 101,10 Light transmitted through the region is heavily dependent on a particle s size so such a system is ideal for detecting antibody-antigen binding and the growth of immune complexes. A comprehensive review of the potential use of lyotropic chromonic liquid crystals for bio-sensing applications was also written Non-optical detection Most previous reports have described optically based measurements as a method of determining changes in LC alignment. Work by Abu-Abed et al. 104 has demonstrated that it is also possible to use capacitance measurements. A LC cell with an array of interdigitated electrodes on one substrate and a plane electrode on the other substrate (alternatively two orthogonally orientated arrays of interdigitated electrodes on a single substrate) allows for capacitance measurements to be matched to numerical models of capacitance as a function of the average director orientation of the LC. Experiments showed slightly different accuracies for the two systems described for different director orientations. Additional work was subsequently performed to modify the system to allow for the more realistic modelling of LCs as a partially disordered system. 105 This technique has also been shown to be capable of measuring anchoring strength by using a Freedericksz transition and changing the concentration of an applied alignment layer. 106 The use of interdigitated electrodes has also been shown to increase the sensitivity of LCs to changes in surface anchoring in the presence of a biological analyte through the application of a bias voltage below the Freedericksz threshold of the system. 107 These results are significant because detection with an electrical signal aids possible automation of biosensor devices based on the technology. Furthermore, removing the need for substrates to be transparent allows cheaper and more durable materials to be used in potentially commercial device construction. 58

59 .5 Wearable sensors Steps to develop a wearable LC sensor for the detection of gaseous pesticides have been made by Adgate et al. 108 An unsealed LC cell filled with the nematic E7 was shown to change alignment in response to organophosphates diffusing into the LC bulk through the open sides of the cell. A short review of the use of liquid crystals for bio recognition and detection was written by Hussain et al Summary In summary a great deal of work has been done in the area in a relatively short time. Nematic, smectic, cholesteric, lyotropic and lyotropic chromonic LCs have all been shown to be able to detect the presence of microscopic (and smaller) amounts of biological analytes on surfaces and at LC-liquid boundaries. They have also been shown to be capable of detecting gaseous analytes in certain cases. This has been shown with variety of optical techniques and also capacitance measurements. There have also been many investigations into the possibilities inherent in tuning the physical properties of these systems to obtain optimal detection. It was modelled by the Abbott group 61 that the effect of particle size and dispersion affects the way surface bound particles influence LC alignment. It was shown by Atherton and Sambles 7 that the energy of a liquid crystal between areas of different surface anchoring is be dependent on the elastic constants of the liquid crystal material. The importance of surface anchoring and the interplay between surface topography and surface chemistry has also been established. 68,69,70 As a result of these reports, the work in this thesis is concerned with measuring the effects of surface perturbations of varying size and density on the alignment of a variety of nematic liquid crystals (using 5CB as a reference). The effect of different surface chemistries is explored and different liquid crystals are used to determine the influence of changing elasticity and birefringence on the response of the liquid crystals to changes in surfaces. These investigations have clear importance to the field of liquid crystal based biosensors. 59

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63 Chapter 3 Liquid Crystal Theory The scope of this work was set out in Chapter 1. It concerns itself with the behaviour and interaction of thermotropic liquid crystals with microscopic features on glass substrates. In order to understand and measure these interactions, certain theoretical concepts must be introduced and explained. This chapter introduces liquid crystal molecules, their structure and some of the more common phases these molecules form. Chirality and how this can affect phase structure is briefly explained and the order parameter is introduced. Optical and electrical measurements of liquid crystals are dependent on two common properties birefringence and dielectric anisotropy. Both of these are a result of the anisotropic shape of liquid crystal molecules and the orientation of their chemical bonds and they are described in detail. Some basic alignments are explained, along with how a liquid crystal's birefringence causes optical textures and structural defects to be observed. Liquid crystal alignment is then explored in terms of the elastic properties within a liquid crystal material and how they can be measured. The aligning anchoring energy applied to the liquid crystal by substrates is also detailed. Lastly the effect of particles suspended in a nematic liquid crystal is illustrated as this has similarities to how liquid crystals respond to particles on surfaces. It will be shown that the interaction between a nematic liquid crystal and a patterned surface is governed by the elastic constants of the liquid crystal, and the anchoring energy at the surface. It is also explained that optical and electrical measurements of this interaction will be dependent on the birefringence and dielectric permittivity of the liquid crystal. 3.1 Introduction to liquid crystals A material may exhibit more than one liquid crystal phase, these are known collectively as mesomorphic phases or mesophases. These phases decrease in order and increase in symmetry as the material changes from a perfectly ordered solid to a completely disordered isotropic liquid. There are two main categories of liquid crystalline material, thermotropic liquid crystals, whose mesophase characteristics 63

64 change with temperature and lyotropic liquid crystals, whose mesophase characteristics change as a function of the concentration of an amphiphile in solution. A common example of a lyotropic liquid crystal is household soap which shows different liquid crystalline properties when dissolved at different concentrations in water. Thermotropic liquid crystals are present in every liquid crystal display (LCD) and it is for this that they are best known and most prevalent in modern life. In both cases the essential feature is that the molecules have some degree of anisotropy, either in their shape such that one molecular axis is significantly different from the other two, or in their chemical composition such that one end of the molecule is soluble in different solvents to the other end. There are also polymer liquid crystals composed of polymerised chains of smaller rigid molecules. 1, As explain in Chapter this work concerns itself with the behaviour and interaction of thermotropic liquid crystals with microscopic features on glass substrates. Thermotropic liquid crystals consist of anisotropic rigid molecules or mesogens. These take many shapes but are split into three broad groups: rod-like or calamitic molecules, disc-like or discotic molecules and the less frequently seen brick or lath shaped sanidic molecules. In this project only thermotropic calamitic mesogens are investigated A calamitic mesogen usually comprises a rigid core and a long flexible hydrocarbon tail. The core is often a pair of ring structures either bonded together or bonded through a rigid link group. This linked pair of rings forms the basis for the rod-like modelling that explains much of the interactions of these molecules. The structure of a typical liquid crystal along with the modelled shape of a prolate spheroid can be seen in Figure

65 y x z CN Figure 3.1 A model of the chemical structure of the liquid crystal 5CB as a rigid rod. The length of the rod in the z axis is longer than in the x and y axes. The dotted line represents the prolate spheroid shape of a usual mesogen model. Calamitic thermotropic liquid crystals may display two main types of mesophase, nematic and smectic. A material with liquid crystalline properties melts from a solid crystal into a liquid crystal phase then clears into an isotopic liquid as the temperature is increased. These temperatures are known as the melting point and clearing point respectively. The clearing point is also referred to as the nematic to isotropic transition temperature, T NI. 3. Liquid crystal phases The nematic phase, N, is the least ordered phase and is usually the first seen when cooling a sample from the isotropic melt (barring the rarer blue phases that can occur for chiral mesogens). It has long-range orientational order, where the long axes of calamitic molecules align in a preferred direction but have no positional order. The local average preferred orientation is defined by a unit vector called the director, n. 3 A representation of the nematic phase may be seen in Figure 3., where θ is the angle between the long axis of the mesogen and the director. 65

66 n θ Figure 3. Orientation of calamitic mesogens in a nematic liquid crystal. More ordered than the nematic phase are the many different smectic phases. In the smectic phases mesogens have the same or greater orientational order as in the nematic phase but also have a degree of positional order. They are arranged in layers within which they have varying degrees of freedom depending on the phase. Also dependent on the phase is the degree of long or short ranged positional order between the layers. It is important to note that these layers are not sharply defined as in a crystal lattice. Rather there is a one dimensional density wave where the average density of the material changes with a wavelength equal to the layer spacing. Furthermore, the nature of the wave is not necessarily fixed and may change even up to the Gaussian form characteristic of an ordered crystal. 4 The two most commonly encountered smectic phases can be seen in Figure 3.3. In the lower order Smectic A phase, SmA, mesogens have similar orientation distributions to the nematic phase yet have the characteristic smectic positional layered distribution. In the higher ordered, smectic C phase, SmC, mesogens exhibit a significant tilt away from the layer normal. 5 66

67 a b Figure 3.3 (a) Schematic of the layered structure of the Smectic A phase. (b) Schematic of the layered structure of the smectic C phase. Many more smectic phases exist for different liquid crystal materials. Additional features, such as hexatic bond orientational order within layers, increases the order of the phases until a crystalline solid is reached. Perhaps most significant are the various phases which have the ferroelectric property of a spontaneous polarisation arising from repeating patterns of mesogen tilt from layer to layer. These are especially interesting as an applied electric field may cause the tilt to switch from one angle to another Chirality A chiral object is one whose mirror image is not transposable upon itself by translation and/or rotation. For example, hands are chiral, the mirror image of a left hand looks like a right hand but this image cannot be superimposed on top of a left hand. Liquid crystal mesogens can be chiral if their molecular structure fits this asymmetrical structure. Where chiral mesogens interact they tend to align at an angle to their neighbours, causing the director to describe a helical superstructure as one moves through a sample along an axis at right angles to the local director. The distance over which this helix repeats itself is known as the pitch length. A nematic phase formed from chiral mesogens is called a cholesteric phase. See Figure

68 n Pitch Length / n n Figure 3.4 The helical orientation of mesogens in a cholesteric liquid crystal. Note, this does not indicate a layered structure, as in the case of smectic phases. The pitch of a phase is dependent on the thermal energy present. Cholesteric pitch decreases with increasing temperature. 1 Where chiral mesogens form a Smectic C phase the tilt angle processes around the layer normal from layer to layer, though the tilt angle does not change, see Figure 3.5. This is known as a chiral Smectic C phase, SmC*. 68

69 Pitch Length Layer Spacing Figure 3.5 Azimuthal rotation of mesogen tilt between the layers of the SmC* phase. 3.4 The nematic order parameter The order of a nematic liquid crystal can in first approximation be described by a scalar order parameter S. S is equal to the average of the second Legendre polynomial, the first non-trivial term in a Legendre expansion of the order distribution function, 3 1 S = P ( cosθ ) = cos θ, (3.1) where θ is the angle between the long axes of calamitic mesogens and the director (as in Figure 3.3.). Triangular brackets denote either the time average of a single mesogen or the average of all local mesogens at a given time. S=1 for completely ordered crystals and S=0 for isotropic liquids. Values of S for nematics vary between 0.4 and Calamitic liquid crystals have cylindrical symmetry about their long axes, and nematic phases formed of these molecules are uniaxial. Furthermore, the symmetry of the mesogens is such that n = -n, the averages of the odd Legendre polynomials are therefore equal to zero. 1 Nematic mesogens that do not have cylindrical symmetry are biaxial and their order parameters are not so easily defined. The order parameters of smectic phases are also significantly more complicated. 69

70 A common method of modelling liquid crystal interactions is to consider the long range electrostatic interactions between molecules and to ignore the short ranged, excluded volume repulsion, forces of the molecules. This mean field approximation is usually known as the Maier-Saupe approach. It assumes that the potential of a liquid crystal molecule can be written as V = vp (cos ). S, (3.) θ where v is a parameter that encompasses the electrostatic interactions between molecules that is dependent on the density of the particles and their polarisability. A statistical average of S for a given temperature can then be written, S = 1 0 d(cosθ ) P (cosθ ). e 1 0 d(cosθ ). e v kbt v kbt, (3.3) where k B is the Boltzmann constant and T is the temperature of the liquid crystal. This is a self consistent field equation which cannot be solved analytically. This model predicts a single relationship of the orientation of liquid crystal molecules at temperatures approaching the nematic to isotropic phase transition. For some nematics this matches experimental data well, it is less good for others. 7,8 It shows the order parameter decreasing as a function of increasing temperature up to the clearing point. 9 At the onset of the isotropic phase the order parameter discontinuously changes to zero. A schematic of the relationship can be seen in Figure

71 S T/T NI Figure 3.6 Orientational order parameter, S, as a function of T/T NI for a typical nematic. [Redrawn from reference 10, pg 133]. More complete descriptions of the Maier-Saupe theory can be found in references 6, 9 and The birefringence of liquid crystals Liquid crystals are often studied in devices with the material sandwiched between parallel plates of glass, generally separated by a few microns and often referred to as sandwich cells. When viewed between crossed polarisers, liquid crystals typically appear coloured due to their birefringence. The colours and textures seen give a lot of information about the structure of the liquid crystal mesophase. 11 Birefringence is an optical property of all anisotropic materials. In all dielectric materials molecules become polarised in the presence an electric field. Because the structure of liquid crystal mesogens is inherently anisotropic the polarisability of the molecules is different in different directions and light will propagate differently depending on its direction of travel and polarisation. 1 In a uniaxial calamitic liquid crystal light propagating in one of three orthogonal directions will experience a different index of refraction than the other two. 1 A material is optically positive if the 71

72 refractive index parallel to the optic axis is greater than the refractive index perpendicular to it. The birefringence, n, is therefore, n = n// n > 0, (3.4) This can be illustrated using the indicatrix, an ellipse with major and minor axes equal to n // and n respectively, for an optically positive medium and vice versa for a negative one (see Figure 3.7). n // Optic axis n // n n Optically positive Optically negative Figure 3.7 Indicatrix of optically positive and optically negative uniaxial mediums. [Figure redrawn from reference 11, pg 36.] The optic axis is the normal to the plane which cuts the indicatrix with a circle. It is the path on which propagating light, of any polarisation, will experience no birefringence. It should be noted that while the indicatrix may look similar in shape to the rod-like spheroid model of a calamitic liquid crystal it is not the same. The indicatrix is a theoretical construct based on the refractive indices of the liquid crystal bulk which is in turn related to the macroscopic orientational distribution and molecular anisotropy of the individual mesogens. 11 An unpolarised beam travelling through a birefringent medium in an arbitrary direction, k, will be split into two perpendicularly polarised beams; the ordinary ray that follows Snell s law and the extra-ordinary ray that does not. They experience different refractive indices n o and n e. This is illustrated in Figure

73 z (Optic axis) k θ n // n e y x Indicatrix n Figure 3.8 Diagram showing how the indicatrix interacts with light propagating in direction k, to give n e. [Figure redrawn from reference 13, pg 87.] Here, n o = n, (3.5) and n// n n e =, (3.6) n cos θ + n sin θ // where θ is the angle between the optic axis and k. 11,13 The relationship between the effective birefringence of a liquid crystal sample (n e -n o ) and the maximum birefringence of the liquid crystal material at that temperature (n // -n ) is therefore highly dependent on the angle of incident light. 3.6 Dielectric anisotropy The relative static permittivity, also known as the dielectric constant is a measure of how an external electric field will induce an electric displacement field in a material 73

74 relative to what it would induce in a vacuum. A vacuum has permittivity of ε 0 ; all materials have a relative permittivity greater than this. As with refractive index the dielectric permittivity of a liquid crystal is affected by the anisotropy of the molecules because it is a result of the ability of the molecules to be polarised by the external field. The value is dependent on the angle between the electric field and the long axis of the molecules. Parallel to the long axis the permittivity is ε //, perpendicular to it the permittivity is ε. The dielectric anisotropy is therefore, 14 ε = ε // ε. (3.7) A material has positive dielectric anisotropy when ε // > ε and negative when ε // < ε. 15 The permittivity of a liquid crystal material can be calculated by measuring the relative capacitance of an empty liquid crystal sandwich cell by coating the inner glass surfaces of the cell with transparent electrodes such as indium tin oxide (ITO). The cell effectively becomes a parallel plate capacitor. The capacitance of this, C empty, is, C empty ε 0 A =, (3.8) d where A is the electrode area and d is the cell thickness. The capacitance of a filled cell, C full, is therefore, C full εε 0 A =. (3.9) d The dielectric constant of the liquid crystal material, ε, can thus be calculated by dividing equation (3.9) by (3.8). C full ε =. (3.10) C empty 74

75 The permittivity calculated is dependent on the alignment of the liquid crystal mesogens within the cell and hence their alignment relative to the plane of the electrodes and the applied field. 3.7 Liquid crystal alignment The alignment of liquid crystal mesogens over length scales larger than the molecular length (and the wavelength of visible light) affects many of the properties of a sample. Birefringence and dielectric anisotropy are both properties of the bulk orientation of the liquid crystal as much as they are of the anisotropy of the molecules themselves. Consequently understanding, identifying and reliably obtaining different alignments is extremely important for the study and application of liquid crystals. Nematic liquid crystals whose optic axes are in the plane of the glass substrates of a sandwich cell are said to have planar alignment. Where the director is not further aligned within this two dimensional plane, long ranged orientational order gives rise to optical textures characteristic of the liquid crystal's phase. These are described in more detail below. Planar alignment where the director alignment is uniform over the whole of the cell is called homogeneous. When the long molecular axis is aligned perpendicular to the substrates the alignment is labelled homeotropic (see Figure 3.9). a b c z y x Figure 3.9 Different alignments of liquid crystal mesogens on glass substrates in the x, y plane. (a) Random planar orientation of mesogens lying in the plane of the substrate. (b) Aligned, homogeneous planar orientation. (c) Homeotropic orientation with mesogens orientated at 90 to the x, y plane. [Figure redrawn from reference 11, pg.] 75

76 Achieving the desired alignment of liquid crystals over domains the size of a device has been the study of much research. The earliest liquid crystal displays were developed in ,17 and the method of producing a homogeneous planar alignment has not changed significantly since then. The technique was developed earlier in the 190s 18 and it is to unidirectionally rub a glass substrate with a velvet cloth or lens tissue. The resultant microscopic grooves in the glass introduce a uniform directionality to the substrate and the director of a nematic liquid crystal is inclined to align parallel to the rubbing direction. This is known as the preferred direction or easy axis of the sample. 19 The uniformity of alignment is improved if some soft alignment layer, usually an organic material such as polyimide, polyvinyl acetate (PVA) or nylon, is deposited in a thin film ( nm thick) on top of the glass before rubbing. 0 Homeotropic alignment can be generated by a layer of surfactant on the substrate. The polar heads of amphiphilic molecules such as lecithin adsorb to the hydrophilic glass, while the two hydrophobic hydrocarbon tails orient perpendicular to the surface. The steric interdigitation of mesogens along the tails provides the aligning mechanism (see Figure 3.10). 1 a Figure 3.10 Surfactant induced homeotropic alignment. (a) Sufficient concentration of amphiphiles allows steric interdigitation with LC mesogens. (b) Too high a concentration of amphiphiles prevents alignment. [Figure redrawn from reference 1, pg 8.] b The director orientation propagates into the bulk of the liquid crystal through the inter-molecular forces responsible for the order of the phase; good alignment can 76

77 generally be obtained across cells up to 50µm thick. Even small disruptions to the alignment layer, such as dirt or scratches, can therefore distort the alignment and optical texture of a sample drastically. 3.8 Liquid crystal textures As mentioned above, a random planar aligned nematic viewed between crossed polarisers produces distinct optical textures. Many phases exhibit characteristic textures that make identification easy, others are more difficult to determine and require a degree of experience to classify. When viewed without polarisers, a homogeneously aligned planar nematic liquid crystal (see Figure 3.9(b)) will have a plain uniform texture. In this configuration, a liquid crystal cell can effectively act as a wave plate. As described earlier, two orthogonally polarised light rays travelling through the sample will experience different refractive indices. One will be retarded relative to the other. The polarisation of light exiting the liquid crystal will be altered depending on the birefringence and thickness of the sample. 13 When observing a homogeneous planar aligned cell between crossed polarisers no variation in the director means that a uniform colour will be seen. In a liquid crystal cell with uniform alignment the intensity of transmitted light varies as, πd I = I0 sin Φsin o λ0 ( n e n ), (3.11) where Ф is the azimuthal angle of the optic axis from one of the polarizer directions, I 0 and λ 0 are the illuminating intensity and wavelength, d is the thickness of the sample and n e and n o are the extraordinary and ordinary indices of refraction of the birefringent liquid crystal (which are related to the absolute birefringence of the liquid crystal (n // -n ) by the angle between the optic axis of the sample and the direction of light propagation). 3 If the sample is rotated such that the director is aligned parallel to one of the polarisers, Ф=0, no light will be transmitted, the sample is described as optically extinct. 77

78 In a homeotropic cell, light travels along the optic axis, perpendicular to the plane of the polarisers, and therefore only experiences one index of refraction. The intensity transmitted through the analyser is zero any rotation of the cell about the optic axis. This optically extinct texture is referred to as pseudo-isotropic. Random planar alignment creates more interesting textures. In a planar aligned liquid crystal cell without a preferred alignment, there is no long range consistency in director orientation and the local average changes over short distances (a few microns). Sudden changes of the director occur at point defects and line defects. These line defects are known as disclination lines. When viewed through crossed polarisers, point defects are joined together by dark brushes called Schlieren textures. 1 The points where the brushes come together are classified by strength, s, which is obtained by dividing the number of brushes originating from the defect by four. The sign of the defect is determined by the motion of the brushes when the crossed polarisers are rotated. Positive defects if the Schlieren brushes turn in the same direction as the polarisers, negative if the opposite direction. These may be seen in Figure In nematic liquid crystals, point defects of s= ±½ and ±1 are observed. 14 This is due to the alignment of the director around a defect with either of the crossed polarisers. The tilted SmC phase also exhibits Schlieren textures. However only singularities of strength s=±1 are seen, this is a way to distinguish SmC phases from nematics. 4 78

79 s = +1 s = +1/ s = -1 s = -1/ Molecular Alignment Schlieren 'brush' textures Crossed Polarizers Figure 3.11 Strength, molecular alignment and Schlieren brushes of the four defect types seen in nematic liquid crystals. [Figure redrawn from references 1, pg 138] Another characteristic of nematics is the thread-like texture; the name nematic comes from the Greek word nema meaning thread. These are produced by disclination lines passing either horizontally or vertically through a sample, ending at one or both of the substrates. They join an s = +½ to an s = -½ point at either end or form a closed loop if the line ends on itself. 4 A similar texture in nematics is formed by surface inversion walls. These form when disclination lines in the bulk are parallel to the viewing plane. A π rotation of the director causes a pair of thin, close black lines to be seen. 11 In homeotropic alignment, a liquid crystal material in the Smectic A phase will appear black as for the nematic phase. Similarly in a uniform homogeneous alignment a SmA phase appears the same as a nematic phase. However, the lower degree of order in a nematic means that the liquid crystal mesogens move with a Brownian motion. A characteristic shimmering is visible in the nematic that is absent in the SmA, this is most easily seen by rotating a sample a few degrees from alignment with a polarizer, away from optical extinction. 1,11 Non uniform, planar alignment of the SmA phase is the most common and creates fan-shaped textures. These are a consequence of the arrangement of the layers in Dupin cyclides; 14 the layers curve around and join to form a series of cooling-tower like structures 5 where the radius of curvature of successive layers is constant. The fan 79

80 shapes are the result of focal conics seen where the Dupin cyclides touch. Illustrations of these can be seen in Figure 3.1. a b Figure 3.1 (a) Vertical cross-section of a pair of Dupin cyclides. (b) Smectic A focal-conic domain. [Figures from reference 1, pg 184 and reference 4, pg 3 respectively] Alternatively, if the ellipse is formed where the focal conics meet in the plane of the substrates, a polygonal texture is seen. This is a space filling structure and is thus more common in thicker samples. An arrangement of focal conics in a liquid crystal cell can be seen in Figure Figure 3.13 Arrangement of tangential focal conics building up polygonal domains. [From reference 14, pg 468.] For more details on the textures of liquid crystal phases see references 11, 13 and 4. 80

81 3.9 Elastic Constants The macroscopic alignment of liquid crystal materials is due to weak intermolecular forces between the mesogens. The energy required to distort liquid crystal alignment is dependent on the nature of the distortion of the director profile, n(r), where r is the relative distance between molecules, and on the elastic properties of the material. The nature of the relationship is also dependent on the phase of the liquid crystal. Three fundamental distortions of a nematic director field are shown in Figure ,6 Glass Surfaces Nematic LC Alignment z y Splay n 0 x n y y n x n x z - y x Twist n n n y y n x n x z n x n y Bend n n z n y LC Alignment at Glass Surfaces Figure 3.14 Schematics of the three fundamental elastic deformations of nematic liquid crystals 9 showing the change in n with respect to x, y and x for each deformation. 6 [Figure redrawn from reference 9, pg 60, and reference 6, pg 1.] Provided that the distance over which major distortions occur, l (l is usually greater than 1µm) is much greater than the molecular length, a (where a~40å), a continuum 81

82 approach can be taken. The distortion free energy per unit volume, in m 3, of a nematic liquid crystal can be written in the form, F ( ) ( ( )) ( ( )) d = K11. n + K n. n + K33 n n, (3.1) K 11, K and K 33 are the elastic constants that correspond to the three distortions shown in Figure 3.14, splay, twist and bend respectively. They are also known as the Frank-Oseen elastic constants. In an ordinary nematic liquid crystal values are of the order N. 1 While in general for a single material nematic K 33 > K 11 > K the magnitude of the differences is such that sometimes an approximation K 11 =K =K 33 =K is made. This is known as the one constant approximation and allows the free energy density to be written as, [(. n) + ( n) ] 1 F d = K, (3.13) For a more detailed mathematical explanation of the elastic constants see references 9 and 14. The elasticity of smectic phases is more complicated than for nematics because the deformation of the liquid crystal layers must also be considered. As this work is only concerned with deformations of nematic liquid crystals, smectic elasticity is not explored any further in this thesis Measuring the elastic constants of nematic liquid crystals Because the elastic constants of a LC affect the energy minimum of the director profile, they may be measured in situations where an external force causes a change in alignment. One of the simplest methods of measuring K 11 and K 33 utilises the Freedericksz effect (explained below). A positive dielectric, homogenously planar aligned nematic liquid crystal exposed to an electric field perpendicular to the plane of alignment will experience an electric torque. This inclines the director to align with the field. Below a certain threshold field, the liquid crystal will remain planar. Because of the symmetry of n=-n, the field cannot exert a torque on a mesogen until a 8

83 non-zero tilt exists. This causes a sudden change in alignment above this threshold. The strength of the field required to buckle the director profile is affected by the elastic constants of the liquid crystal and its dielectric anisotropy. The voltage required to produce this field is known as the threshold voltage or critical voltage, V 0. At increasing field strengths above this threshold, the director will begin to align in the direction of the field, until at large fields the alignment is highly homeotropic. The effect is usually measured using liquid crystal materials held in cells as described above. A diagram of such a set up can be seen in Figure z Glass Substrates z n x α n x V LC Material a b Figure 3.15 A planar aligned nematic liquid crystal cell. (a) With no electric field. (b) With an electric field perpendicular to the plane of the substrates with V>V 0. [Figure redrawn from reference 1. pg 09.] Original measurements of the Freedericksz effect were made using a magnetic aligning field. 7 However, the magnitude of the magnetic field required to completely re-align a liquid crystal is very large (over 0.T, depending on cell gap). The same deformation can be achieved with much more moderate electric fields. 10 The Freedericksz effect can be measured optically, using the induced change in alignment to alter the intensity of light transmitted by a sample. Capacitance measurements of a liquid crystal may also be used, by calculating the change in the dielectric permittivity of the liquid crystal as it aligns with the field. The profile of the permittivity along with the threshold voltage can be seen in Figure

84 Permitivity V 0 Voltage (V) Figure 3.16 The behaviour of the permittivity of a planar nematic liquid aligned cell in response to a potential difference across the cell. Before the threshold voltage, the permittivity profile is flat and the permittivity is measured at right angles to the director of the planar sample, therefore ε measured =ε. Above the threshold, the permittivity increases linearly with increasing field until almost all mesogens are aligned with the field and increasing field strength has a reduced effect. At very high voltages, the sample is almost perfectly homeotropically aligned and ε measured ε //. However, a more accurate value of ε // would be obtained by measuring the capacitance of a truly homeotropic cell. The type of distortion created by the electric field can be calculated from an analysis of the geometry of the cell and the field. The elastic constants can be derived by minimising the energy of the distorted state. The total energy per unit volume is given by: 84

85 U = F d + U e, (3.14) where F d is the distortion energy per unit volume from equation 3.1 and U e is the electric energy per unit volume. For this geometry, U e 1 = ε 0. χ ee sin α, (3.15) where χ e is the electric susceptibility anisotropy of the liquid crystal, E is the electric field strength and α is the angle between n and the x-y plane. From Figure 3.14 the director can be seen to have components in the x and z directions such that, n x = cos[ α( z)], n = 0 and = sin[ α( z)]. y n z Substituting these into equation 3.1 and then substituting for F d and U e, equation 3.14 becomes, U dα 1 [ K cos α + K sin α ]. ε. χ E α 1 = e sin. (3.16) dz Since α= α(z) the function of α that minimises the free energy per unit area as a function of z, F A, may be found by evaluating F A = d 0 U. dz, (3.17) where d is the thickness of the sample. By calculus of variations using Euler's equation and by recognising that α(z) is small just above the threshold field, E th, the field may be defined in terms of one elastic constant by: 85

86 E th π = d K ε χ 0 e. (3.18) Because χ e = ε and V=E.d, a threshold voltage may be defined that is independent of the sample s thickness: K V 0 = π. (3.19) ε ε 0 This was first shown by Gruler and Meier in A more rigorous mathematical derivation of this along with an explanation of calculus of variations and the application of Euler s equation can be found in reference 1. Similar equations may be derived for K and K 33 for corresponding geometries. (A twisted cell for K and a homeotropically aligned cell for K 33 ). However, the geometry required to measure K 33 requires either a strong magnetic field or an inplane electric field. This is difficult to generate uniformly. In 1979, Raynes et al. 9 derived equations that allowed K 33 to be calculated for the planar geometry above (among others). They showed that, ( C C ) C = K 33 ε ε + K 11 V V. ε V 0 0, (3.0) where C is the capacitance of the sample and C is the capacitance of the sample in its undeformed planar state (i.e. the state in which ε is measured). Immediately following the threshold voltage the relationship between voltage and capacitance (or permittivity) is linear ( C C ) V V 0 = g, (3.1) 86

87 where g is the gradient of the profile. This method of calculating the physical parameters of a liquid crystal is sometimes not as accurate as fitting the entire permittivity curve to the energy equation (see Chapter 5) Anchoring energy The orientation of liquid crystal mesogens relative to a surface is dependent on two properties of the surface: surface chemistry and surface topography Surface chemistry The relative importance of the two was conclusively proved by Creagh and Kmetz in They showed that on substrates of identically smooth tin oxide, the liquid crystal 4'-methoxybenzylidene-n-butylanilin (MBBA), will align homeotropically when the substrate is completely clean of all carbon. Where the substrate were not been cleaned as effectively, carbon was detected on the surface by Auger spectroscopy and the liquid crystal aligned homogeneously. This was backed up by work by Proust et al. 31 who experimented using a surfactant, hexadecyltrimethylammonium bromide, as a coating on glass substrates. A close packed monolayer of this surfactant presents a methyl group at the surface with a low surface energy on which MBBA aligns homeotropically. A more diffuse monolayer of the same surfactant lying parallel to the glass presents a methylene-carbonyl surface with a high surface energy. In this case MBBA aligns homogeneously. Further experiments showed that completely clean substrates produced homeotropic alignment both with and without a grooved topography but that if some homogeneous inducing surfactant was present planar alignment in the direction of the grooves would be achieved. What they had effectively shown was that for substrates where the surface energy is low, the intermolecular elastic energy of the liquid crystal dominates and perpendicular alignment will tend to be observed. Where the surface energy is large, the elastic energy of the liquid crystal will be less important and the energy of the system will be minimised for planar alignment. The importance of surface chemistry in determining liquid crystal alignment has been confirmed and expanded upon more recently in work by Abbott et al. 3,33,34 and Evans et al. 35,36 87

88 A common way to illustrate the energy of surface anchoring is through a pure twist state model. The previous section concerned itself with the energy associated with a bulk distortion of a nematic; a more complete description of the total energy must also include terms to account for surface interactions, the boundary conditions. A nematic liquid crystal is held between parallel glass substrates, treated to give uniform planar alignment. To induce a twist the rubbed directions or easy axes of the substrates are separated by an angle τ, see Figure z τ Substrate Ф n t d Ф 1 n y x Substrate 1 Figure 3.17 Schematic of a pure twist cell. [Figure redrawn from reference 1, pg 14.] The easy axes of substrates 1 and are aligned with the x axis and vector t, respectively. At the substrates, the director n deviates from x and t by Ф 1 and (τ - Ф ). Throughout the cell there is no polar deviation of the director from the x, y plane, α=0. In the one constant approximation, the total free energy for the twist state becomes, 1,37 F d 0 1 dφ 1 1 = K + 1Φ1 + dz W W τ dz ( Φ ), (3.) F a b F a S where F a b is the anisotropic (angle dependent) bulk energy and F a S is the anisotropic surface energy. W 1 and W are the energies required for maximum deviation of the 88

89 director away from the easy axis in the plane of each substrate. W 1 corresponds to substrate 1 and W corresponds to substrate. These are also called the azimuthal anchoring energies and have units J.m -. (A more detailed derivation can be found in reference 1 and a more general case where the polar anchoring is also considered is explained in reference 37.) For, W 1, Ф 1 0, there is no deviation from the aligned direction at the surface of substrate 1; similarly for W, (τ - Ф ) 0. For finite W, Ф=0 for a virtual value 13, 1 z=-k/w. This defines the extrapolation length, K b =, (3.3) W b characterises the relation between the anisotropic, surface energy, F a S and the bulk elastic energy (or intermolecular interaction energy), F a b. 13,1 F b ~ a, (3.4) F b a S a where a is the mean molecular size. For strong anchoring, the surface energy is comparable to the bulk intermolecular interactions and b~a. For 'weak anchoring F S b a <<F a and the extrapolation length is much greater than the mean molecular size, b>>a. That the anchoring strength of a liquid crystal to a surface affects the propagation of director distortions into the liquid crystal bulk has important implications for potential biosensor designs Surface topography: grooved surfaces The alignment of nematics along an easy axis is best explained by considering a periodic grooved surface (wavevector q) with strong polar anchoring, W p, i.e. the director is tangential to the surface at z=0. 38 An illustration of this can be seen in Figure

90 Ф 0 =π/ Ф 0 =0 z x (a) π/q (b) Figure 3.18 The director of a nematic liquid crystal on a grooved glass substrate. (a) With the director aligned perpendicular to the grooved direction. (b) With the director aligned parallel to the grooves, out of the page. [Figure redrawn from reference 39, pg 13.] Φ 0 is the angle between the direction of the grooves and the director. For a liquid crystal to align perpendicular to the grooves requires an amount of energy. This was first calculated by Berreman. 38 He assumes a surface profile defined by: z = Asin qx, (3.5) where A is the amplitude and q is the wavevector of the grooves. It is also assumed that the director can only lie in a plane perpendicular to the grooves and that the elastic constants of the liquid crystal are equal, i.e. the one constant approximation. 39 The excess elastic energy density of the distortion is given by, F d ( z) = K α x α + z, (3.6) where K is the elastic constant in the one constant approximation and α is the polar angle between the director, n and the x axis. 90

91 F d is minimised when α α = 0 +. (3.7) x z (See Jägemalm. 13 ) Considering the boundary condition of the surface and that α 0 for z, the solution for α takes the form, qz α ( z, x) = Aq cos( qx) e. (3.8) Substituting equation 3.8 into equation 3.6 gives the dependence of the elastic energy density on z, 39 qz ( Aq ) e K Fd ( z) =. (3.9) The total excess energy of the deformed state, F is given by the integral of the elastic energy density, ( z) = F dz KA q 4 0 F d =. (3.30) For arbitrary azimuthal orientation, F ( z) = KA q sin Φ0, (3.31) 4 which is minimised for Ф 0 =0 or π, along the grooves. For more detailed explanations see, Jägemalm 13, de Gennes and Prost 14, Sonin 1, Berreman 38 and Blinov and Chigrinov 39. Similar calculations can be made to show why long chain amphiphiles homeotropically anchored to a substrate can induce homeotropic alignment through steric interactions

92 This thesis is concerned with the orientation of liquid crystals on surfaces presenting topographical defects and is related to many previous works referenced in Chapter on surfaces with SAMs presenting alternating surface anchoring. When examining more complex geometries of director field deformation, the above equations are not necessarily sufficient. In a departure from the one constant approximation, Batalioto et al. 40 derived equations for the anchoring energy of a nematic liquid crystal held between two micro-textured periodically patterned substrates. The pattern induces planar anchoring with a rapidly changing director orientation across the periodicity of the pattern. A schematic of the micro-texture is shown in Figure L/ L/ -Φ 1 +Φ 1 y x Figure 3.19 A Schematic one of the planar micro textured surface used by Batalioto et al. [Figure redrawn from reference 40, pg 1.] L is the periodicity of the texture and the diagonal lines represent the easy directions of the nematic mesogens in the plane of the substrates, inclined at an angle of ±Φ 1 to the x axis. They showed that as the director field is examined over more than one period, the azimuthal angular distribution of the director, φ, is described by the splay and bend elastic constants rather than twist as might be expected; 9

93 dφ( x) dx W = d K 1 sin sin ( φ( x) τ ) ( φ( x) ) + K cos ( φ( x) ) 3. (3.3) W=W s, where W s is the surface anchoring energy at each surface, d is the substrate separation and τ is the angle between the easy direction and the x axis. This is valid when the groove width of the aligning layer is much greater than the mean molecular length. 3.1 Particles in liquid crystals The distortion of a liquid crystal director at a surface decorated with microscopic topological structures will be related to the distortion of the director around a similarly sized particle suspended in the bulk of a liquid crystal. Much depends on the nature and strength of the anchoring of the liquid crystal to the surface of the particle. A schematic of a possible distortion for homeotropic anchoring on a sphere can be seen in Figure 3.0. z β ξ r Figure 3.0 Schematic of a possible director distortion about a spherical particle with homeotropic anchoring producing a quadrupole deformation with a disclination loop. [Figure redrawn from reference 41, pg 959] Using the one constant approximation, it has been shown by Ruhwandl and Terentjev 41 that for particles with homeotropic surface anchoring, the angular distortion of a uniform director field can be described by equation.30, 93

94 3 WR R β = sinξ. (3.33) 4K r This holds where the radius of the particle, R, is smaller than ~3-4µm. r and ξ define the position at which β is calculated; r is the radial distance from the particle and ξ is the angular distance away from the z axis. For homeotropic anchoring to spherical particles there are three main director configurations (see Figure 3.1). (a) (b) (c) Figure 3.1 Three different director configurations around a particle with homeotropic anchoring. (a) Dipole deformation with hedgehog defect. (b) Quadrupole with Saturn ring disclination loop (represented by the dotted line). (c) Quadrupole without disclination loop (weak anchoring). [Figure from redrawn from reference 4, pg 168.] It has been shown by Poulin et al. 4 that when the surface energy is dominant, i.e. WR >>KR (in the one constant approximation, where R=radius of the particle), dipolar hedgehog distortions form, Figure 3.1 (a). Weaker surface anchoring allows quadrupole deformations with and without a disclination loop to form, Figure 3.1 (b) and Figure 3.1 (c), respectively. It can be noted that the quadrupole surface ring in Figure 3.1 (b) is the same defect structure as is displayed in Figure 3.0. For planar anchoring at a particles surface, tangential alignment is seen. This causes the formation of two boojum defects either side of the particle. This is illustrated in Figure

95 Figure 3. The director profile around a particle with planar anchoring. The two surface defects or boojums are generated to meet the surface boundary conditions. [Figure from reference 43, pg 66.] Further work by Stark 44 demonstrates that dipolar conformations are heavily affected by the elastic constants K 11 and K. In cases where K <K 11 the dipolar conformation will exhibit a twist about the hyperbolic hedgehog. However, a large value of the saddle-splay elastic constant K 4 can induce a quadrupolar surface ring even for strong anchoring. The saddle-splay constant is a measure of the elastic contribution of the surface anchoring to the total free energy of a nematic liquid crystal that is particularly important for non-planar anchoring Summary In this chapter, the liquid crystal state of matter has been described. Some of the different mesophases were identified along with how these phases change if formed from chiral mesogens. The order parameter of nematics was simply defined in terms of the director n. The director, along with the anisotropic shape of the molecules, was linked to the birefringence and dielectric anisotropy of liquid crystals and these terms were explained. Different alignments of liquid crystals were shown as well as how these alignments can be identified by the observation of optical textures. The elastic continuum theory of nematic liquid crystals was used to introduce the elastic constants and techniques by which these can be measured using the Freedericksz effect were explained. Finally the effect of surface chemistry and surface topography on the alignment of liquid crystal on substrates and around suspended particles was described. It has been shown that the reaction of liquid crystals to particles or substrate topography will be dependent on the elastic constants of the liquid crystals, particularly K 11 and K 33, as well as the surface anchoring. In addition, the magnitude 95

96 of any optical or electrical measurements made will be dependent on the values of n and ε of the liquid crystal phase. 1 Collings, P. J. and Hird, M. (1997), Introduction to Liquid Crystals Chemistry and Physics, Taylor and Francis, London. Callister, W.D. (007), Materials Science and Engineering: An Introduction (Third Edition), Johin Wiley & Sons Inc, New York. 3 Barón, M. (001), Pure Appl. Chem., 73, no. 5, pg Khoo, I-C. and Simoni, F. (1991), Physics of Liquid Crystalline Materials, Gordon and Breach Science Publishers, Reading. 5 Goodby, J.W., Blinc, R., Clark, N.A., Lagerwall, S.T., Osipov, M.A., Pikin, S.A., Sakurai, T., Yoshino, K. and Zeks, B. (1991), Ferroelectric Liquid Crystals: Principles, Properties and Applications, Gordon and Breach Science Publishers, Reading. 6 Vertogen, G. and de Jeu, W.H. (1998), Thermotropic Liquid Crystals, Fundamentals, Springer- Verlag, Berlin Heidelberg New York. 7 Luckhurst, G.R. and Zannoni, C. (1977), Nature 67, Collings P.J. (1990), Liquid Crystals, Nature s Delicate Phase of Matter, Princeton University Press, Princeton. 9 de Gennes, P.G. (1974), The Physics of Liquid Crystals, Oxford University Press, London. 10 Kelker, H. and Hatz, R. (1980), Handbook of Liquid Crystals, Verlag Chemie Gmbh, Weinheim. 11 Dierking, I. (003), Textures of Liquid Crystals, Wiley-VCH, Weinheim. 1 Murthy, A.R. Giridhar, A.R. and Rangacharyulu, M. (008), Chinese Journal of Physics, 46, no. 1, Jägemalm, P. (1999), Phd Thesis, On the Optics and Surface Physics of Liquid Crystals, Chalmers, Götborg. 14 de Gennes, P.G. and Prost J. (1993), The Physics of Liquid Crystals ( nd edition), Oxford Science Publications, Oxford. 15 Luckhurst. G.R. and Veracini, C.A. (1994), The Molecular Dynamics of Liquid Crystals, Kluwer Academic Publishers, Dordrecht. 16 Williams, R. (1963), Nature, 199, Williams, R. (1963), J. Chem. Phys, 39, Zocher, H. (195), Naturwissenschaften, 13, (Referenced in: Hoogboom, J., Elemans, J.A.A.W., Rowan, E.A.E., Raising, T.H.M. and Nolte, R.J.M., (007), Phil. Trans. R. Soc. A., 365, ). 19 Musevic, I., Nieuwkerk, C. and Rasing, T. (004), Surfaces and Interfaces of Liquid Crystals, Springer, New York. 0 Hoogboom, J., Elemans, J.A.A.W., Rowan, E.A.E., Raising, T.H.M. and Nolte, R.J.M., (007), Phil. Trans. R. Soc. A., 365, Sonin, A.A. (1995), The Surface Physics of Liquid Crystals, Gordon and Breach Publishers, Amsterdam. Naemura, S., (1978), Appl. Phys. Lett. 33, no 1, Kleman, M. and Lavrentovich, O. D. (003), Soft Matter Physics An Introduction, Springer, New York. 4 Elston, S. and Sambles, R. (1998), The Optics of Thermotropic Liquid Crystals, Taylor and Francis, London. 5 Lydon, J. Lecture given at BLCS Winter Workshop, Hull University, December Frank, C.F. (1958), Discuss. Faraday Society 5, Fréedericksz, V. and Zolina, V. (1933), Trans. Faraday Soc. 9, Gruler, H. and Meier, G. (197), Mol. Cryst. Liq. Crys., 16, Raynes. E.P., Tough, R.J.A. and Davies, K.A. (1979), Mol. Cryst. Liq. Cryst., 56 (letters), Creagh, L.T. and Kmetz, A.R. (1973), Mol. Cryst. Liq. Crsyt., 4, Proust, J.E., Ter-Minassian-Saraga, L. and Guyon, E. (197), Sol.St. Commum., 11, Drawhorn, R.A. and Abbott, N.L. (1995), J. Phys. Chem., 99, Yang, K.L., Cadwell, K. and Abbott, N.L. (004), J. Phys. Chem. B, 108, Cadwell, K, Alf. M.E. and Abbott, N.L. (006), J. Phys. Chem. B, 110,

97 35 Evans, S.D., Allinson, H., Boden N. and Henderson, J.R. (1996), Faraday Discuss., 104, Alkhairalla, B., Boden, N., Cheadle, E., Evans, S. D., Henderson, J. R., Fukushim, H., Miyashita, S., Schonherr, H., Vancso, G. J., Colorado jr, R., Graupe, M., Shmakova, O. E. and Lee, T.R. (00), Europhys. Lett., 59 (3), pp Sugimura, A., Le Masurier, P.J., Miyamoto, T. and Tsuji, M. (1998), Thin Solid Films 331, Berreman, D.W. (197), Physical Review Letters, 8, no. 6, Blinov, L.M. and Chigrinov, V.G. (1996) Electrooptic Effects in Liquid Crystal Materials, Springer, New York. 40 Batalioto, F., Bechtold, I. H., Oliveira, E. A. and Evangelista, L. R. (005), Phys. Rev. E, 7, Ruhwandl, R.W. and Terentjev, E.M. (1997), Phys. Rev. E 55 (3), Mondain-Monval, O., Dedieu, J.C., Gulik-Krzywicki, T. and Poulin, P. (1999), Eur. Phys. J. B, 1, Poulin P. and Weitz D. A. (1998) Phys. Rev. E, 57, Stark, H. (1999), Eur. Phys. Jour. B, 10, Faetti, S. (1994), Phys. Rev. E 49, no 5,

98 Chapter 4 Modelling a Biological Analyte with Latex Beads This chapter details some initial experiments investigating the effect of surface bound particles on the orientation of liquid crystals. In a review of the literature in Chapter it was shown that the alignment of liquid crystal films is sensitive to the presence of biological particles at adjacent surfaces. 1 This has potential for biosensor design; liquid crystal alignment change could be used to detect biological analytes as they bind to surfaces. It was also shown that the size and concentration of the particles is important. Latex beads were chosen as a model for the biological particles seen to bind to surface in Chapter. Beads with diameters of 50nm were used at different surface concentrations to investigate the effect of their presence at surfaces on the alignment of nematic liquid crystals and to show that liquid crystal alignment change can be used to detect the presence of particles too small to be viewed directly with a microscope. This chapter introduces the materials used in these initial experiments; the Latex beads, the biological interaction that binds them to the surfaces and the liquid crystals used to detect their presence. The optical equipment and the physical techniques used to measure the system are detailed. The optical textures seen for two nematic liquid crystals (5CB and ZLI 1695) for decreasing concentrations of particles are presented and lower detection limits are suggested. The inherent limitations of the experimental methods are investigated and discussed. These are all gathered in a single chapter because they comprise a number of small experiments that have a great influence on the subsequent direction of investigation of this research. Most importantly the results of this chapter inform the choice of the more ordered model of a potential biosensor detailed in Chapter 5 which was used to investigate the critical physical properties of the system in the rest of the thesis. 4.1 Introduction Small (sub-micron) Latex beads were used to model similarly sized biological particles (such as bacteria and viruses) that cannot be easily seen by eye or normal optical microscopy. Nano-scale surface topography has been shown to directly affect 98

99 liquid crystal anchoring and alignment 3 and the binding of these beads to surfaces has some similar effects. The beads were bound to the surfaces with a biotin-streptavidin bond (see below). Biotin tagged beads were dispersed in an aqueous suspension and deposited onto streptavidin coated substrates via pipette. The suspending liquid was allowed to evaporate. Different concentrations of the beads in suspension were used to change the concentration of beads at the surfaces to assess the effect of particle concentration on alignment change. The substrates were used to construct cells which were subsequently filled with nematic liquid crystals. The beads caused distortions in the orientation of the liquid crystal samples which were observed by polarising microscopy. The beads were also labelled with a blue fluorophore to allow their surface position to be identified independently from the liquid crystal reaction. It was intended that the biotin tagged beads would disperse and bind evenly across the streptavidin coated substrates forming a monolayer similar to that seen for biological analytes in the literature. 4,5 The concentration of the particles could then be measured by the intensity of fluorescence from the surface and linked to quantifiable measurements of liquid crystal director distortions. Limitations in the experimental techniques, particularly the drying dynamics of the bead suspensions, made this comparison impossible. This is explained below. 4. Materials used 4..1 Biotin coated beads and streptavidin coated surfaces Biotin, also called vitamin H is found in all natural cells. Avidin is a protein derived from chicken egg white that is known to bond strongly to biotin. More commonly used in reactions is streptavidin, a bacterial equivalent to the protein avidin. The bond between biotin and streptavidin is the strongest known non-covalent bond, with a dissociation constant, Kd, 6,a of order Kd= mol/l. 7 The disassociation constant is a measure of the strength of the binding between two substances. When considering a protein binding to a ligand (or biotin binding to surface immobilised streptavidin) Kd a Dissociation constant: a measure of the strength of binding between two substances A and B by the ratio of association to the rate of dissociation of the complex AB. 6 Kd = [A][B] / [AB]. Relatively weak binding corresponds to Kd=10-6 mol/l, strong binding Kd=10-9 mol/l. Water molecules at 5 C have Kd= mol/l. 99

100 is the concentration of a substance in solution, at which half of the available bond sites are occupied. 8 Smaller values of the disassociation constant for a reaction correspond to stronger bonds. The extremely high strength of the biotin-streptavidin bond is in part because streptavidin molecules pack together more closely when bound to biotin molecules than without the binding. 9 Biotin and streptavidin are bound by multiple weak Van der Waals forces at points of contact between the two molecules. The compound strength of the bond is due to the large number of contacts this is because shapes of the molecules fit together very closely, they can be said to have a high degree of chemical complementarity. 10 The structure of biotin can be seen in Figure O H O S H N N H O Figure 4.1 The chemical structure of Biotin. The beads used were 50nm in diameter, carboxylate-modified, biotin-labelled, polystyrene beads with a blue fluorophore attached and were purchased from Sigma- Aldrich (product code L7655). The stated absorption and emission wavelengths of the fluorophore were 360nm and 400nm respectively. The beads are delivered as a 1% solid in a buffered aqueous suspension (10mM PBS, ph 7.1, mm NaN 3 ). 1 The bead suspension was diluted with distilled water, using an Eppendorf Research µl pipette. Suspensions were placed in an ultrasonic bath for 5 minutes prior to deposition on substrates. This was to reduce aggregation and to increase the uniformity of the bead dispersion. 100

101 The slides used were SuperStreptavidin Substrates TM, supplied by ArrayIt (product code SMS). 13 They were composed of microscope slides with a streptavidin layer covalently bonded to the glass. The stated streptavidin density was streptavidin molecules per mm. 4.. Liquid crystals The two liquid crystals used in this experiment were 5CB, a pure compound and ZLI1695, a mixture of cyano-cyclohexylcyclohexanes. 14 Both are thermotropic nematic liquid crystals. They were chosen because each melts from the crystal to nematic phase (K-N) around or below room temperature and they have low nematic to isotropic (N-I) transition temperatures. Their phase sequences are: 5CB; K-N 4 C, N- I 35.3 C and ZLI 1695; K-N 13 C, N-I 7 C). b ZLI 1695 was specifically chosen because it was observed not to fluoresce after exposure to ultraviolet light (see below). Both materials were provided by Merck. The chemical structure of 5CB is given in Figure 4.. C 5 H 11 CN Figure 4. Chemical structure of 5CB. 4.3 Cell construction Prior to assembly, 1µl of diluted bead suspension was pipetted by hand onto the Streptavidin substrates to form a circular area with a radius of approximately -3 mm. These were then allowed to dry at room temperature for a period of approximately two hours. The liquid crystal cells were constructed as shown in Figure 4.3. Thin (~1mm) strips of Mylar film 1µm thick were used to separate the streptavidin substrates from the glass coverslips. These were secured with ultraviolet curing glue (Norland Optical b Transition temperatures provided by Merck data sheets. 101

102 Adhesive 71). The cells were filled with the liquid crystals in their isotropic phase by capillary action. Marienfeld no. 1 coverslips were placed in a hot ultrasonic bath with soapy, distilled water for 15 minutes. They were then transferred to pure, distilled water and replaced in the bath for 15 minutes; this procedure was repeated with fresh water six times. The coverslips were then cleaned again in acetone in a hot (~50 ) ultrasonic bath for a further 15 minutes. Finally they were immersed in methanol for approximately one minute and then dried with a stream of nitrogen gas. Throughout the process the coverslips were secured by a PTFE (polytetrafluoroethylene) holder to prevent scratching. 18(±0.1) mm Alignment layer Coverslip 9(±1) mm 1 µm Mylar spacer, U.V. curing glue 5(±0.) mm ~1 µl suspension of L7655 biotin labelled nano-spheres (Sigma- Aldrich) Super Streptavidin Substrate TM (ArrayIt) 11(±1) mm Figure 4.3 Schematic of cell construction. Alignment layers were deposited on to the coverslips by spin coating. Planar alignment was achieved with a solution of 0.5% PVA in distilled water. 0.1% lecithin dissolved in chloroform was used for homeotropic alignment. Five to six drops of the solutions were pipetted from a height of approximately 4cm dropped onto a substrate spun at 80rps for planar alignment and 60rps for homeotropic alignment. The coverslips and SuperStreptavidin Substrates TM were cut using a diamond tipped scriber. After cutting, the coverslips measured 18(±0.1) mm by 9(±1) mm, the SuperStreptavidin Substrates TM measured 5(±0.) mm by 11(±1) mm; glass 10

103 fragments and dust were removed with a stream of nitrogen gas. The PVA coated coverslips were rubbed with a clean velvet cloth to promote planar alignment Measurements of cell thickness The cells thicknesses were calculated by measuring the interference fringes from normally reflected light from wavelengths of nm. This is possible because an empty cell can be modelled as a Fabry-Perot etalon. It is important to note that for the model to hold it is assumed that the refractive index of air is constant and equal to one for all illuminating wavelengths. Furthermore, the illuminating light must be at normal incidence to the plane of the cell. If these are true, or close to true, constructive interference is obtained for mλ = d, (4.1) where λ is the illuminating wavelength, m is an integer and d is the cell gap. The spectrum of reflected light was measured by a Chromex 500IS imaging spectrometer and fed to a computer for analysis. The experimental technique and apparatus used are described in more detail in previous works by Guillou, and Roberts, Two widely spaced maxima or minima are examined and the number of fringes in between are counted. Hence two equations are generated; m λ d, (4.) 1 1 = and m λ d. (4.3) = Where m 1 and m are the integer values of the edge maxima or minima (note because this is the integer number of wavelengths in the path difference m 1 >m ) and λ 1 and λ are the wavelengths (λ 1 <λ ). Thus the cell gap d can be calculated: 103

104 λ λ = M λ λ 1 d, (4.4) 1 where M=m 1 -m. 17 Measurements of the cell thickness by this technique were accurate to approximately ±0.1µm. Using the above construction technique cells were manufactured to thicknesses of ~15(±1)µm across the area of the cell. 4.4 Optical polarized microscopy Due to the optical behaviour of liquid crystals, optical polarized microscopy is often the easiest and best technique for study. This is mainly due to both its simplicity and its relative cost efficiency. In addition to this it offers easy access to the sample being studied in-situ, allowing other experimental techniques to be applied at the same time. The binding of Latex beads to the substrates changes the anchoring of the liquid crystal at the surface similar to how biological analytes are reported to do in the literature. 18 This causes a distortion of the local director away from the alignment of the liquid crystal in areas of the cell without beads. 19 This is observable by polarising optical microscopy because of the birefringence of the liquid crystal materials. Deviation of the director away from the overall alignment of the liquid crystal within the cell (see Chapter 3) changes the angle the optic axis of the liquid crystal makes with the direction of light propagation through the sample. Orthogonal polarisations of light will experience different refractive indices and this can be visualised with optical polarising microscopy when contrasted with the light passing through the rest of the cell. This is most clear in cells with homeotropic alignment, or planar alignment where the optic axis lies parallel to one of the directions of polarisation, as they appear dark or optically extinct 0 (see Chapter 3) when viewed between crossed polarisers. It was reported in the literature that a critical concentration of a biological analyte was needed to change the orientation of adjacent liquid crystal films. 1 Different concentrations of beads at the surface can be seen to induce different director distortions and hence transmit different intensities of light through the otherwise dark cells. 104

105 Optically extinct planar alignment can be easily identified by rotating the sample so that the optic axis is no longer parallel to the polarizer/analyser. It can be difficult to distinguish a well aligned, dark homeotropic nematic phase from a black isotropic melt. Applying a small stress to a sample (e.g. by poking it) can solve this as there will be a director distortion at the point of stress. This can be clearly seen as a birefringent flash in a homeotropic phase. 0 Where this is either not possible, or not desirable, conoscopy can be used. Conoscopy is also a good method of ascertaining the quality of homeotropic alignment (see below). The standard microscope set up for these experiments can be seen in Figure 4.4. Digital camera Beam splitter U.V. light source Removable analyser Objective Condenser Liquid crystal sample on rotatable stage Rotatable polarizer Light source Figure 4.4 Schematic of optical observation by polarising microscopy. The addition of the ultra violet arm is specific to this investigation. The microscope used was an Olympus BH research microscope with a DeltaPix DP 00 digital camera attached. An Olympus, infinity corrected, 10x magnification objective was used. The ultra violet light source used was an Olympus BH RFCA attachment. The purpose was to measure the density of beads deposited on the streptavidin coated substrate via their fluorescence intensity with a photodiode and to match this to the director distortion of the liquid crystal. Beads with ultra violet absorption were chosen 105

106 so that reflection of the exciting light would not interfere with the detection of the fluorescence emission or the transmitted optical light. Many of the physical properties of the thermotropic liquid crystals used are highly dependent on temperature. The temperature of the samples was kept constant with a Linkham hot-stage and Linkham TMS91 temperature controller. This was capable of controlling and measuring the temperature of the sample to an accuracy of 0.1K Conoscopy Conoscopy is the imaging of the back focal plane of the objective. It gives an image of the Fourier transform of the structure of the material. When a birefringent sample is illuminated with highly convergent light, each point on the focal plane is illuminated from a different single direction. This requires an objective with a high numerical aperture. The conoscopic image formed is viewed most easily by simply removing the focussing eyepiece of the microscope. However, better imaging can be achieved with the addition of a Bertrand lens. Focal plane Analyser Ordinary ray Extraordinary ray Sample Polariser Microscope axis Figure 4.5 Schematic diagram of the light paths that form a conoscopic image. [Figure redrawn from reference.] Arbitrarily polarized light passing the birefringent sample is split into orthogonally polarised ordinary and extraordinary rays (see Figure 4.5) that experience different refractive indices and so travel different paths. When the path difference between the rays is equal to an integer multiple of wavelengths the sample acts as a full waveplate; 106

107 the polarization of the light remains unchanged and will therefore be blocked by the analyzer, 3 conoscopic images will have dark areas at these points known as isochromes. The simplest case is a uniaxial, homeotropically aligned, nematic with the optic axis of the sample coinciding with the direction of light propagation. When illuminated with monochromatic light, the isochromes form dark concentric circles which can be seen in the back focal plane. These are centred on the optic axis. In addition to this, cylindrical symmetry means that where the projection of the incident wavevector is parallel to one of the polarizer directions only one refractive index is experienced by the transmitted wave. These dark areas are called isogyres and form the characteristic Maltese cross in the centre of the focal plane, see Figure 4.6.,4,5 Crossed polarisers Figure 4.6 Characteristic Maltese cross and concentric dark circles of a uniaxial, homeotropic liquid crystal under conoscopic observation. [Figure redrawn from reference 5, pg 16.] Well aligned homeotropic samples produce clear, sharp crosses centred in the middle of the focal plane. More in-depth discussions of conoscopy can be found in references, 3, 4 and Results The aim of the work presented in this chapter was to demonstrate that liquid crystals could be used to image the binding of sub-micron sized particles to surfaces. The lower limit of detectable particle concentration on the surface was also investigated. 107

108 4.5.1 Testing alignment layers As mentioned above, changes in liquid crystal anchoring and director orientation are most easily viewed optically when contrasted with a uniform alignment across the area of a cell. The streptavidin substrates were not able to have alignment agents applied without affecting the streptavidin-biotin binding. Three different alignment regimes for the cells coverslips were investigated: plain glass, a planar alignment agent and a homeotropic alignment agent. The aim was to discern which would provide the most uniform alignment for the liquid crystals in cells comprising one coverslip and a streptavidin coated substrate. Optical polarising microscopy images of three cells each with a different alignment layer can be seen in Figure 4.7. a b Figure 4.7 Polarized microscopic images of cells with: (a) Plain glass coverslip, at an angle of minimal optical transmission relative to the polariser directions. (b) PVA coated coverslip, rubbed left to right, at an angle of optical extinction. (c) Lecithin coated coverslip; the circular defect is the result of a water mark on the glass and is included as a reference for the dark appearance. c In each case the liquid crystal is 5CB, cell thickness is 18.0(±1)µm and the polarisers are orientated up-down and left-right in the images. A plain glass coverslip showed that there was an inherent directionality to the streptavidin substrates but that this was not well defined across the whole of a cell. The image in Figure 4.7(a) was taken with the cell at an azimuthal angle in the plane of the polarisers that minimised the transmitted light intensity. This direction was found to be common to all substrates cut from the SuperStretavidin slides. In Figure 4.7(b) a PVA coated coverslip was used. It was rubbed with a velvet cloth with the rubbing direction parallel to the directionality of the streptavidin substrate. The cell is also orientated at an angle of minimum optical transmission. This is 108

109 noticeably darker than the cell constructed with plain glass and closer to an optically extinct texture obtainable with uniform planar alignment. The streaks in the lower half of the image are due to the poorly defined directionality of the streptavidin substrate. Lecithin coated coverslips were found to give good homeotropic alignment, verified conoscopically, despite the anisotropy of alignment at the streptavidin substrate. This is shown in Figure 4.7(c). The dark appearance contrasts sharply with the watermark included in the image. Lecithin coverslips were used in the investigations of bead detection because they gave a more uniform alignment then the other alignment regimes. This gave a better background contrast by which to judge the effect of director distortions caused by changes in liquid crystal anchoring at the bead decorated surfaces Imaging beads with 5CB The effect of decreasing concentrations of beads on the alignment of 5CB is shown in Figure 4.8. The concentrations are given as the concentration of beads in suspension (percentage solids) that was deposited onto the surface by pipette. The lowest concentration of beads found to cause an observable alignment change was 0.01%. During deposition the bead suspensions dry to form a circular pattern with a radius of approximately -3mm. The edges of these patterns and their effect on the alignment of 5CB in the nematic phase can be seen in Figure 4.8. The drying process appears to draw the beads to the edge of the circle in a coffee stain effect rather than forming a uniform layer across the area of suspension deposition. 6 This is particularly apparent at lower suspension concentrations. Similar effects and particle patterns have been reported for the drying dynamics of droplets of similarly sized particles in suspensions of similar concentrations. 7,8 This drying effect appears to occur despite the strong binding between the biotin tagged beads and the streptavidin coated substrate. 109

110 a b c d e f g h i j k l 00µm Figure 4.8 Microscopic images of the edge of the circular bead stain for cells filled with 5CB. (a, d, g and j) White light transmission without polarisers. (b, e, h and k) UV illumination in reflection without polarisers. (c, f, i and l) White light transmission through crossed polarisers. The bead concentrations in suspension prior to deposition are: (a-c) 1% (d-f) 0.5%, (g-i) 0.05%, (j-l) 0.01%; the images were taken at 5 C (nematic phase). Figure 4.8(a), (d), (g) and (j) show the transmission of light through the samples with sequentially reduced bead concentration without polarization. The aggregation of the beads is visible at these concentrations without the effect of director distortions. 110

111 The position of the beads can also be seen in reflection when they are illuminated with UV light (Figure 4.8(b), (e), (h), and (k)). It is interesting to note that the beads appear to fluoresce red rather than the blue stated emission wavelength of 400nm. In contrast the edges of air bubbles in Figure 4.8(b) and (e) fluoresce purple and the edge of an air bubble in the liquid crystal in Figure 4.8(h) appears bright blue. This may in part be caused by the liquid crystal 5CB which appears to be sensitive to exposure to UV illumination (see below). The effect of the beads on the transmission of polarized light by the liquid crystal can be seen in Figure 4.8(c), (f), (i) and (l). It can be seen that cells transmit light in areas where beads are bound to the substrates, this contrasts with the dark areas without beads. This is most easily seen in Figure 4.8(l). The alignment on the clean glass was shown to be homeotropic via conoscopy. It is clear that the presence of beads on the substrates distorts the director profile of 5CB. At high concentrations, 1%, 0.5%, 0.05% solid in suspension, the director distortion appears to extend to areas of the substrate where beads were not deposited. It is possible that this is a result of much lower concentrations of beads, dispersed outside the circular stain but not seen without the liquid crystal. This is partly supported by the purple tint to the fluorescent images outside the red stain in Figure 4.8(b) and (e) as this could be a compound effect of the red beads and the blue liquid crystal Sensitivity of 5CB to UV illumination To illustrate the UV sensitivity of 5CB, a cell was constructed from two lecithin coated coverslips without any beads. This was found to give good homeotropic alignment across the area of the cell when illuminated with white light. This was confirmed by conoscopic observation. The cell was then exposed to the UV light source, initially no change was seen. However, after two minutes of UV illumination the liquid crystal could be seen to shine blue. 111

112 a b 00µm Figure 4.9 Images of an air bubble in 5CB. (a) White light illumination in transmission through uncrossed polarisers. (b) White light transmission through crossed polarisers after minutes UV exposure. In Figure 4.9 the edge of an air bubble in the in the cell can be seen. Before exposure to UV light the cell was uniformly black when viewed between crossed polarisers, no distinction between the air bubble and the liquid crystal could be seen. After exposure to the ultraviolet light source, the edge of the bubble could be seen as a bright blue line and the liquid crystal as a light blue next to the black air bubble. This indicates that 5CB is sensitive to exposure to UV light. It is possible that because of this the emitted fluorescence of low concentrations of beads may not be distinguished from the background of the liquid crystal. This makes 5CB an unsuitable liquid crystal for experiments involving UV light Imaging beads with ZLI 1695 The liquid crystal ZLI 1695 was chosen to continue experiments. It comprises a mixture of cyclohexylcyclohexanes instead of the biphenyl structure of 5CB. ZLI 1695 was not observed to react optically to exposure to UV light over a time period of several minutes. Cells with varying concentrations of beads, similar to those used for 5CB, showed that ZLI 1695 could be used to image lower concentrations was possible with 5CB. 11

113 a b c d e f g h i j 00µm Figure 4.10 Microscopic images of the edge of the circular bead stain for cells filled with ZLI (a, c, e, g and i) White light transmission without polarisers (b, d, f, h and j) White light transmission through crossed polarisers. The bead concentrations in suspension prior to deposition are: (a+b) 0.01%, (c+d) 0.005%, (e+f) 0.005%, (g+h) %, (i+j) %. Bead concentrations below this did not cause a visible alignment change. Figure 4.10 shows optical images of the response of ZLI 1695 to surface bound beads. As in Figure 4.8 the polarisers are orientated up-down and left right in the images. At 113

114 the lower bead concentrations used the fluorescence intensity from the beads is too weak to be photographed and images for UV illumination are not shown. When viewed with white light between crossed polarisers the cells could be seen to have homeotropic alignment in areas outside of the area of bead deposition. This was verified conoscopically. However, light is clearly transmitted through the outer edges of the ring of beads, indicating an alignment change away from homeotropic. This is clear for suspension concentrations of beads down to % which is significantly lower than is visible using 5CB. As explained in Chapters and 3 there are a number of factors that could cause the difference in apparent sensitivity of the two liquid crystals. The anchoring energy and tilt angle of the liquid crystals to the surface of the beads will determine whether they change the anchoring energy of the substrate in areas where they are bound. 9 The elastic constants of the liquid crystal along with the anchoring energy, determine how far from the surface of the beads any director distortion will propagate into the liquid crystal. 30 The effective birefringence of the liquid crystal over the region of the director distortion and the thickness of the liquid crystal cell will determine the intensity of light transmitted. 31 Difference in these factors between the two liquid crystals would be expected to cause a change in their apparent optical response to a given concentration of beads. (These factors are investigated and discussed in more detail in the rest of the thesis.) However, perhaps the most crucial factor is that the concentration of beads bound to the surface is not effectively controlled between different cells. The concentration of beads at the edge of the circular area of deposition can be seen to be higher than in the centre of the circles from the images taken without polarisers shown in Figure This is observation matches predictions based on the current understanding of the drying of colloidal suspensions. 6 Because of the drying dynamics of the bead suspensions and because of the unpredicted (red) fluorescence behaviour of the beads the actual concentration of beads at the edge can't be easily predicted or measured. This is a critical flaw in the experimental technique used. 114

115 4.6 Investigation into bead-surface binding patterns Attempts to achieve a more even surface coverage of beads were not successful. Pipetting away excess liquid after deposition of the suspensions was ineffective and drying rings were still observed. Rinsing substrates immediately after suspension deposition was found to prevent all surface binding. Delaying the rinse by varying amounts of time was met with mixed success. Time periods of less than two minutes were found to be insufficient for any surface bound beads to be detectable. Longer than two minutes appeared to allow the initial formation of a ring pattern (see Figure 4.11). This was observed for concentrations of beads in suspension too low to be seen with white light illumination with a microscope. Instead samples of beads on substrates were placed in an Amersham Biosciences, Typhoon Trio + Variable Mode Imager. The beads were seen to measurably fluoresce when illuminated with a red 633nm wavelength laser and observed with a 670nm Band Pass 30nm (BP30) filter. Excitation with the blue and green lasers did not produce any fluorescence from the beads and this matches earlier observations. The positions of the bound beads for a rinsed sample can be seen in Figure µl of % solid suspension of the beads was pipetted onto a SuperStreptavidin substrate and left to bind for two minutes before rinsing for 30 seconds in detergent. c During rinsing, the substrate was tilted with the upper edge seen in Figure 4.11 held lowest. The image is shown in extremely low contrast greyscale with fluorescence intensity as dark. The substrate is positioned in the centre of the image; the straight dark lines mark the edges with the lighter areas to the sides showing the scanner bed. c Detergent solution: 1 M NaCl, 0.01% TWEEN 0, 10 mm Tris (ph 8.0). 115

116 Circular ring stain of beads Dirt and grease on the scanner bed 10mm Figure 4.11 Fluorescence image from Amersham Biosciences, Typhoon Trio + Variable Mode Imager. The image was taken with illumination from a 633 nm laser and 670nm BP30nm filter. Extremely low contrast imaging shows initial binding of biotin beads to substrate post rinsing. It can be seen that after two minutes of binding a drying ring has already begun to form leaving a circle of beads surrounding an empty (clean) area of the substrate. It is also clear that the beads have aggregated into clumps as individual beads with diameters of 50nm are too small to be seen with optical wavelengths. The action of tilted rinsing appears to have allowed some particles to bind to the substrate in a fine spray extending upwards from the ring. However, this concentration of beads emits very little fluorescence. At the contrast necessary to distinguish them the dirt and grease on the scanner bed shows up darker (more fluorescent) than the beads. In addition to this, the substrate itself fluoresces as it is clearly darker than the surrounding clean scanner bed. Drying of the suspensions under conditions of controlled humidity similar to the work by Zhang et al. 3 was not performed due to time constraints. 4.7 Summary It has been shown that liquid crystals allow the optical detection of particles too small to be viewed directly with a microscope. Furthermore it has been shown that different liquid crystals react differently to the same topographical distortions (within experimental methods), ZLI 1695 is more sensitive than 5CB to low concentrations of surface bound particles. However, it has also been shown that there are serious limitations to these experimental techniques. It is clear that the particles are aggregating as they bind to the 116

117 substrates (individual nanoscopic particles should not be visible in Figure 4.11) and that the aggregates sizes are not known. Also the particles do not form an even monolayer across the area of deposition; drying dynamics generate an unavoidable circular coffee stain formation where the concentration of particles in the edge ring is not known. This means that it is not trivial to estimate the particle concentrations at a point on the surface and so particle concentration cannot be matched to changes in liquid crystal anchoring at the surfaces. For bio-sensing applications it is very important to have reproducible results and to quantitatively understand the relationship between the input and output of a sensor. The current model does not allow the relationship between liquid crystal response and particle size or density to be investigated. Furthermore, without the ability to closely control these variables, the importance of the different physical properties of the liquid crystal cannot be quantitatively assessed and the different optical responses of 5CB and ZLI 1695 cannot be explained. The preliminary experiments in this chapter show that experiments with nanoscopic beads are not a simple way to investigate the important physical parameters of a potential biosensor. Because of this, the decision to move to a different model was made. The new model replaces latex beads with photo-lithographically deposited gold micro dots on silicon substrates. The position and size of the gold dots is very well controlled which allows arrays of dots to be created with known dot size and surface density. This allows the effects of different array properties on the optical response of a liquid crystal to be assessed, and steps towards understanding the limits of detection of a biosensor to be made. It also allows the effects of the elastic constants, birefringence and anchoring energy of a liquid crystal on its optical response to be independently measured and quantitatively evaluated. 1 Gupta, V.K., Skaife, J.S., Dubrovsky, T.B and Abbott, N.L. (1998), Science 79, Guzmán, O., Abbott, N.L. and de Pablo, J.J. (005), J. Chem. Phys. 1, Skaife, J.J. and Abbot, N.L. (1999), Chem. Mater. 11, Bi, X. Huang, S. Hartono, D. and Yang, K.L. (007), Sens. Actuators B 17, Bi, X. and Yang, K.L. (007), Colloid Surf A 30, Freitas, R. A. Jr. (1999), Nanomedicine Volume 1: Basic Capabilities, Landes Bioscience, Georgetown, TX, ( accessed on 13/06/06). 117

118 7 Holmberg, A., Blomstergren, A., Nord, O., Lukacs, M., Lundeberg, J. and Uhlén, M. (005), Electrophoresis 6, Livnah, O., Bayer, E.A., Wilchek, M. and Sussman, J.L. (1993), Proc. Natl. Acad, Sci, USA 90, Williams, D.H., Stephens, E. and Kahn, M. (003), Journal of Molecular Biology 39(), Menikh, A., MacColl, R., Mannella, C.A. and Zhang, X.C. (00), Chem. Phys. Chem. 3, no 8, Weber, P.C., Pantoliano, M.W. and Salemme, F.R. (1995), Acta. Cryst D51, Sigma-Aldrich Product Information Sheet L7655data sheet, (available at 1.File.tmp/l7655pis.pdf accessed 09/1/009). 13 Arrayit product information. (available at streptav.html, accessed 4/06/011). 14 Pulkkinen, A., Jokisaari, J. and Väänänen, T. (1986), J. Mol. Struct. 144, no 3-4, Guillou, J.P.S. (000), An experimental Study of the Selective Reflection Band from a Chiral Nematic Liquid Crystal Device, MSc Thesis, University of Manchester, Department of Physics and Astronomy. 16 Roberts, N.W. (003), Optical Properties and Polarization Sensitivity of Self-Assembled Systems, PhD Thesis, University of Manchester, Department of Physics and Astronomy. 17 Jenkins, F.A. and White, H.E. (1981), Fundamentals of Optics (Fourth Edition), McGraw-Hill International Editions, Maidenhead, Berkshire, Bramble, J.P., Evans, S.D., Henderson, J.R., Anquetil, C., Cleaver, D.J. and Smith, N.J. (007), Liq. Cryst. 34, No. 9, Grollau, S., Guzmán, O., Abbott, N.L. and de Pablo, J.J. (005), J. Chem. Phys. 1, Collings, P. J. and Hird, M. (1997), Introduction to Liquid Crystals Chemistry and Physics, Taylor and Francis, London. 1 Lai, S.L., Huang, S., Bi, X. and Yang, K.L. (009), Langmuir 5, Wahlstrom, E. (1969), Optical Crystallography, John Wiley and Sons, New York. 3 Oswald, P. and Pieranski, P. (005), Nematic and Cholesteric Liquid Crystals, Taylor and Francis, London. 4 Bloss, F.D. (1990) An Introduction to the Methods of Optical Crystallography, R.A.N. Publishers, Marietta, OH, de Gennes, P.G. and Prost, J. (1993), The Physics of Liquid Crystals ( nd edition), Oxford Science Publications, Oxford. 6 Deegan, R.D., Bakajin, O., Dupont, T.F., Huber, G., Nagel, S.R., and Witten, T.A. (1997), Nature 389, Parisse, F and Allain, C. (1996), J. Phys. II France 6, Deegan, R.D. (000), Phys. Rev. E 61, no Lee, Y.J., Gwag, J.S., Kim, Y.K., Jo, S.I., Kang, S.G., Park, Y.R. and Kim, J.H. (009), Appl. Phys. Lett. 94, Ruhwandl, R.W. and Terentjev, E.M. (1997), Phys. Rev. E 55 (3), Kleman, M. and Lavrentovich, O. D. (003), Soft Matter Physics An Introduction, Springer, New York. 3 Zhang, J., Sun, Z. And Yang, B. (009), Curr. Opin. Colloid. In. 14, no,

119 Chapter 5 Modelling a Biological Analyte Using Gold Microdots 5.1 Introduction Due to the complexity with the experimental model detailed in Chapter 4, an alternate model was required. An array of microscopic raised circular gold dots on a silicon substrate was chosen as a model of a monolayer dispersion of biological particles bound to a substrate at specific binding sites. The aim remained to use liquid crystals to detect microscopic topological features. Defects or distortions of the liquid crystal bulk caused by these features are detectable optically as a consequence of the birefringence of the liquid crystals. There are several advantages of this method over the previous work using biotin tagged beads. The controlled photo-lithographic deposition of the gold dots (see section 5.5) allows their exact position to be known without the use of a secondary detection method. Furthermore, precise control of the dot size allows direct quantitative assessment of an individual dot s effect on any defects or director distortion produced. Neither of these was possible whilst the binding and aggregation of the beads was not controllable. In addition, controlling the properties of arrays of micro-sized dots (e.g. array pitch and total percentage of gold coverage) in tandem with dot size and shape, allows the macroscopic effect of a whole array on the liquid crystal alignment to be measured. In this thesis five different nematic liquid crystals are examined. The purpose of the investigation is to identify the liquid crystal with which the response to an array of dots is most clearly detectable. Furthermore, the importance of the physical properties of the liquid crystals when determining the response of the alignment to an array was quantitatively analysed. If an optimal combination of physical properties could be identified for particle detection, an "ideal" liquid crystal could be specified or designed. This chapter outlines the experimental techniques used to characterise these liquid crystals and details the design and manufacture of the gold patterned substrates themselves. In Chapter 3 the presence of a foreign body, such as a latex bead or gold particle, was shown to change the director profile of an ambient liquid crystal. The nature of the distortion and any defects formed are affected by the nature and strength of the 119

120 anchoring of the liquid crystal to the body; whilst the propagation of a distortion into the liquid crystal bulk is largely determined by the elastic constants of the liquid crystal. Two of the liquid crystal elastic constants, K 11 and K 33, were identified as being significantly important. If such a distortion is measured by optical means then the magnitude of any measurement is affected by the liquid crystal's birefringence as well as the thickness of the sample. Preliminary investigations showed that the clearest response to the substrate based arrays occurs at, or close to, the nematic to isotropic phase transitions of the liquid crystals, as seen in Figure 5.1. a b 100 µm c Figure 5.1 Polarised optical micrographs of the behaviour of 5CB on a silicon substrate with raised gold dots as the liquid crystal is heated through the nematic to isotropic transition. (a) 30 C. (b) 35.3 C (=T NI ). (c) 36 C. (The images were taken in reflection with a homeotropically aligned coverslip.) Two arrays of dots measuring 3x3µm (top) and 3x6µm (bottom) are shown, along with the clean silicon area between them. In the nematic phase, Figure 5.1(a), the liquid crystal is largely homeotropic, with areas of tilted alignment over the gold (see section 10

121 5.8 for more in depth discussion). However, at the nematic to isotropic transition, Figure 5.1 (b), a grid-like array of defects that mimics the array of gold dots can be seen. These fade and disappear as the liquid crystal melts into the isotropic phase, Figure 5.1 (c). Similar responses are seen when using other nematic liquid crystal materials. The method by which these images were taken is detailed below. As a result of these observations the physical properties of the liquid crystal materials were measured over a range of temperatures up to their clearing points, T NI. This chapter presents the experimental techniques used to measure the birefringence and the elastic constants K 11 and K 33 of the liquid crystals at temperatures approaching their nematic to isotropic phase transitions. The methods of fabricating the gold patterned substrates with different surface chemistries and of constructing the liquid crystal cells with different thicknesses are detailed. Finally the optical polarising microscopy techniques used to observe the cells are explained. An Abbé refractometer was used to measure the birefringence of each liquid crystal, whilst the elastic constants were calculated from measurements of the capacitance of liquid crystal cells using the method based on the Freedericksz transition as described in Chapter 3. The results of these measurements are given in Chapter 6. The response of the liquid crystals to arrays of gold microdots was measured using optical polarized microscopy, using both images and the intensity of reflected laser light from the liquid crystal as it undergoes a phase transition between the nematic and isotropic phase. The results of these measurements are presented in Chapters 7, 8, 9 and Introduction to liquid crystals used The liquid crystals used were the single component material 5CB and the mixtures E7, ZLI 1695, ZLI 113 and MDA (Merck, GmbH). All of these are thermotropic with room temperature nematic phases. The chemical structures of the liquid crystals can be seen in Figure 5.. 5CB is a single component material and ZLI 1695 is a mixture of different cyanocyclohexylcyclohexanes. E7 is a mixture comprising 51% 5CB, 5% 7CB, 16% 8OCB (4-octyloxy-4 -cyanobiphenyl) and 8% 5CT (4-pentyl-4 cyanoterphenyl). 1 ZLI 113 is 11

122 a mixture of cyano-phenylcyclohexanes and the composition of MDA is currently proprietary knowledge of Merck. a C 5 H 11 CN b C 7 H 15 CN c C 8 H 17 O CN d C 5 H 11 CN e R CN f R CN Figure 5. Schematic diagrams of the chemical structures of the liquid crystals and their components. (a) 5CB, (b) 7CB, (c) 8OCB, (d) 5CT, (e) cyano-cyclohexylcyclohexane, (f) cyano-phenylcyclohexane. 3 R represents the different alkyl chains of the molecules. The physical properties of the liquid crystals known before the investigation are summarised in Table 5.1 5CB and ZLI 1695 were used to allow ease of comparison with the previous experiment (see Chapter 4). E7 was chosen because of its similarity to 5CB except for higher values of K 11 and K 33. ZLI 113 was chosen because it has elastic constants very similar to E7 but a significantly lower birefringence. MDA was selected for its extremely low value of K 33 /K 11, while its dielectric anisotropy ( ε) remains similar to that of the other materials. Since all of the selected liquid crystals, with the exception of 5CB, are not pure materials, there is a biphasic region: a temperature range over which both the nematic and isotropic phases are able to stably co-exist. 1

123 Previously Known Physical Properties of the Liquid Crystals Liquid Melting Clearing n ε K 11 (pn, K 33 (pn, Width of Crystal point point, T NI (0 C, (0 C, 0 C) 0 C) biphasic ( C) ( C) 590nm) 1kHz) region ( C) 5CB ZLI N/A N/A 0.5 E ZLI MDA 01- N/A 79.5 N/A Table 5.1 Previously known physical properties of the nematic liquid crystals used. The values are from Merck data sheets. The elastic constants data are from reference 4. Other values for MDA are from reference 5. The known values given in Table 5.1 are reported for room temperature, not at the isotropic to nematic transition for each material. 4,5 It is important to note that there is some variation within the literature for values of the elastic constants. This is explored in more depth in Chapter Refractive index measurements The birefringence of each liquid crystal was measured using an Abbé 60 Refractometer (Bellingham and Stanley). 6 A schematic of its operating principle can be seen in Figure 5.3. A liquid crystal sample is sandwiched between two prisms where the upper prism is hinged to allow access to the sample area. The upper surface of the lower prism is coated with a homeotropic alignment layer, in this case formed from 0.1% lecithin dissolved in chloroform. The prisms are temperature controlled using a Neslab Endocal refrigerated circulation bath. 13

124 Incident Monochromatic Light Liquid Crystal Sample (40-50 µm thick) Illuminating Prism (ground lower surface, also temperature controlled) θ c Diffuse Lower Surface Field Stop Refracting Prism (very smooth upper surface, also coated with alignment layer) Light Dark Figure 5.3 Schematic of the prisms of an Abbé Refractometer. Incident monochromatic light from a.8mw laser diode of wavelength λ=670nm, passes through the first prism which has a roughened lower surface. This diffuses the light so that each point of the surface acts as an individual point source. The light then passes through the sample and is refracted at the smooth upper surface of the lower prism. For a sample with a single refractive index, a critical angle, θ c, is observed. Beyond this angle, light is totally internally reflected at the sample-glass interface. This can be seen by a clear dark-light division in the viewing lens. Positioning the cross-hairs of the viewing field on the dividing line and reading the position on a Vernier scale allows the refractive index of the sample to be read from the tables supplied with the refractometer. Thus it is important that the refractive index of the lower prism be very well known to ensure the accuracy of calculations. 7, 8 When using a birefringent liquid crystal sample, two refractive indices are present. For this reason is it important that the liquid crystal is homeotropically aligned between the glass prisms and that this alignment is of high quality. Light polarised in the plane of the glass surface at right angles to the homeotropic director is refracted at the surface due to the ordinary refractive index n o. Light polarised at 90 to this direction is refracted by the extraordinary refractive index n e. There are, therefore, two different critical angles and two dividing lines in the field of view. The alignment of the liquid crystal between the prisms is such that these are equal to the absolute refractive indices n and n // of the liquid crystal material. These are read off separately to calculate the 14

125 birefringence. More details of the function of a refractometer can be found in references 6, 7 and 8. Due to the large and bulky nature of the refractometer spin-coating an alignment layer is not possible. Instead, the alignment layer must be deposited by carefully wiping a lens-cleaning tissue, moistened with the 0.1% solution of lecithin in chloroform, a single time across the surface of the prism. Since it is extremely important that the surface is as clean as possible before this is done, the glass was cleaned with optical grade methanol seven to eight times before deposition of the alignment layer. Approximately 1- µl of a liquid crystal was then pipetted onto the surface without allowing the pipette to touch the glass. The upper prism was then secured and the sample left for 3-4 hours to allow the liquid crystal to orient itself. This lengthy period is necessary because the liquid crystal sample is very thick (~50µm) relative to more usual sandwich cell viewing geometries (5-0 µm). 5.4 Capacitance measurements using commercial cells In Chapter 3, the method by which values of K 11, K 33, ε // and ε may be calculated from capacitance measurements was outlined. Measurements were carried out using commercial cells obtained from EEV, Chelmsford. The cells had anti-parallel alignment and were 5.5µm thick. The thickness of each cell was confirmed using the method of measurement described in Chapter 4 before they were filled with liquid crystal. In order for the capacitance measurements to be taken, wires were soldered to the cells using indium shot. a The glass was cleaned with acetone prior to a base layer of indium being deposited. Wires were then soldered to this layer, rather than to bare glass, as this was found to increase the strength of the soldered link and increase the durability of the finished cell. The cells were subsequently filled with the liquid crystal in the nematic phase by capillary action. Filling was performed in an evacuated bell jar in order to remove air bubbles trapped by the influx of the liquid crystal and any air dissolved in the LC. a Indium, shot, -5 mm diameter, % metal basis. Sigma Aldrich, product number: G. 15

126 Subsequently the cells were sealed with U.V. curing glue b and cured in an ultra-violet oven. All areas of the filled cell not covered by glue were screened from the ultraviolet light by black card during the procedure to limit any degradation due to U.V. exposure of the liquid crystal Elastic constants calculated from capacitance measurements The capacitance measurements were carried out using a Wayne Kerr Electronics Precision Component Analyser 6430A which applies a sinusoidal field at 10kHz over a voltage range 0-10Vrms. The field was applied out of plane of the cell, thus at a right angle to the alignment of the liquid crystal, in order to use the Freedericksz effect to calculate the elastic constants (see Chapter 3 for more details). The dielectric permittivity, ε, was calculated by measuring both the empty, C empty, and filled, C full, capacitances of the liquid crystal cells. Previous work by Clark et al. 9 showed that edge effects and stray capacitance in similar cells without guard rings amounts to ~10% of the empty capacitance of the cell and that this is approximately constant for varying permittivities. Thus C ε = C full empty X X, (5.1) where X represents the edge effects and the stray capacitance of the cell and is equal to 10% of C empty. The component analyser was controlled by a LabView program and the capacitance measurements were recorded by a PC. The calculated dielectric permittivities were then analysed using a MATLAB program to obtain values for ε //, ε, K 11 and K 33 as detailed below. As explained in Chapter 3, measurements of the dielectric permittivity of a planar aligned liquid crystal can be used to calculate its elastic constants by increasing the applied voltage above the Freedericksz threshold. However, measurements of the b Norland Optical Adhesive, U.V. Curing Glue

127 threshold voltage V 0 and the gradient of the ε vs. V curve do not give the best results when calculating K 11 and K 33. This is because the electric field within a liquid crystal cell will not be completely uniform and the liquid crystal molecules will be slightly tilted away from perfect alignment with the substrates. Instead the entire permittivity curve was used to find these parameters. For the purposes of the following derivation it is assumed that the liquid crystal is confined by a cell of thickness d with strong anti-parallel anchoring, α is the angle between the director, n, and the x-y plane. A sketch of the system can be seen in Figure 5.4. This is the same set-up as is required to make the measurements described in Chapter 3 but is shown here for clarity. a V=0 d n z y x n b V>V 0 n α x Figure 5.4 Schematic of the director profile of a planar aligned cell filled with nematic liquid crystal. (a) with no applied voltage (b) with a voltage greater than the Freedericksz threshold applied between the surfaces of the cell. The following equations were derived by Welford and Sambles 10 and build upon the work by Deuling. 11 Values of K 11, K 33, ε // and ε are found that minimise the Gibbs free energy by fitting the permittivity measurements to values calculated from the energy equations. The Gibbs free energy of a liquid crystal, G, in an electric field is given by G d = + 0 ( F F ) el diel dz, (5.) 17

128 where F el is the energy contribution per unit volume from the elastic deformation of the liquid crystal and F diel is the energy contribution per unit volume of the electric field acting on the dielectric permittivity of the liquid crystal. Expanding equation 5. therefore gives G 1 dα dz d = // 0 1 ( K cos α + K sin α ) ε E ( ε sin α + ε cos α ) dz. (5.3) The Euler-Lagrange equation of calculus of variations: d df df =, (5.4) dz dα dα d dz where F is the energy per unit volume and is defined by dg F = ' (5.5) dz is then used to give: d α ( K dz, 11 cos α dα + K33 sin α) + 33 K11 dz ( K ) D sinα.cosα = ε 0 ( ε ε ) ( ε sin α + ε cos α ) // // sinα.cosα (5.6) where D is the electric displacement field in the z direction, related to the electric field, E, by D=ε 0.ε.E or, ( ε sin α + ε α ) D = ε. (5.7) 0 // cos 18

129 From Figure 5.4 the system is seen to have symmetry about z=d/. Using the boundary conditions that for z=d/, dα/dz=0 and α= α max, an equation may be derived for reduced voltage as a function of α max, γ and K. V V ( 1 + γ sin α ) 1 α max 1 + K sin α = max 0 π 0 max max sin ( 1 + γ sin α )( sin α α ) 1 dα, (5.8) ε // ε K 33 K11 where γ = and K =. V 0 is the threshold voltage and is defined by ε K // 11 K11 V 0 = π. (5.9) ε 0 ( ε ε ) // Gruler 1 derived an expression for the capacitance in a similar fashion: ( 1 + K sin α )( 1 + γ sin α max ) ( sin α sin α ) α max dα ε 0ε 0 max C =. (5.10) 1 d α max + 1 K sin α ( )( ) dα γ sin α max sin α max sin α 1 Equations 5.8 and 5.10 are combined to give ( 1 + K sin α )( 1 + γ sin α max ) ( sin α sin α ) 1 α max ε ( ) ( ) ε α = + max 1 γ sin α max d α. (5.11) π 0 max 1 For more detailed descriptions of these derivations see references 10 and 11. The fitting program was written by Dr. Paul Brimicombe of the Nonlinear and Liquid Crystal Physics group at The University of Manchester. It uses approximate values of K 11, K 33, ε // and ε to calculate a value of α max from equation 5.8, for all voltages in the measurement range. This is then used to calculate ε from equation 5.11 for the same voltages. These are compared to the experimentally obtained values and the X error calculated. The MATLAB non linear curve fitting function lsqnonlin 13 is then used to 19

130 adjust K 11, K 33, ε // and ε in order to minimise this error. For a more detailed explanation of the function lsqnonlin see reference 13. The calculations here and the fitting program are explained in more detail in Appendix A and Appendix B respectively. 5.5 Substrate construction The substrates consist of circular gold micro-dots, varying in diameter from 1µm to 16µm, raised approximately 50nm from a silicon oxide wafer. The wafers are pure silicon with a 90nm layer oxide on top with a surface roughness ~1nm. They were fabricated with the aid of Dr Peter Blake and Dr Tim Booth from the Condensed Matter Physics group at The University of Manchester. a Imaging Resist Lift-off Resist Mask U.V. Illumination ~ -3 µm Silicon Oxide Wafer b Au Film ~50nm Thick Figure 5.5 A side profile of the photolithographic process used to manufacture the Au-Si substrates. (In reality the mask is much closer to the top layer of photo-resist than it appears here and diffraction of the incident radiation has been exaggerated for clarity.) (a) Ultraviolet light passing through the mask softens and breaks down the top layer, the imaging resist. Developer is then used to remove the patterned imaging resist along with a slightly larger area of lift-off resist. (b) An Au film is then deposited, by vapour deposition, over the whole area of the wafer. The bi-layer, under-cut resist profile promotes discontinuous deposition between the top and bottom layers of gold. All remaining resist is then removed leaving just the bottom island of gold. The substrates were constructed using bi-layer photolithography, see Figure 5.5. Two different layers of photo-reactive polymer, known as photo-resist or simply resist, are deposited onto the silicon wafer by spin coating. Between each stage high temperature baking was used to ensure no moisture on the substrate interferes with the layering. 130

131 The lower layer is the lift-off resist, polymethylglutarimide or PMGI from MicroChem. 14 This was softened using ultraviolet light before the imaging resist, S1805 from Shipley Company, was applied. 15 After both layers were deposited the photo-resist was exposed to ultraviolet light through a patterned photolithographic mask. c The substrate was then immersed in Microposit MF-319 developer fluid, 16 which removes the areas of the imaging resist that have been affected by the ultraviolet light and a slightly larger area of the pre-softened lift-off resist below. A 50nm thick layer of gold was vapour-deposited onto the entire substrate. The distinctive under-cut resist profile promotes discontinuous deposition over the holes in the resist layers. Subsequently, the remaining resist along with the upper layer of the gold was removed with developer, leaving the gold micro-dots alone on the surface of the silicon. More information on the photolithographic process can be found in references 14 and 15. Each substrate supported two sets of arrays as can be seen in Figure 5.6. Each set comprises arrays with a range of different spot sizes and spot separations (array pitch). The array parameters were 1µm diameter spots with.5µm array pitch (these arrays were labelled 1s.5p), µm spots with 5µm array pitch (s5p), 4µm spots with 10µm array pitch (4s10p), 8µm spots with 0µm array pitch (8s0p), and 16µm spots with a 40µm array pitch (16s40p). These parameters were chosen to provide a range of spot sizes for a constant percentage of gold surface coverage. Arrays with parameters: 4µm spots with 7µm array pitch (4s7p), 4µm spots with 10µm array pitch (4s10p), 4µm spots with 0µm array pitch (4s0p) and 4µm spots with 40µm array pitch (4s40p) were used to investigate the effect of increasing spot separation (decreasing gold surface coverage) for constant spot size. c The photolithography mask was supplied by Photronics, Inc. 131

132 Array Series 1 Array Series A B C D E F G H I J Array Key A: plain gold B: 8s0p(a) C: 4s10p D: s5p E: 1s.5p (not formed) F: 8s0p(b) G: 4s40p H: 4s0p I: 4s7p J: 16s40p Figure 5.6 Schematic of the layout of the arrays on each substrate. Array Series 1 and are duplicates. The arrays measured 1.5mm by 1.5mm to ensure they covered the whole of the viewing area of the microscope (see section 5.8). They were separated from each other by 1mm to enable determination of the alignment on the plain silicon oxide substrates by inspection and by conoscopy. Plain un-patterned gold coated substrates were prepared to test the effects of different surface chemistries. Gold was evaporated onto clean glass microscope slides. Half of each slide was covered by an aluminium mask in contact with the glass. This produced slides that illustrated the difference between the effect of the gold layer with controlled surface chemistry and the glass on the alignment of supported liquid crystal films. The resultant gold layers were approximately 500nm thick. This was a much cheaper and more efficient method than using the photolithographic method of fabricating the arrays. 5.6 SAM construction It has been shown many times in the literature that liquid crystal alignment is susceptible to surface chemistry. It is also known that the surface chemistry of gold is readily changed by exposure to biological materials. 17,18 One consequence of this is that gold surfaces can easily be contaminated and that this can cause unpredictable effects in adjacent liquid crystal films. To avoid this problem, self assembled monolayers (SAMs) of alkanethiols were created on the substrates. This ensures that consistent surface chemistry is presented across the gold arrays. Alkane thiols were used because they have a sulfur group (SH) at one end of the alkyl chain. This sulfur is known to bind covalently to gold surfaces and the alkyl chains of the thiols orient 13

133 perpendicular to the gold surface. 19 A schematic diagram of a thiol SAM on a gold surface can be seen in Figure 5.7. R R R R R R R R S S S S S S S S Au Figure 5.7 Schematic diagram of a thiol SAM on a gold surface, the hydrocarbon chain length and functional R group differs between thiols. The high degree of uniformity and order in a SAM is due to two chemical processes: the reversible nature of the gold-sulphur bond and the Van der Waals forces that exist between the hydrocarbon chains of the thiols. 0,1 The reversible process of thiol absorption to gold can be summarised by the chemical equation: ( CH ) SH Au s R( CH ) S Au 1 s H R n + n +, (5.1) where R(CH ) n SH is the unbound thiol in solution, Au s is a binding site on the gold surface, and R(CH ) n S-Au s is the thiol bound to the gold. 0 Initial binding of the sulphur to the gold is random with no organisation of hydrocarbon chains. An exchange between thiols bound and in solution continues until Van der Waals forces between parallel hydrocarbon chains stabilises the organic layer. The free energy of the monolayer is minimised where the chains orient perpendicular to the gold surface and this causes the SAM to present a uniform surface of chemical end groups. 1 The effects of two thiols on liquid crystal alignment were investigated. 3-Mercapto-1- propanol (which terminates in a alcohol, OH, group) and 3-Mercaptopropionic Acid (carboxylic acid, COOH, terminated) were used because they have the same alkyl chain length but present different end groups to the liquid crystal. The chain length was kept constant to avoid possible steric interactions affecting the comparison. 133

134 Alcohol and acid terminated SAMs were used because they have both been reported in the literature to induce planar alignment in a variety of nematic liquid crystals which contrasts with the homeotropic alignment observed on the silicon oxide wafers. The chemical structures of these thiols can be seen in Figure 5.8. O HS OH HS OH a b Figure 5.8 Chemical structures of the two thiols used: (a) 3-Mercapto-1-propanol, (b) 3-Mercaptopropionic Acid. Figures from Sigma-Aldrich product data sheets. SAMs were constructed by immersing patterned substrates in a 5mM solution of the thiol in ethanol for 1 hours. They were then rinsed copiously in pure ethanol and dried with nitrogen gas. They were rinsed a final time for 0 seconds in a 0.1M solution of hydrochloric acid and dried a second time. This method is described in the literature and shown to produce uniform SAMs on gold surfaces for the purpose of controlling LC alignment Cell fabrication The substrate cells were constructed using cover-slips treated with homeotropic alignment layers. These were prepared using the method described in Chapter 4. Homeotropic alignment was chosen to contrast with the planar alignment promoted by the SAM coated gold. The induced hybrid aligned nematic (HAN) director distortion was chosen because this was found to give the greatest optical contrast between topographical perturbations and flat surfaces in Chapter 4. In Chapter 4, a solution of 0.1% lecithin dissolved in chloroform was used as an alignment agent. However, lecithin is a fatty, organic compound 4 that does not covalently bind to the surface of the glass. At the relatively high temperatures (>70 C) required to reach the nematic to isotropic phase transitions of some of the liquid crystals used it dissociates from the surface and dissolves into the liquid crystal bulk. Instead a solution of 0.5% cetyl trimethyl ammonium bromide, CTAB, in distilled 134

135 water was used. CTAB alignment layers also do not covalently bond to glass but are more stable at high temperatures. Homeotropic alignment was used because of the ease with which uniform alignment can be obtained. This is true even in cases where the lower substrate's anchoring is not uniform, (see Chapter 4) as in this case where different chemical and topographical structures exist on the surface. A diagram of a completed cell can be seen in Figure µm polystyrene spacer beads Liquid Crystal Coverslip Homeotropic alignment layer (CTAB) Cell Thickness 7-10µm Silicon substrate Gold micro-dots ~50nm thick Figure 5.9 Schematic of a liquid crystal cell constructed with a patterned gold-silicon substrate. The coverslips were separated from the substrates using 5µm diameter polystyrene beads and secured using U.V. curing glue (Norland Optical Adhesive 71). Cell thickness was varied by replacing the beads with 10µm beads and strips of 0µm thick Mylar film. The thickness of the cells was measured using the interference technique detailed in Chapter 4. The thicknesses were found to be between 7 and 10µm for the 5µm beads and varied by less than 1µm across the area of the cell. The cells were filled with the liquid crystals in their isotropic phase by capillary action. After filling, the cells were heated to 0 C above the phase transition of the liquid crystal and held there for one hour. This was to remove filling induced anisotropy in the alignment. 5.8 Optical polarising microscopy Microscopic observations and measurements of the liquid crystal samples on the goldsilicon substrates were carried out using a Leitz LABOURLUX 1POLS polarising microscope with a reflection arm attached. A schematic of the experimental set up can be seen in Figure

136 Neutral Density Filters Diffuser Photodiode / Digital Camera.8mW, 670 nm laser diode / white light source for normal observations Linear Polarisers Interchangeable Laser/White Light Holder Sample Temperature Controlled Hot Stage Figure 5.10 Schematic of optical polarised microscope set up for measuring the effect of Au-Si patterned substrates on liquid crystal alignment. The reflection arm normally incorporates a white light source for reflection studies of materials. However, in this case it was customised to allow the additional use of a.8mw, λ=670nm laser diode. The laser beam passes through a diffuser to create a uniform intensity distribution across the sample. Neutral density filters were added to modulate the intensity of the light further to prevent saturation of the photodiode. The response of the photodiode was tested using the reflection of the laser from a mirror. The response of the diode was plotted against cos θ, where θ is the angle between two polarisers in the beam path. The relationship was shown to be linear from 0-10V. The temperature of the samples was controlled with a Linkham hotstage and Linkham TMS91 temperature controller described in Chapter 4. These are capable of controlling and measuring the temperature of the sample to an accuracy of 0.1K. Images of the liquid crystal cells in-situ were taken using the white light reflection source and the same DeltaPix digital camera used in Chapter 4. Measurements of the light reflected from the cells were taken using illumination from the laser diode detailed above with the photodiode mounted in place of the camera. Initial images taken showed that 5CB exhibits a tilted alignment on the gold spots in the nematic phase. In Figure 5.11 images of a cell with homeotropically aligned 5CB on a gold patterned silicon substrate can be seen. The brightness of the gold spots can be seen to increase and decrease as the cell is rotated, indicating a planar component to 136

137 the liquid crystal alignment. It should be noted that the change in brightness is not consistent across different gold spots. This indicates that any tilted alignment does not have a uniform direction across the array. 100µm Polariser Directions Figure 5.11 Polarised optical images of the behaviour of 5CB in the nematic phase on an array of 3x6µm Au spots. The tilted planar alignment of the liquid crystal on the spots can be seen as the sample is rotated. (The images were taken in reflection with a homeotropically aligning coverslip and a 0x objective. There is a 0 rotation between frames. The large defect on the clean area of the substrate is included as a reference point.) Following the observation that an array of gold spots can produce an array of brightly textured defects at the nematic to isotropic transition, see Figure 5.1, it was decided to quantify the response of the liquid crystals by measuring the intensity of light reflected from the array. A laser diode was used instead of white light illumination to avoid issues arising from the different dispersion relations of the different liquid crystals. The intensity of light reflected from the liquid crystal sample was normalised using the intensity of unpolarised laser light reflected from a mirror. This was initially found to saturate the photodiode and so a specific combination of neutral density filters was used to reduce the intensity to a measurable level. The laser's output was measured over a period of eight hours. It was found to reduce in intensity during the first hour and to vary by approximately 0.1% after that time. 137

138 Measurements were recorded by an Agilent 34401A 6½ Digital Multimeter and compiled by a PC using a standard GPIB port. The temperature controller was steered using a LabView program through a PC serial port. An example graph for the reflected intensity of a cell filled with MDA can be seen in Figure Biphasic Region Normalised Intensity (Arbitrary Units) Nematic Phase Isotropic Phase Temperature ( o C) Figure 5.1 The reflected light intensity from homeotropically aligned MDA on an array of circular plain gold microdots 8µm in diameter, separated by 0µm. The sample was cooled at a rate of 1 C.min -1. As the cell is cooled from the isotropic phase into the nematic phase, a peak in the intensity is recorded at the phase transition. The width of the peak roughly corresponds to the temperature range of the biphasic region of the material. It should be noted that the intensity of reflection in the nematic phase is slightly higher than in the isotropic phase. This may be explained by imperfect homeotropic alignment due to flaws in the aligning coverslip and the tilted anchoring to the gold microdots. The samples were heated and cooled at a rate of ±1 C.min

139 5.9 Summary In this chapter, the equipment and techniques used to measure the physical properties of the liquid crystals used and their response to arrays of gold microdots were described. Details of the gold patterned substrates and the methods by which they were manufactured were outlined. In Chapters 8, 9 and 10 the results obtained from these substrates are presented and analysed. 1 Merck Data Sheets, Merck KGa, Darmstadt, Germany. Saunders, F.C. (1988), Electro-optic modulator, European Patent Application no , filed 4 October Chemical Book, website ( accessed on 17/19/11). 4 Brimicombe, P.D., Kischa, C., Elston, S.J. and Raynes, E.P. (007) JAP 101, Strömer, J.F, Raynes, E.P. and Brown, C.V. (006) APL 88, Bellingham and Stanley Ltd., Tunbridge Wells, Kent, ( accessed 13/01/10). 7 Jenkins, F.A. and White, H.E. (1981), Fundamentals of Optics (Fourth Edition), McGraw-Hill International Editions, Maidenhead, Berkshire, Hanson, J. (006), Refractometry: Theory, ( accessed 13/01/10). 9 Clark, M.G., Ranyes, E.P., Smith, R.A. and Tough, R.J.A. (1980), Journal of Physics D: Applied Physics 13, Welford, K.R. and Sambles, J.R. (1987), Mol. Cryst. Liq. Cryst. 147, Deuling, H.J. (1987), Mol. Cryst. Liq. Cryst. Lett. 19, Gruler, H., Scheffer, T.J. and Meier, G. (197), Z. Naturforsch, 7 A, The MathWorks, ( accessed on 08/0/10). 14 MichroChem Product data sheet, ( accessed on /01/10). 15 Shipley Company MSDS, ( accessed on /01/10). 16 Shipley Company MSDS, ( accessed on 4/01/10). 17 Zhang, X. (010), Electrochem. Commun. 1, Issue 10, Gupta, V.K., Skaife, J.S., Dubrovsky, T.B and Abbott, N.L. (1998), Science 79, Sellers, H., Ulman, A., Shnidman, Y. and Eilers, J.E. (1993), J. Am. Chem. Soc. 115, Schlenoff, J.B., Li, M. and Ly, H. (1995), J. Am. Chem. Soc. 117, Love, J.C., Estroff, L.A., Kriebel, J.K., Nuzzo, R.G. and Whitesides, G.M. (005), Chem. Rev. 105, no 4, Alkhairalla, B., Allinson, H., Boden, N., Evans, S.D. and Henderson, J.R. (1999), Phys. Rev. E 59, no 3, Luk. Y.Y., Yang, K.L., Cadwell, K. and Abbott, N.L. (004), Surf. Sci. 570, Levene, P.A. and West, C.J. (1917), The Laboratories of the Rockefeller Institute of Medical Research, Downloaded from The John Rylands University Library, ( accessed 5/01/10). 139

140 Chapter 6 Ancillary Results Physical Properties of Liquid Crystals In this chapter the measurements of birefringence ( n) and the elastic constants, K 11 and K 33, of the five liquid crystals used are presented. These results are necessary to understand the optical measurements of the liquid crystals at temperatures approaching the nematic to isotropic transition on patterned substrates. In particular,the birefringence may be expected to influence the optical signal observed, while K 11 and K 33 define the elastic energy associated with the formation of defects. Although the room temperature values are known (see Table 5.1) specific values at the nematic to isotropic phase transitions of the liquid crystals are not easily available. 6.1 Refractive index measurements Refractive index measurements were taken with an Abbé Refractometer as described in Chapter 4. Calibration tables were used to convert readings taken from the Abbé into refractive index values. These tables are designed to be used for measurements taken at 0 C and with a 589.6nm light source. However the measurements for this thesis were taken using a 670nm wavelength laser diode and over a temperature range of 0-75 C. Calculations were therefore performed to modify the calibration tables to account for these changes, following the guidelines detailed in the equipment manual. 1, The Abbé Refractometer is capable of accuracies in the measurement of refractive index of ± However, the error in manually determining the optical extinction angles of the prism was consistently greater than this and was found to be ~±0.00. This is due to a hazy bright-dark boarder that is cause by imperfect liquid crystal alignment within the Abbé. It was particularly unclear at temperatures greater than approximately 60 C because lecithin was used as the alignment agent and this is known to dissociate from the glass at high temperatures. (Lecithin had to be used to facilitate cleaning of the Abbé between measurements.) The standard deviation of multiple measurements taken at the same temperature was calculated and a standard error was derived. In most cases the error in the measurement of the refractive index, n, is included within the symbols of the graphs (the exception of E7 is explained 140

141 below). The temperature measurements of the Abbé are self consistent to ±0.1 C. However, the absolute temperature and thus the reduced temperature, of the liquid crystals, needs to be adjusted with reference to the clearing point of each liquid crystal, T NI. In the case of 5CB this was easily determined as there is a sharp transition between the phases that is easily distinguishable by eye. It was determined that the clearing point of 5CB could be determined to within ±0. C. The other liquid crystals used are mixtures and therefore exhibit a biphasic region (a temperature range where the nematic and isotropic phases co-exist stably). The clearing point was determined to be the temperature for which the nematic phase could no longer be observed and taken as the temperature at which two refractive indices, could no longer be measured. For these mixtures it was found that the temperature of the transition could not be measured more accurately than ±0.5 C and so this was used for the approximate uncertainty of the temperature measurements. This error is omitted from the graphs below for clarity. E7 was chosen as a reference material to test the validity of the measurement technique because it is a well understood liquid crystal and its physical properties have been recorded by many individuals. Measurements of its refractive indices as a function of temperature were also available. Measurements of n e and n o for E7 are shown in Figure 6.1. It can be seen that there is good agreement between these data and that taken by Allinson

142 1.75 n o n e 1.70 Allinson n o Allinson n e Refractive Index Temperature ( o C) Figure 6.1 Variation of refractive index with temperature for E7, including a comparison with results from reference 3. The errors in the measurement of n e and n o can be seen to be less than the size of the data symbols in most cases. However, as the temperature approaches the nematicisotropic transition, the uncertainty in n o increases. This is because at high temperatures the optical boundary at the second angle of extinction becomes more difficult to discern and the variation between measurements becomes greater. 14

143 The birefringence of E7 can be seen in Figure 6. this also shows excellent agreement with Allinson s data. 0.0 Birefringence Allinson Birefringence 0.15 Birefringence Temperature ( o C) Figure 6. Birefringence of E7, measured values compared with those from reference 3. Values of n e and n o for 5CB are shown in Figure

144 n o n e 1.66 Refractive Index Temperature ( o C) Figure 6.3 Variation of refractive index with temperature for 5CB. The temperature profiles of n o and n e seen here for E7 and 5CB are typical for nematic liquid crystals at temperatures below the isotropic phase. Examples of this can be seen in many liquid crystal text books. 4,5,6 The other liquid crystals show slightly different temperature profiles, possible reasons for this are explained below. 144

145 Values of n e and n o for ZLI 1695 are shown in Figure n o n e Refractive Index Temperature ( o C) Figure 6.4 Variation of refractive index with temperature for ZLI The behaviour of n o here is different from that seen for E7 and 5CB. In the previous two cases, n o was seen to increase slowly as a function of increasing temperature. In this case, and in the case of ZLI 113 (see Figure 6.5), n o initially decreases as the temperature rises until it reaches a minimum and then increases slightly close to the phase transition. This matches the behaviour of other multi-component materials in the ZLI line observed by Soorys et al. 7 and for the single component liquid crystal 5PCH by Li et al. 8 This can be explained by competition between two of the liquid crystals' physical properties that both contribute to the refractive index: the order parameter and the polarisability. The order parameter of the nematic phase decreases as a function of temperature and causes the value of n o to increase. However, the polarisability of the liquid crystal mesogens is also a function of temperature. The lower the polarisability, the lower the refractive index of both n e and n o. If the effect on the refractive index of a decrease in the polarisability is greater over a given 145

146 temperature range than the effect of the order parameter, it could cause the value of n o to decrease in this manner. Values of n e and n o for ZLI 113 are shown in Figure n o n e Refractive Index Temperature ( o C) Figure 6.5 Variation of refractive index with temperature for ZLI 113. Here, the initial decrease in n o is less significant than for ZLI This may reflect a different relationship between polarisability and temperature. 146

147 Values of n e and n o for MDA are shown in Figure n e n o 1.64 Refractive Index Temperature ( o C) Figure 6.6 Variation of refractive index with temperature for MDA It should be noted that it was not possible to reach the nematic-isotropic transition for MDA This is because the transition temperature, 79.5 C, is outside of the operating range of the ABBÉ refractometer. The result of this is that it was not possible to calculate a true reduced temperature for this material for comparative purposes. This is accommodated by increasing the error in the temperature for MDA to ±1 C. 147

148 Birefringence as a function of temperature is shown for each of the five liquid crystals in Figure CB E7 0.0 ZLI 1695 ZLI MDA Birefringence Reduced Temperature (K) Figure 6.7 Comparison of the birefringence of the liquid crystals as a function of reduced temperature as they are heated towards the isotropic phase. Error bars for n are contained within the symbols for all materials. The errors bars for temperature are contained for all materials except MDA It can be seen that the values of birefringence for 5CB, E7 and ZLI 113 appear to collapse to the same point when plotted as a function of reduced temperature. This might be expected for the first two, as 5CB is a major component of the mixture that comprises E7. However, ZLI 113 is a mixture comprising multiple phenylcyclohexanes. 9 ZLI 1695 comprises a mixture of cyanocyclohexylcyclohexanes 10 and it was chosen because of its extremely low value of n at room temperature; this is carried through towards the transition. It is harder to extrapolate the value of birefringence for MDA at the transition but it appears to be similar to those of the higher four liquid crystals rather than that of ZLI

149 6. Elastic constants measurements It was shown in Chapter 3 that the distortion of LC alignment induced by shaped surfaces and/or particles is partly dependent on the elastic constants of the LC. In order to understand the behaviour of different liquid crystals on arrays of raised spots at the nematic-isotropic transition, it is necessary to have information on their elastic constants at these temperatures. As described in Chapter 5, capacitance measurements were taken in 5.5µm thick homogenously aligned cells filled with each of the five liquid crystals at temperatures approaching the phase transition. The transition was determined optically as the point at which no more of the nematic phase was visible between crossed polarisers. This gives an error in the measurement of the temperature of ±0.1 C, the same as the temperature accuracy of the hotstage and temperature controller. The size of this error is covered by the size of the symbols on the following graphs. The permittivity of the system, ε, was calculated from the capacitance and the fitting method described in Chapter 5 and Appendix A was used to derive values for ε //, ε, K 11 and K 33. The errors in the values derived by the program are also consistently smaller than the symbols on the following graphs. The values of ε //, ε were found to have good agreement with existing data available for both 5CB and E7. A comparison between the fitted values of K 11 and existing data taken by different methods can be seen for E7 in Figure 6.8. Measurements are plotted against Reduced Temperature which is defined as the difference between the absolute temperature of the measurement and the nematic to isotropic phase transition of the liquid crystal (T-T NI ). 149

150 1 This work K 11 Allinson K 11 Bancroft K Raynes K 11 8 K 11 (pn) Reduced Temperature (K) Figure 6.8 Comparison of fitted values of K 11 for E7 as a function of reduced temperature with results obtained by others (see references 3, 11 and 1). The fitted data is compared with measurements taken by Allinson 3, Bancroft 11 and Raynes et al. 1 Allinson obtained measurements by using a magnetic field to re-orient the director of E7 in thick cells (~47µm) and the optical retardation of the LC. Values of K 11 and K 33 were obtained by measurements of the gradient of the optical retardation as a function of magnetic field strength and extrapolated to give the critical field. Bancroft used a dynamic light scattering method and Raynes et al. used capacitance measurements on thinner (5µm) twisted nematic cell to calculate the elastic constants based on a model by Gruler et al. 13 The fitted data appear to lie within the variation of others measurements and within fitting errors of the results of Bancroft and Raynes. 150

151 The fitted values of K 33 are compared with data from Allinson and Raynes in Figure This work K 33 Allinson K 33 Raynes K K 33 (pn) ReducedTemperature (K) Figure 6.9 Comparison of fitted values of K 33 for E7 with results obtained by others (see references 3 and 1). Again the fitted data obtained here shows good agreement, within error, with the data reported by Raynes et al. It is noted by Allinson that significant systematic error arises from different equipment used even in cases of the same experimental technique. 151

152 Comparison data was also available for K 11 values for 5CB and is shown in Figure This work K 11 Hopwood K 11 Bancroft K 11 5 K 11 (pn) ReducedTemperature (K) Figure 6.10 Comparison of fitted values of K 11 for 5CB with values obtained by others (see references 11 and 14). The fitted data of this thesis lie within errors of the data reported by Hopwood 14 and Bancroft. Hopwood performed experiments using both electric and magnetic fields to induce a director distortion and measured the threshold fields by optical retardation observations. Hopwood also collated data from a variety of sources for measurements of K 11 and K 33 for 5CB. He showed that there is a variation of ~10% in values reported by different people using different techniques. The results obtained here by the fitting of capacitance measurements vary by <10% from those obtained by others. Values of K 33 for 5CB can be seen in Figure Values of K 11 and K 33 for ZLI 1695, ZLI 113 and MDA can be seen in Figure 6.1, Figure 6.13 and Figure 6.14 respectively. 15

153 8 7 6 K 33 (pn) R educed Tem perature (K) Figure 6.11 Calculated values of K 33 for 5CB as a function of reduced temperature K 11 K Elastic Constants (pn) Reduced Tem perature (K) Figure 6.1 Fitted values of K 11 and K 33 for ZLI 1695 as a function of reduced temperature. 153

154 0 18 K 11 K 33 Elastic Constants (pn) R educed Tem perature (K) Figure 6.13 Fitted values of K 11 and K 33 for ZLI 113 as a function of reduced temperature. Elastic Constants (pn) K 11 K R educed Tem perature (K) Figure 6.14 Fitted values of K 11 and K 33 for MDA as a function of reduced temperature. 154

155 MDA is unusual in that K 11 is consistently greater than K 33. This was expected and was the reason that MDA was included in the experiments. It was not possible to calculate the elasticity of MDA for low values of reduced temperature close to the phase transition. This was because, as the temperature increases into the biphasic region, capacitance measurements become considerably noisier and it was not possible to fit predicted values of the physical parameters to the resultant permittivity curves. A comparison of K 11 for the five different nematics is shown in Figure It can be seen that, as a function of reduced temperature, the values of K 11 for four of the five LCs collapse to a single curve. This might be expected for 5CB and E7 due to their relative compositions but the compositions of ZLI and ZLI are significantly different. Values for MDA are significantly below the spread of the data for the other materials. 7 5CB K 11 E7 K 11 6 ZLI 1695 K 11 ZLI 113 K 11 5 MDA K 11 K 11 (pn) Reduced Temperature (K) Figure 6.15 Comparison of fitted values of K 11 for the five LCs investigated as a function of reduced temperature. 155

156 The spread of data for K 33 across the five nematics (see Figure 6.16) is significantly larger than for K 11. Again 5CB and E7 appear to have similar values close to the phase transition but the spread among the other materials shows clearly different behaviour and values for MDA can be seen to be much lower than for the other materials. 14 5CB K 33 E7 K 33 1 ZLI 113 K ZLI 1695 K 33 MDA K 33 K 33 (pn) Reduced Temperature (K) Figure 6.16 Comparison of fitted values of K 33 for the five LCs investigated. It has been reported in the literature that the ratio of K 33 /K 11 also has an effect on the ease with which liquid crystal alignment can be influenced. 15 This ratio for each of the five liquid crystals is plotted against reduced temperature in Figure

157 ..0 5CB K33/K11 E7 K33/K11 ZLI 113 K33/K11 ZL1695 K33/K11 MDA K33/K K33/K Reduced Temperature (K) Figure 6.17 Comparison of the fitted values of K 33 /K 11 for the five LCs investigated. The relationship between the ratio of the elastic constants and temperature appears to be more complicated than either of the constants alone. However, a clear spread of values at the phase transition can be seen between the different liquid crystals. 6.3 Summary The birefringence and elastic constants of the five liquid crystals have been measured as a function of reduced temperature. Comparison of values obtained for E7 and 5CB with results reported by others have shown good agreement within the errors derived from the fitting method and within the spread of similar data from literature. This suggests that the values obtained are accurate and reliable enough for comparative purposes between the liquid crystals measured. This data allows the effect of differing elastic constants and birefringence on the optical behaviour of LCs at topologically patterned surfaces to be assessed. 157

158 1 ABBE 60 Series Refractometer Operators Manual, Bellingham and Stanley Ltd. (199), Tunbridge Wells. Calibration Tables for ABBE Refractometer Model 60/ED, Bellingham and Stanley Ltd. (199), Tunbridge Wells. 3 Allinson, H. (1994), PhD Thesis, A study of Photochromic Fulgide Doped Liquid Crystals, University of Manchester. 4 Collings, P.J. (1990), Liquid Crystals: Nature s Delicate Phase of Matter, Princeton University Press, Princeton. 5 Vertogen, G. and de Jeu, W.H. (1998), Thermotropic Liquid Crystals, Fundamentals, Springer-Verlag, Berlin Heidelberg New York. 6 Kelker, H. and Hatz, R. (1980), Handbook of Liquid Crystals, Verlag Chemie Gmbh, Weinheim. 7 Soorys, T.N., Gupta, S., Kumar, A., Jain, S. and Arora, V.P. (006), Indian J. Pure Ap. Phy. 44, Li, J., Gauza, S. and Wu, S.T., (005), J. Appl. Phys. 96, No. 1, Saunders, F.C. (1988), Electro-optic modulator, European Patent Application no , filed 4 October Pulkkinen, A., Jokisaari, J. and Väänänen, T. (1986), J. Mol. Struct. 144, no 3-4, Bancroft, M. (1989), PhD Thesis, Dynamic Light Scattering Studies of Some Nematic Liquid Crystals, University of Manchester. 1 Raynes, E.P., Tough, R.J.A. and Davies, K.A. (1979), Mol. Cryst. Liq. Cryst. 56 (Letters), Gruler, H., Scheffer, T. J. and Meier, G. (197) Z. Naturforsch, 7A, 966. (Referenced from: Raynes, E.P., Tough, R.J.A. and Davies, K.A. (1979), Mol. Cryst. Liq. Cryst. 56 (Letters), ) 14 Hopwood, A.I. (1985), PhD Thesis, Electro-Optic Effects in Polymer Liquid Crystal Solutions, University of Manchester. 15 Kuo, C.L., Miyashia, T., Suzuki, M. and Uchida, T. (1996), Appl. Phys. Lett. 68, no 11,

159 Chapter 7 The Effect of Controlling Surface Chemistry Using Thiols The main focus of this thesis is an investigation into the effect of arrays of raised gold spots on silicon wafers on the alignment of supported LC films. In this chapter, the effect of surface chemistry will be explored. It has been shown many times in the literature that gold surfaces can be easily functionalised by exposure to biological materials. 1, This approach allows substrates to be prepared with consistent surface chemistry, which is particularly useful when investigating the behaviour of liquid crystals in proximity to topological structures. An unfortunate consequence of the ease with which gold surfaces can be functionalised is that it is difficult to obtain and preserve untainted gold surfaces. The difficulty of effectively cleaning metal surfaces of all contamination and the sensitivity of the alignment of LC films supported on chemical surfaces has also long been known. 3,4 For the purposes of investigating the response of liquid crystals to topological structures it is important to ensure that surface chemistry and surface topography are controlled. An array of gold spots on a silicon wafer is unlikely to maintain constant surface purity under exposure to different environments and will obviously have a different surface chemistry to the underlying silicon. As a result it, was decided that creating SAMs over the whole of the patterned substrates would ensure consistent surface chemistry and protect the gold surfaces from contamination. Control experiments using unpatterned gold surfaces, both unadorned and coated with SAMs of the alkane thiols 3-Mercapto-1-propanol (OH terminated) and 3- Mercaptopropionic Acid (COOH terminated), are presented in this chapter. OH and COOH terminated SAMs were used as they have both been shown to promote planar anchoring in a variety of nematic liquid crystals 5 and this is likely to produce interesting effects when paired with the topological influence of the gold spots. The liquid crystal 5CB was used as it is well understood and its behaviour on a variety of substrates is well documented. Unpatterned gold coatings, approximately 500nm thick, were applied to glass slides and SAMs were formed on the gold by the processes described in Chapter 5. It should 159

160 be noted that this is significantly different from the 50nm thick gold layers of the arrays of spots and that this is due to the difference in gold deposition techniques used. The substrates were combined with homeotropically aligning glass slides and 5µm spacer beads to construct liquid crystal cells as detailed in Chapter 5. This was done as soon as possible (within an hour of gold deposition/sam construction) to reduce the potential for environmental contamination. Cell thickness was measured by interferometry, as explained in Chapter 4, and was found to be ~10µm. The thickness of the cells was found not to have good consistency across the area of the cell, varying by approximately ±µm over 10mm. It is believed that this has an effect on some of the results as described below. The difficulty in obtaining cells of consistent thickness was due to the challenge of constructing cells with the uneven gold-glass substrates used. 7.1 Images of the behaviour of the 5CB on the surfaces Images taken with polarised microscopy show the behaviour of the liquid crystal on these surfaces both in the nematic phase and as the material is heated through the isotropic phase transition. The images were taken through an Olympus BH research microscope with a DeltaPix DP 00 digital camera and 10x magnification objective as described in Chapter 4. The camera uses an automatic exposure adjustment and is manually focused through the microscope. All images are to the same scale and a reference length is included in Figure

161 7.1.1 Plain Au Gold surfaces without SAMs were measured to give context to the results for functionalised surfaces. The edge of the gold layer in a cell can be seen in Figure 7.1. a Figure 7.1 Microscopic images of a ~10µm thick 5CB cell in the nematic phase. a) With no polarisers. b) With crossed polarisers. The left half of the bottom substrate is coated in a layer of gold ~500nm thick. T-T NI =-4.8K. b 00µm It can be seen that the boundary between the gold and the glass is diffuse. This is present for all cells made in this manner and is due to imperfect contact between the glass and the glass holder during the gold deposition (see Chapter 5). Between crossed polarisers, the nematic phase appears dark. Homeotropic alignment on and off the gold was verified conoscopically. However, at the edge of the gold, a faint bright line can be seen (Figure 7.1 (b)). This is clearly follows the gold-glass boundary and indicates some degree of tilted alignment at this point. This is consistent with a more granular gold layer from an oblique angle of deposition at the glass-holder contact. Angled gold evaporation has been shown to induce clearly defined, tilted alignment. 6 Closer to the nematic isotropic transition, this line becomes more clear (see Figure 7.). Figure 7.1 (b) is in the same orientation as the 0 image in Figure

162 µm Figure 7. Polarised microscopy images of the edge of the Au layer as the substrate is rotated between the polarisers. T-T NI =-0.8 C The bright line at the edge of the gold-glass boundary can be seen to have a planar component on rotation of the cell between crossed polarisers. Extinction is almost achieved for the 110 position, indicating a minimal twist deformation through the cell. The line is clearer at higher temperatures. This could be due to a reduction in anchoring energy as a function of increasing temperature that causes an anchoring transition 7, a change in the elastic constants of the liquid crystal, or a change in birefringence. The possible causes of this change are discussed later. 16

163 Polarising microscopy images of the cell as the LC is heated and cooled are shown sequentially in Figure 7.3 and Figure 7.4 respectively. a b c Figure 7.3 Microscopic images of the gold-glass border of a ~10µm thick 5CB cell as it is heated through the nematic-isotropic transition at 1 C.min -1. (a) No polarisers. (b-d) Crossed polarisers for sequential heating. d 00µm 163

164 a b c Figure 7.4 Microscopic images of the gold-glass border of a ~10µm thick 5CB cell as it is cooled through the nematic-isotropic transition at -1 C.min -1. (a) No polarisers. (b-d) Crossed polarisers for sequential cooling. d 00µm It can be seen that the LC behaves distinctly differently on and off the gold and that there are distinct textures associated with the gold-glass boundary. Despite good homeotropic alignment in the nematic phase, defects and colours more commonly associated with random planar alignment are seen at the transition to and from the isotropic phase and are particularly obvious on the gold. The different colours that can be seen at the same time are possibly due to a combination of a small temperature gradient (>0.1 C) across the cell and a small difference in the thickness of the cell (~0.1µm) at different points. 164

165 7.1. Alcohol thiol: 3-mercapto-1-propanol Images taken with polarising microscopy of a cell with a SAM formed from the alcohol terminated thiol are shown in Figure 7.6. a b c Figure 7.5 Microscopic images of the gold-glass border of a 5CB cell ~10µm thick. The cell has an alcohol terminated SAM on the gold surfaced substrate. (a) No polarisers. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers for heating through the nematic-isotropic transition at 1 C.min -1. (d) Crossed polarisers for cooling through the isotropic-nematic transition at -1 C.min -1. d 00µm No sequential images are shown for this surface as the nematic-isotropic transition appears more smoothly with fewer distinct textures. In contrast with the plain goldglass surface, no significant deviations from homeotropic alignment can be seen across the area of the cell. This is true for all angles of rotation and persists up to T-T NI ~- 0.1 C. Furthermore, on heating and cooling, no birefringence is seen on the glass surface. On the gold surface, the transition on heating is optically dark. Small flashes of light from the edges of biphasic bubbles can be seen. This is particularly clear close to the gold-glass border. On cooling, the whole of the gold area shows up brightly and 165

166 the nematic defects that form do not appear to be linked to topographical defects in the gold layer. The textures formed on cooling are much brighter and more uniform than those formed on heating and the interference colours seen for a plain gold-glass surface are not present here Acid thiol: 3-mercaptopropionic acid Images taken with polarising microscopy of a cell with a SAM formed from the acid terminated thiol are shown in Figure 7.6. Similar to the cell constructed with an alcohol terminated SAM; no significant deviations from homeotropic alignment can be seen across the area of the cell in the nematic phase. Also, no significant birefringence can be observed on the glass surface. On heating, large bright defects can be seen on the gold and on cooling a very bright uniform reflection can be seen across the whole of the gold surface. The boundary between the gold and the glass is much more distinct for the acid terminated SAM on heating and cooling. Possible causes for these observations are discussed below. 166

167 a b c d e Figure 7.6 Microscopic images of the gold-glass border of a 5CB cell ~10µm thick. The cell has an acid terminated SAM on the gold surfaced substrate. (a) No polarisers. (b) Crossed polarisers in the nematic phase. (c-d) Crossed polarisers for sequential heating through the nematic-isotropic transition at 1 C.min -1. (e-f) Crossed polarisers for sequential cooling through the isotropic-nematic transition at -1 C.min -1. f 00µm 167

168 7. Reflection of monochromatic light as a function of temperature The intensity of light reflected from the cells at the nematic to isotropic transition is measured by the method described in Chapter 5, along with the method of normalising the intensity of reflected light. The aim is to obtain an objective average measure of the optical reaction of a dynamic system that is reproducible despite unpredictable dark defect formation. Intensity measurements were taken every 50ms and the temperature was changed at a rate of ±1.0 C.min -1. Normalised measurements are consistent from cell to cell within this chapter. (Note: the reflected intensity from these unpatterned gold surfaces was considerably higher than that from arrays of gold spots. As a result, additional filters were used to prevent saturation of the photodiode and the normalised measurements in this chapter are not consistent with those from arrays of spots presented in the rest of the thesis.) 7..1 Plain Au Control measurements from a cell, approximately 7.7µm thick, constructed with a plain gold coated substrate are shown below. The reflected intensity on heating (see Figure 7.7) shows no signal above a background level of noise. This is interesting because there appears to be activity in the optical images shown in Figure 7.3. However, since the images were taken with an automatic exposure, the apparent brightness of the images is not an objective measure for comparison. 168

169 0.01 Normalised Intensity (Arbitrary Units) Temperature ( o C) Figure 7.7 Reflected intensity of 5CB on a plain gold substrate as it is heated through the nematic-isotropic transition. The cell is 7.9µm thick. The dotted line represents the nematic to isotropic transition. On cooling the same area of the cell shows a peak in intensity significantly higher than the background noise (see Figure 7.8). 169

170 0.14 Normalised Intensity (Arbitrary Units) Temperature ( o C) Figure 7.8 Reflected intensity of 5CB on a plain gold substrate as it is cooled from the isotropic to the nematic phase at a rate of -1 C.min -1. The area of measurement is 7.9µm thick. The peak in the reflected intensity occurs at the temperature of the isotropic to nematic transition and the width of the peak corresponds to the temperature range of the transition of 5CB (~0.1 C). Approximately 100 measurements are taken over each temperature step of 0.1 C and the variation of the measurements is smaller than the size of the symbols on the graphs. In considering the measurements of the peak in the reflected intensity, it is important to examine the influence of: the orientation of the sample with respect to the crossed polarisers (Figure 7.9), differences in the reflected intensity from areas of the same cell with different thicknesses (Figure 7.10) and the stability of the height of the peak with respect to time (Figure 7.11). The peak in reflected intensity exhibits a variation over repeated measurements and also a rotational dependence as shown in Figure

171 0.15 Normalised Intensity (Arbitrary Units) Angle (Degrees) Figure 7.9 Reflected intensity of 5CB on a plain gold coated substrate as it is rotated between crossed polarisers. The spread of data at a single point is shown at 0 rotation. The area of measurement is 7.9µm thick. The lines above and below each point represent the variation in intensity for repeated measurements at a single angle (~±0.003). They are not true errors but do serve to give an indication of the spread of the data. The variation with rotation is consistently larger than this. The variation between different areas of the same cell is illustrated by Figure

172 0.8 Normalised Intensity (Arbitrary Units) Angle (Degrees) Figure 7.10 Reflected intensity of 5CB on a plain gold coated substrate as it is rotated between crossed polarisers. The area of the cell analysed is different from that in Figure 7.9. The spread of data at a single point is shown at 0 rotation. The area of measurement is 7.7µm thick. The maximum intensity measured for the second area is approximately double that of the first cell but the variation in intensity for the same angle is also an order of magnitude larger (~±0.0). This may in part be due to the change in thickness from 7.9µm to 7.7µm (the effect of cell thickness is discussed in more detail in Chapter 8). The intensity of the reflection is also not stable over a long period of time (see Figure 7.11). 17

173 1. Normalised Intensity (Arbitrary Units) Time (minutes) Figure 7.11 Reflected intensity of 5CB on a plain gold coated substrate at the angle of maximum intensity. Measurements are taken for the same area over a long period of time. The area of measurement is 7.9µm thick. The biggest variation in the reflected intensity is with respect to time. This is probably due to changes in the plain gold surface due to chemical interactions with minor impurities. Therefore plain gold is clearly unsuitable in examining these systems with respect to their critical physical parameters and would be problematic in a sensor device. 7.. Alcohol thiol: 3-mercapto-1-propanol The reflected intensities of a cell constructed with an alcohol terminated SAM as it is heated and cooled can be seen in Figure 7.1 (a) and (b) respectively. Similar to plain gold cells no signal above background noise is observed for heating but a significant peak is recorded on cooling. 173

174 Normalised Intensity (Arbitrary Units) Temperature ( o C) Temperature ( o C) a b Figure 7.1 Reflected intensity of 5CB on a gold substrate with an alcohol terminated SAM as it is (a) heated and (b) cooled through the nematic-isotropic transition. The area of measurement is 6.0µm thick. (The dotted line marks the nematic to isotropic transition temperature on heating.) Normalised Intensity (Arbitrary Units) The slight difference in the temperature of the transition peak between this cell (34.7 C) and that shown for plain a gold substrate in Figure 7.8 (34.9 C) can be explained by an imperfect thermal contact between the different areas of the cell and the hot-stage. The temperature can be seen to vary by as much as ±0.5 C for the same liquid crystal on different occasions with the same instruments. The behaviour of the reflected intensity as a function of rotation and time is shown in Figure Two different areas of the same cell were measured two days apart. Both show clear rotational dependence of the intensity as the cell is rotated between crossed polarisers. However, different areas of the same cell exhibit distinctly different angles of maximum intensity. 174

175 Normalised Intensity (Arbitrary Units) Angle (Degrees) Normalised Intensity (Arbitrary Units) Angle (Degrees) a b Figure 7.13 Reflected intensity of 5CB on a gold substrate with an alcohol terminated SAM as it is cooled from the isotropic to the nematic phase. The substrate is rotated between crossed polarised. (a) First area, day one, 6.0µm thick. (b) Second area, two days later, 7.7µm thick. The planar component of the alignment is much more pronounced for the alcohol terminated SAM than for plain gold and a 90 rotation period can be seen. The angle of maximum intensity is clearly different for different areas of the same cell. The spread of data at a single angle is ~±0.01, shown for 0 in Figure 7.13 (a). This is ~3% of the maximum signal strength, which is smaller than the maximum error seen for plain gold (Figure 7.10, ~15%). More importantly, different areas of the same cell show good consistency over a time period of two days, within the variation of data for a single point taken within a time period of minutes Acid thiol: 3-mercaptopropionic acid Figure 7.14 shows reflected intensity measurements for a cell constructed with an acid terminated thiol on heating and cooling at the angle of maximum intensity. In contrast with the other two surfaces measured, this SAM produces a significant peak on heating through the phase transition. This can be explained by the bright textures that can be seen on the gold surface on heating in Figure 7.6 (d). 175

176 Normalised Intensity (Arbitrary Units) Temperature ( o C) Temperature ( o C) a b Figure 7.14 Reflected intensity of 5CB on a gold substrate with an acid terminated SAM as it is (a) cooled and (b) heated through the nematic-isotropic transition. Measurements are shown at the angle of maximum intensity. The area of measurement is 1.5µm thick. Normalised Intensity (Arbitrary Units) The difference in temperature of the peaks on heating and cooling can be explained by the different defects that nucleate on heating and cooling (Figure 7.6) and because the nematic to isotropic phase transition is of first order and will be subject to a degree of hysteresis and supercooling. The height of the intensity peak for two different areas of the same cell as it is rotated between crossed polarisers can be seen in Figure Normalised Intensity (Arbitrary Units) Angle (Degrees) Angle (Degrees) a b Figure 7.15 Reflected intensity of 5CB on a gold substrate with an acid terminated SAM as it is cooled through the isotropic-nematic transition. (a) First area, 1.5µm thick. (b) Second area, 1.5µm thick. Data were taken on the same day, approximately 30 minutes apart. Normalised Intensity (Arbitrary Units)

177 The variation in measurements at a single angle is approximately the same as the symbol size. The angle of maximum intensity for the two areas appears to be more similar than for the alcohol SAM but the maximum intensity itself exhibits a greater variation between two areas of the same cell. A 90 rotation period is also apparent. Measurements of the time stability of the system are shown in Figure The variation in the reflected intensity from the acid terminated SAM over a period of two days is approximately the same as that seen over a period of 30 minutes Normalised Intensity (Arbitrary Units) Time (Minutes) Figure 7.16 Reflected intensity of 5CB on a gold substrate with an acid terminated SAM as it is cooled through the isotropic-nematic transition. Data was taken from the same area over a two day period. The variation between days is within the difference in a single day. The cell is 1.5µm thick. This gives a measure of the variation of intensity for a single point to be approximately 5-10% of the signal strength. The difference in intensity between different areas of the same cell also falls within this error. 177

178 7.3 Discussion It is clear that a plain gold surface prepared in the above manner is not a good substrate to use for consistent measurements of the behaviour of liquid crystals at the nematic to isotropic phase transition. Different areas of the same cell have reflection intensities that differ by an amount much greater than the distribution of points for the same area. Furthermore, cells constructed with plain gold surfaces appear not to give consistent reading over time periods greater than 30 minutes. Cells made with SAMs formed from alcohol and acid terminated thiols both appear to be stable for time periods long enough for systematic measurements of patterned substrates to be taken (approximately one day is required). The SAMs also give consistent surface chemistry across the cell and under this condition different areas of the same cells appear to give results that are within the variation of a single area. It is possible that the difference in thickness (~5µm) between the alcohol and acid terminated SAM cells plays an important role in the magnitude of the reflected intensity. The effect of cell thickness on reflected intensity is investigated in Chapter 8. That the reflected intensity shows a rotational dependence is interesting. The cells appear to be homeotropic in the nematic phase when viewed optically and this was confirmed conoscopically for each area studied. It appears that there must be a planar component to the surface alignment that is only apparent close to the phase transition. This implies a hybrid alignment to the cells, with strong homeotropic alignment at the top surface and weaker tilted alignment at the SAM. It is unlikely that this tilt direction is a filling artefact (it is known that filling cells by capillary action can impart a planar direction to the alignment of the liquid crystal), as these cells were heated sufficiently highly into the isotropic phase to remove such anisotropy. In addition to this the angle of maximum intensity varies across the cell by approximately 70. Directionality imparted by filling would be more uniform. Both surface chemistry and surface topography influence the anchoring orientation of liquid crystals. In this case, there is an interaction between the SAM and the underlying gold layer. The gold layer does not have any intended anisotropy from its evaporation but local regions of anisotropy are likely. The anchoring of xcb nematic 178

179 liquid crystals on acid and alcohol terminated thiols has been reported in the literature. This is discussed below. Luk et al. 8 showed that 5CB will orient homogeneously on obliquely deposited gold films supporting COOH terminated SAMs. They also showed that the azimuthal orientation of the mesogens would be parallel or perpendicular to the underlying surface anisotropy depending on the length of the alkyl chain of the thiol molecules. They found that a chain length of 10 induced alignment parallel to the surface grooves but that a chain length of 15 induced perpendicular alignment. The alkane thiol in this thesis, 3-Mercapto-1-propanol, has a chain length of three, which suggests that it would not alter any underlying anisotropy. It is believed that the mechanism controlling the alignment is hydrogen bonding between the acid group and the nitrile end group of the liquid crystal. Cheng et al. 9 showed that a film of 7CB will exhibit random planar alignment on an unpatterned acid terminated SAM but orient homeotropically on an alcohol terminated SAM, both with a chain length of 10. Similar results were shown for the behaviour of 6CB. 10 That the chain length for the SAM used here is so much shorter suggests that the surface chemistry does not effectively mask the surface topography and that there is a combined effect of the SAM and the gold on the liquid crystal orientation. It is possible that changes in the birefringence and elastic constants of the liquid crystal 5CB at the nematic-isotropic transition have the effect of amplifying the tilted deformation of the alignment. The effects of changing birefringence and elastic constants are explored in Chapter 9. This allows the gold surface to show up brightly at the transition whilst remaining dark (and apparently homeotropic) in the nematic phase. It is also known that the surface anchoring of a liquid crystal changes as a function of temperature. 7 The interaction of anchoring and elasticity plays a crucial role in determining defect nucleation and director distortion propagation. This is discussed in more detail in Chapters 9 and Summary For the purpose of the investigation into cell thickness and array properties, the acid terminated SAM was chosen over the alcohol terminated SAM. This is because, whilst 179

180 there appears to be little difference between the two chemicals in terms of time stability and consistency between areas of the same cell, the acid terminated SAM exhibits a peak in the reflected intensity on heating as well as cooling. This gives the opportunity for additional analysis, which would not be possible using the alcohol terminated SAM. 1 Zhang, X. (010), Electrochem. Commun. 1, no 10, Gupta, V.K., Skaife, J.S., Dubrovsky, T.B and Abbott, N.L. (1998), Science 79, Creagh, L.T. and Kmetz, A.R. (1973), Mol. Cryst. Liq. Cryst., 4, Proust, J.E., Ter-Minassian-Saraga, L. and Guyon, E. (197), Sol.St. Commun. 11, Alkhairalla, B., Allinson, H., Boden, N., Evans, S.D. and Henderson, J.R. (1999), Phys. Rev. E 59, no 3, Skaife, J.J. and Abbott, N.L. (1999), Chem. Mater. 11, Blinov, L.M. and Chigrinov, V.G. (1996) Electrooptic Effects in Liquid Crystal Materials, Springer, New York. 8 Luk, Y.Y., Yang, K., Cadwell, K. and Abbott, N.L. (004), Surface Science 570, Cheng, Y.L., Batchelder, D.N., Evans, S.D., Henderson, J.R., Lydon, J.E. and Ogier, S.D. (000) Liq. Cryst. 7, No. 10, Critchley, K., Cheadle, E.M., Zhang, H.L., Baldwin, K.J., Liu, Q., Cheng, Y., Fukushima, H., Tamaki, T., Batchelder, D.N., Bushby, R.J. and Evans, S.D. (009), J. Phys. Chem. B 11,

181 Chapter 8 The Effect of Cell Thickness To assess the effect of cell thickness on the reflected intensity, cells of different thicknesses were constructed as described in Chapter 5. The cells were filled with the nematic liquid crystal 5CB and optical polarising microscopy images and monochromatic reflected intensity measurements were taken as it was heated and cooled through the nematic to isotropic phase transition. Measurements were of areas of the cells that present arrays of microscopic gold spots to investigate the effect of thickness on the defects that form at these spots. Cell thicknesses were measured by interferometry on areas of the cells immediately adjacent to the arrays of interest. This ensured that measurements were as accurate as possible and that any variation in thickness between areas of the same cell was accounted for. The cells were measured to have nominal thicknesses of 7.5, 10.0, 1.7 and 40.0µm. The thinner cells were constructed using 5 and 10µm thick polystyrene spacer beads. The differences in the thickness between the cells and the beads are accounted for by the slightly different amounts of glue used in the cells' construction. The 40.0µm cell was made using strips of 0µm thick Mylar spacer sheet. The greatly increased thickness for this technique is a result of the increased difficulty in constructing cells with Mylar strips in comparison to polystyrene beads. 5CB was used as a standard liquid crystal because of its well understood physical properties and because it had been used to demonstrate the time stability of the acid terminated thiol SAMs. The arrays used for this part of the investigation had a spot size of 8µm and a pitch length between spots of 0µm. This configuration was chosen because the relatively large spot size and separation ensured that multiple arrays on the same substrate (and within the same cell) would be clean and usable following cell construction. Despite the fact that peaks in reflected intensity were observed on heating through the nematic to isotropic transition on areas of plain gold (shown in Chapter 7), no consistent peaks were seen in the reflected intensity on heating over the arrays of spots. Consequently, only the equivalent peaks in reflected intensity observed on cooling were used to 181

182 compare the response of different cells. The cells were all cooled through the transition at a rate of 1 C.min -1. As described in Chapter 5, each substrate presents two duplicates of a series of arrays of gold spots with different spot sizes and spot separation. Within each series, the array of spot size 8µm and pitch length of 0µm is reproduced twice, giving a total of four of these arrays on each substrate. This allowed multiple measurements of the effect an array with these properties on the optical textures and reflected intensity to be made without constructing and filling additional cells. A schematic diagram of the silicon substrates, the relative positions of the duplicated arrays, and the positions at which the cell thickness was measured can be seen in Figure 8.1. Areas of thickness measurements Array Series 1 1 Array of interest Other arrays 3 Array Series 4 Silicon substrate Figure 8.1 A schematic of the silicon substrates showing the relative position of the arrays of interest and the positions of the thickness measurements. For the purposes of this chapter the four arrays with 8µm spots and 0µm pitch will be referred to as Arrays 1,, 3 and 4 as indicated in the figure. Measurements of cell thickness showed a measurable difference (~1µm) between Array Series 1 and Array Series. A rather larger difference in thickness was measured between series for the 40µm thick cell observed below. This is a result of its different construction technique. The difference in thickness between arrays within the same series was found to be 18

183 approximately 0.1µm. This enabled the effect of two distinct thicknesses to be measured for each cell, one for each array series. The chapter will first present optical microscopy images of Array 1 for a cell of a certain thickness. These will be without polarisers, with crossed polarisers in the nematic phase, with crossed polarisers as the cell is heated through the phase transition and with crossed polarisers as the cell is cooled through the transition. Images of Arrays 1,, 3 and 4 on cooling will then be shown to illustrate the reproducibility of the optical textures across multiple arrays. Reflected intensity profiles of the cells as they were cooled will then be presented. This is shown for each cell in sequence of increasing cell thickness with the specific thickness of each array noted. A summary and discussion of the results along with an analysis of the effect of changing thickness closes the chapter. 8.1 Nominal 7.5µm thickness In Figure 8. polarised microscopic images of a cell with a nominal thickness of 7.5µm can be seen. Images were taken as the cell was heated and cooled through the isotropic to nematic phase transition. 183

184 a b c Figure 8. Microscopic images of a cell filled with 5CB and an acid terminated SAM. The nominal thickness is 7.5µm. Images show Array 1 with spot diameter 8µm and array pitch 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. Images were taken with white light. d 00µm No consistent alignment can be seen on the gold spots in the nematic phase, Figure 8. (b). The flaws in the homeotropic alignment that show up as bright spots do not appear to be centred on the gold in any regular manner. On heating through the nematic to isotropic phase transition, the gold spots shine brightly, Figure 8. (c). Immediately after this, an array of small cross defects can be observed to form above the spots. The centre of each of the defects appears to be positioned over the spots. The transition on cooling appears much brighter and the gold shows up clearly, Figure 8. (d). However, there does not appear to be a spatial relationship between any defects that form and the spots. The cooling transitions of four identical arrays are shown in Figure

185 a b c Figure 8.3 Polarising microscopy images of a cell with a nominal thickness of 7.5µm filled with 5CB and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1, 7.7µm thick. (b) Array, 7.7µm thick. (c) Array 3, 7.4µm thick. (d) Array 4, 7.4µm thick. Images were taken with white light. d 00µm The image of Array 1 shown in Figure 8.3 (a) is the same as that shown in Figure 8. (d). This is done for ease of comparison with the other arrays. The cell is 7.7µm thick over Array Series 1 and 7.4µm thick over Array Series. Similar behaviour can be seen on Array 1, Figure 8.3 (a) and Array 3, Figure 8.3 (c) despite the difference in thickness of 0.3µm at these points. However, different transition behaviour can be seen for Array, Figure 8.3 (b) and Array 4, Figure 8.3 (d). The difference in thickness between arrays within the same array series is <0.1µm. This is much less than the difference in thickness between arrays on different array series (0.3µm in this case). To explain the similarities seen for arrays at different thicknesses and the differences seen for arrays at the same thickness, there must be other factors that have a significant influence on the reflected intensity. These optical textures are reproducible over repeated observations of the transition. The intensity of monochromatic light reflected 185

186 from these arrays on cooling through the transition can be seen in Figure 8.4. Results are shown for the angle of maximum intensity for each array which was determined by repeating the reflection measurements for different azimuthal angles of the sample between the crossed polarisers. Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) b Normalised Intensity (Arbitrary Units) Temperature ( o C) c Normalised Intensity (Arbitrary Units) Temperature ( o C) Figure 8.4 Reflected intensity of monochromatic light from a cell filled with 5CB on cooling. (a) Array 1, 7.7µm thick. (b) Array, 7.7µm thick. (c) Array 3, 7.4µm thick. (d) Array 4, 7.4µm thick. d The variation in the magnitude of the reflected intensity peak over repeated measurements of the same array is approximately ±0.03 or 5% of the signal. The difference in intensity between the different arrays (with supposedly identical spot size of 8µm and spot separation of 0µm) at the same thickness is much larger than this. The Array 1 and Array measured in Figure 8.4 (a) and (b) have the same thickness to within ±0.1µm. However, the difference in intensity of the reflected monochromatic light from the two arrays is ~60% of the signal of Array 1. The lower intensity observed for Array can be matched to the generally dark texture seen in Figure 8.3 (b). The difference in intensity between Array 1, Figure 8.4 (a) and Array 3, Figure 8.4 (c) is interesting given the similarity in the textures seen in Figure 8.3 (a) and (c). 186

187 8. Nominal 10.0µm thickness Polarised microscopy images of a cell with a nominal thickness of 10.0µm are shown in Figure 8.5. a b c Figure 8.5 Microscopic images of a cell filled with 5CB and an acid terminated SAM. The nominal cell thickness is 10.0µm. Images show Array 1 with spot diameter 8µm and array pitch 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. Images were taken with white light. d 00µm In the nematic phase, some of the gold spots show up brightly, Figure 8.5 (b), whereas the alignment of the liquid crystal on the surrounding silicon was confirmed by conoscopy to be homeotropic. This is a significant difference from the cell with nominal thickness of 7.5µm and the thickness dependence of this effect is discussed later. The bright reflection from the gold spots in the nematic phase is interesting because the cell is otherwise homeotropically aligned and this indicates that some degree of tilted alignment is induced by the gold surface. It was shown in the initial investigation of these substrates (described in Chapter 5, Figure 5.8) that any tilted 187

188 component in the alignment of the liquid crystal over the gold spots does not have a uniform direction from spot to spot within each array. This is observed by the irregular brightening and darkening of different spots as the array is rotated between crossed polarisers and the effect of this can be seen in Figure 8.5 (b) by the patchy nature of the brightness of the gold spots. As the cell is heated through the phase transition an array of small cross defects can be seen centred on the gold spots, Figure 8.5 (c). This is similar to that previously observed for the 7.5µm thick cell, Figure 8. (c), though this effect is clearer and more widespread in this thicker cell. The cooling transition is less uniform and there is not a clear link between defect formation and spot position, Figure 8.5 (d). The optical textures of cooling on multiple arrays are shown in Figure 8.6. a b c Figure 8.6 Polarising microscopy images of a cell with an nominal thickness of 10.0µm, filled with 5CB and an acid terminated SAM. Four different arrays of 8µm gold spots separated by 0µm are observed. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1, 9.4µm thick. (b) Array, 9.4µm thick. (c) Array 3, 8.5µm thick. (d) Array 4, 8.5µm thick. Images were taken with white light. d 00µm 188

189 The image shown of Array 1 in Figure 8.6 (a) is the same as that shown in Figure 8.5 (d). As above, this is done for ease of comparison with the other arrays. The cell is 9.4µm thick over Array Series 1 and 8.5µm thick over Array Series. The optical textures seen in Figure 8.6 (a-c) appear to be qualitatively similar. The cross defects that do form do not appear to be anchored to the gold spots in any way. However, the textures seen for Array 4 in Figure 8.6 (d) are distinctly different. Large cross defects centred on the spaces between squares of four spots grow as the temperature decreases and merge together over time into a square lattice. At lower temperatures, these ordered textures break down. The intensity of light reflected from these arrays is shown in Figure Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) b Normalised Intensity (Arbitrary Units) Temperature ( o C) Normalised Intensity (Arbitrary Units) Temperature ( o C) c d Figure 8.7 Reflected intensity from of monochromatic light from a cell filled with 5CB on cooling. (a) Array 1, 9.4µm thick. (b) Array, 9.4µm thick. (c) Array 3, 8.5µm thick. (d) Array 4, 8.5µm thick. Measurements were taken at the angle of maximum intensity as for the previous thickness. However, as there is a non-zero intensity of reflection in the nematic phase, the angle was determined by rotation at a constant temperature below the clearing 189

190 point. The differences in intensity of the reflection between arrays in the nematic phase can be explained by the irregular nature of the tilted alignment of the liquid crystal over the gold spots. If the azimuthal angle of tilt is random from spot to spot within an array, then at the angle of maximum reflection (averaged over the whole array), different numbers of spots will be aligned with the polarisers for different arrays. This would cause a variation in the reflected intensity depending on the distribution of the azimuthal angle of the tilt across each array. The intensity profiles here are very different from those seen for the 7.5µm thick cell. The high reflected intensity below the phase transition is a result of the brightness of the gold spots in the nematic phase. It is possible that this is also masking the distinct sharp peak seen at the phase transition in the thinner cell. It is interesting that there is no clear difference between the intensity profile of Array 4, Figure 8.7 (d), where defect nucleation can be linked to gold spots and the profiles of those arrays with random textures. 190

191 8.3 Nominal 1.7µm thickness Polarised microscopy images of a cell with a nominal thickness of 1.7µm are shown in Figure 8.8. a b c Figure 8.8 Microscopic images of a cell filled with 5CB and an acid terminated SAM. The nominal thickness is 1.7µm. Images show Array 1 with spot diameter 8µm and array pitch 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. Images were taken with white light. d 00µm Here the gold spots appear dark in the nematic phase, Figure 8.8 (b), but the same array of cross defects appears on heating through the phase transition, Figure 8.8 (c). On cooling each spot shines brightly and is surrounded by a distinctive light and dark checked pattern, Figure 8.8 (d). These checks meet the patterns from adjacent spots to form a very regular square lattice. This texture can be seen for three of the four arrays shown in Figure 8.9 (a), (b) and (d) as they are cooled through the transition. 191

192 a b c Figure 8.9 Polarising microscopy images of a cell with a nominal thickness of 1.7µm, filled with 5CB and an acid terminated SAM. Four different arrays of 8µm gold spots separated by 0µm are observed. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1, 13.0µm thick. (b) Array, 13.0µm thick. (c) Array 3, 1.7µm thick. (d) Array 4, 1.7µm thick. Images were taken with white light. d 00µm As above the image of Array 1 shown in Figure 8.9 (a) is a duplicate of that shown in Figure 8.8 (d) for ease of comparison between the arrays. The cell is 13.0µm thick over Array Series 1 and 1.5µm thick over Array Series. It is clear that Array 3 shown in Figure 8.9 (c) exhibits slightly different behaviour from the other arrays. Regular defects nucleate on each of the gold spots but do not merge together uniformly. The intensity of light reflected from these arrays (see Figure 8.10) has a sharp peak at the phase transition and very low levels at temperatures below it. This would be expected from the dark appearance in the nematic phase shown above. 19

193 Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) b Normalised Intensity (Arbitrary Units) Temperature ( o C) Normalised Intensity (Arbitrary Units) Temperature ( o C) c d Figure 8.10 Reflected intensity of monochromatic light from a cell filled with from 5CB on cooling. (a) Array 1, 13.0µm thick. (b) Array, 13.0µm thick. (c) Array 3, 1.7µm thick. (d) Array 4, 1.7µm thick. There does not appear to be a clear link between the textures seen above and the magnitude of the intensity peaks shown here. The results were taken at the angle of maximum intensity as for the 7.5µm thick cell. Good reproducibility (within ~5% of the peak height) is seen for repeated measurements of the same array at the maximum angle. However, the variation in peak height between different arrays of the same thickness (Figure 8.10 (a) compared with (b) and Figure 8.10 (c) compared with (d)) is approximately 50% of the peak height of the highest peaks. 193

194 8.4 Nominal 40.0µm thickness Polarised microscopy images of a cell with a nominal thickness of 40.0µm can be seen in Figure a b c Figure 8.11 Microscopic images of a cell filled with 5CB and an acid terminated SAM. The nominal thickness is 40.0µm. Images show Array 1 with spot diameter 8µm and array pitch 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. Images were taken with white light. d 00µm As for the 10.0µm thick cell the gold spots here show up brightly, Figure 8.11 (b). This is the first cell where the optical textures on heating do not appear to be related to the position of the gold spots and the cross defects are not observed, Figure 8.11 (c). The behaviour on cooling does not appear to be influenced by the presence of the gold spots either, Figure 8.11 (d). The optical textures for multiple arrays (see Figure 8.1) are more consistent than for thinner cells. 194

195 a b c Figure 8.1 Polarising microscopy images of a cell with a nominal thickness of 40.0µm filled with 5CB and an acid terminated SAM. Four different arrays of 8µm gold spots separated by 0µm are observed. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1, 40.0µm thick. (b) Array, 40.0µm thick. (c) Array 3, 36.5µm thick. (d) Array 4, 36.5µm thick. Images were taken with white light. d 00µm The cell is 40.0µm thick over Array Series 1 and 36.5µm thick over Array Series. The different colours seen are likely to be the result of a small temperature gradient across the cell. This is plausible because the colours appear in bands that would mimic isothermal contours. The intensity profiles from these arrays are shown in Figure

196 Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) b Normalised Intensity (Arbitrary Units) Temperature ( o C) c Normalised Intensity (Arbitrary Units) Temperature ( o C) Figure 8.13 Reflected intensity of monochromatic light from a cell filled with from 5CB on cooling. (a) Array 1, 40.0µm thick. (b) Array, 40.0µm thick. (c) Array 3, 36.5µm thick. (d) Array 4, 36.5µm thick. d The high intensity of these arrays at temperatures below the phase transition corresponds to the bright gold spots in the nematic phase. This allowed the angle of maximum intensity to be ascertained as for the 10.0µm thick cell. Unlike the 10.0µm cell, the higher nematic reflection does not appear to mask the peak in intensity at the transition. Initial analysis of these results shows that visually similar graphs have been produced by measuring the Brewster angle of 9CB on patterned SAMs by Bramble et al. 1 Evanescent wave ellipsometry (EWE) was used to show that there is a peak in the Brewster angle of liquid crystal films supported on SAMs with alternating (homeotropic-planar) striped surface anchoring, as they are heated and cooled through the isotropic to nematic transition. However, this implies a quite different physical response to that observed here: a peak in the Brewster angle indicates homeotropic alignment within the liquid crystal cell. In this case the peak observed is indicative of a 196

197 random planar alignment or the formation of significant defects. The difference may be in part caused by the heating and cooling rates used (±1.0 C.min -1 here and ±0.1 C.min -1 by Bramble et al. 1 ). A slower system, in thermal equilibrium, might be more inclined to settle into uniform alignment. 8.6 Discussion A summary of the optical textures and reflected intensity at the phase transitions is detailed in Table 8.1. Each of these observations is discussed in turn. Optical Response at Different Thicknesses Nematic phase texture Textures on heating Textures on cooling Reflected Intensity on Cooling (Arbitrary Units) ~7.5µm thick ~10.0µm thick ~1.7µm thick 36.5µm thick 41.8µm thick Dark Bright gold Dark Bright gold Bright gold Cross defects on gold spots Random planar texture Cross defects on gold spots Random planar texture (one array shows defect nucleation between gold spots) Cross defects on gold spots Square grid texture centred on the gold spots Random planar texture Random planar texture Random planar texture Random planar texture 0.5± ± ± ± ±0.04 Table 8.1 A summary of the optical response observed on heating and cooling through the nematic to isotropic phase transition at different cell thicknesses. It is interesting that some arrays show gold spots brightly in the nematic phase and some do not. For the arrays where the gold shines, there is clearly a hybrid alignment with the homeotropic coverslip and a tilted alignment on the gold. It is not clear whether the same surface alignment is present on the gold spots that do not shine. Since the gold spots support SAMs that were constructed identically, the surface chemistry is likely to be very similar. Different distributions of the azimuthal tilt of the alignment on the gold will account for a variation in intensity as the arrays are rotated but the dark arrays are dark for all angles. Thicker cells might be expected to be influenced by the surface anchoring less as the bulk nematic energy could dominate the system. However, the 40.0µm thick cell shows consistently bright gold on all four 197

198 arrays over two distinct thicknesses. A more continuous thickness variation would be useful before drawing conclusions about this effect. Optical textures centred on the gold spots only appear consistently on cooling for one thickness of all thicknesses observed. In contrast, cross defects centred on the gold appear on heating for all of three thinnest cells. It is possible that thickness does affect the nucleation of defects on heating and that at a certain thickness these will no longer appear. This could be an also be effect of the interaction between surface anchoring and the elastic energy of the liquid crystal bulk. More data would be required to state this conclusively. The highest intensities of reflected light were measured on the arrays where gold centred defect nucleation was observed. This only occurred consistently for the cell with an approximate thickness of 1.7µm, though it occurred for both Array Series 1 and with thicknesses 13.0µm and 1.5µm respectively. The single array on the 10µm thick cell, for which defect nucleation was observed, also corresponds to the array with the highest reflected intensity measured for this cell. (Though in this case the increase in reflected intensity for this array over the next highest array in the cell is only 0.05.) The thickness at this array is 8.5µm. which is inconsistent with the idea of a possible ideal thickness for defect nucleation. It might be suggested that the large variation in reflected intensity from these arrays is due to variations in the manner in which the grid-like defect structures nucleate Intensity vs. thickness In discussing the effect of cell thickness on reflected intensity an explanation of the effect of thickness on a normal birefringent medium is required. The intensity of light transmitted through a birefringent medium is given by equation 3.11 from Chapter 3: πd I = I0 sin Φ. sin o λ0 ( n e n ), (3.11) Where Ф is the azimuthal angle of the optic axis from one of the polarizer directions, I 0 and λ 0 are the incident illuminating intensity and wavelength, d is the thickness of 198

199 the sample and n e and n o are the extraordinary and ordinary indices of refraction of the birefringent material. In reflection, the transmission will be a function of d, as light will pass through the sample twice. In a liquid crystal medium, the relationship between n e and n o and the values of n // and n are governed by equations 3.5 and 3.6 from Chapter 3: n o = n, (3.5) and n// n n e =, (3.6) n cos θ + n sin θ // where θ is the angle between the optic axis and the direction of light propagation. In a planar aligned liquid crystal cell (θ=90 ) n o =n and n e =n //. (See Chapter 3 section 3.5 for a more complete description of the optics here). However, in a liquid crystal cell with a more complicated tilted alignment, such as that observed on these substrates, the angle between the optic axis and the direction of light propagation may not be known. In this case, the azimuthal angle of maximum intensity, Ф, is found by repeating measurements of an array as it is rotated between crossed polarisers, for comparative purposes, this is assumed to be constant between different arrays. At the phase transition, the orientation distribution of the LC mesogens is not defined and as a result values of θ and n e cannot be calculated. For analysis purposes, the approximation that n e =n // is made. This is clearly not true but the assumption that the alignment of the liquid crystal at the surface of the gold spots is similar for different cell thicknesses and for different arrays is reasonable because the same liquid crystal is used each time and the arrays were constructed using the same technique. The average director configuration through the bulk of the liquid crystal will be different for changing thickness and this is accepted as a flaw in the model. 199

200 The assumption that n e -n o = n // -n means that the effective birefringence (which is actually dependent on the director tilt) is equal to the absolute birefringence of the liquid crystal, n, (which is independent of the director orientation). This lets the reflected intensity be written as a function of sin (πd. n/λ 0 ), where the value of birefringence is that measured for 5CB at its transition temperature in Chapter 6. This is shown in Figure Normalised Intensity Peak Height (Arbitrary Units) sin (πd n/λ 0 ) Figure 8.14 Monochromatic reflected intensity peak height plotted against sin (πd. n/λ 0 ). The birefringence used is 0.07, the lowest reduced temperature value measured for 5CB, and λ 0 is 670nm, the wavelength of the illuminating laser diode. The values of the normalised intensity peak height are averages of the repeated measurements at each of the different cell thicknesses. Different points are plotted for each specific thickness, accounting for the change in thickness between the two Array Series in each cell. The lines above and below each data point represent the variation in the peak height observed between measurements of different arrays at exactly the same cell thickness (this is clearly much greater than the variation of 5% of the peak height seen for repeated measurements of the same array). The variation between measurements is 00

201 not constant between thicknesses; for one data point the variation is smaller than the symbol size. These are not true errors but serve to give an impression of the spread of the data. It is clear that the variation between measurements at certain thicknesses (particularly 13.0µm and 1.5µm) is as great as the variation for changes in thickness of up to 30µm. It is interesting that the greatest variation in peak height occurs for the arrays at the thickness where defect nucleation is anchored to the gold spots most consistently. Furthermore, the smallest variations in measurements are recorded for the thickest cells where the effect of the surface on the system is minimised. This suggests that factors other than thickness play an important role in determining the intensity reflected from the cells at the phase transition. 8.7 Summary From Figure 8.14, it can be seen that the retarding effect of cell thickness and birefringence is not a dominant factor in determining the reflected intensity from the liquid crystal cells as they are cooled. There is too great a variation in intensity between measurements of arrays at the same thickness to be able to make statements about the effect of thickness from this data. Comparing these results with those presented by Bramble et al., 1 for substrates presenting alternating surface anchoring, suggests that there is a difference in anchoring energy between the gold spots and the silicon substrates. This is not surprising since there is a difference in surface chemistry between the acid terminated SAMs on the gold spots and the silicon oxide surface. This is potentially an important result in the development of a liquid crystal biosensor. If small changes in the optical retardance of a device as a function of device thickness are less important to the function of the device than other parameters, it would allow devices to be tuned more effectively. However, this is not to say that thickness does not play a role in determining how the nematic phase nucleates near gold spots. If the nature of defect nucleation at the gold spots is a determining factor in the reflected intensity, then the elastic constants of the liquid crystal at temperatures close to the phase transition will be important factors. The interaction of surface energy and elastic energy (in part dependent on the liquid crystal bulk) is crucial in determining the formation of defects. It has been shown in 01

202 the literature that the formation of defects on micro-scale particles in liquid crystals is dependent on the nature and strength of the surface anchoring and the elastic constants of the liquid crystal medium.,3,4 It has also been shown that the alignment of liquid crystals on surfaces with patterned surface chemistry is dependent on the interaction of surface energy and elasticity. 5 In the next chapter the effect of the birefringence and elasticity of the liquid crystal on the optical textures and reflected intensity are investigated. This is done by filling cells of the same thickness with different liquid crystals with different values of birefringence and elastic constants. 1 Bramble, J.P., Evans, S.D., Henderson, J.R., Anquetil, C., Cleaver, D.J. and Smith, N.J. (007), Liq. Cryst. 34, No. 9, Mondain-Monval, O., Dedieu, J.C., Gulik-Krzywicki, T. and Poulin, P. (1999), Eur. Phys. J. B, 1, Poulin P. and Weitz D. A. (1998) Phys. Rev. E, 57, Stark, H. (1999), Eur. Phys. Jour. B, 10, Atherton, T.J. and Sambles, J.R. (006), Phys. Rev. E 74,

203 Chapter 9 The Effects of Different Liquid Crystals In this chapter, the effects of elasticity and birefringence on the optical textures and reflected intensity of liquid crystal cells as they are heated and cooled through the isotropic to nematic phase transition are investigated. The cells were made from patterned substrates with acid terminated SAMs as described in Chapter 5. They were filled with different nematic liquid crystals with different physical properties. The liquid crystals used were 5CB, E7, ZLI 1695, ZLI 113 and MDA Their physical properties at room temperature are described in Chapter 5, Table 5.1, and the values of their birefringence and elastic constants at temperatures approaching the phase transition are detailed in Chapter 6. The cells were constructed with 5µm polystyrene spacer beads which were found to give the smallest variation in thickness between different areas of the same cell. The thicknesses were measured by interferometry and found to be approximately 10µm. Arrays with a spot size of 8µm and spot separation of 0µm were used as they had the most consistently reproduced in the substrate fabrication process. Similar to the investigation into the effect of cell thickness in Chapter 8, four identical arrays within each cell were examined and are referred to as Arrays 1,, 3 and 4. The relative positions of these arrays on each substrate are shown in Figure 8.1. The cells were heated and cooled at a rate of ±1 C.min -1, as for the results shown in Chapters 7 and 8. This chapter presents results for each liquid crystal in turn. As for Chapter 8, white light optical microscopy images of Array 1 for each cell filled with a different liquid crystal are shown. Images of the arrays without polarisers, with crossed polarisers in the nematic phase, with crossed polarisers as the cell is heated through the nematic to isotropic phase transition, and with crossed polarisers as the cell is cooled through the transition are presented. Images of the phase transition on heating and cooling are then shown for Arrays 1,, 3, and 4 for that cell to demonstrate the reproducibility of the transient optical textures. The measurements of the reflected intensities of monochromatic light from the arrays as they are heated and cooled are then given. The results are summarised and discussed as they 03

204 are compared with the physical properties of the liquid crystals that were measured in Chapter CB For images of 5CB in the nematic phase and detailed discussion of its behaviour on cooling, see Chapter 8. In the nematic phase the gold shows up brightly and the cell presents liquid crystal alignment with an average planar component. This was used to discern the angle of maximum reflection for the measurements of intensity on heating and cooling. The cell has an average thickness of 9µm (±0.5µm). Images of the textures that form as 5CB is heated through the phase transition on the four substrate arrays are shown in Figure 9.1. The phase sequence of 5CB is nematic-35.3 C-isotopic. 1 As a single component material, it does not have a biphasic temperature range. 04

205 a b c d 00µm Figure 9.1 Polarising microscopy images of a cell ~9µm thick filled with 5CB and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. At the phase transition, the gold shows up brightly and cross defects nucleate on the gold spots as described for this cell in Chapter 8. The measurements of the intensities of monochromatic light with a wavelength of 670nm reflected from the four arrays as they are heated are shown in Figure

206 Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) b Normalised Intensity (Arbitrary Units) Temperature ( o C) Normalised Intensity (Arbitrary Units) Temperature ( o C) c d Figure 9. Reflected intensity from a cell filled with 5CB on heating through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The bright gold spots in the nematic phase correspond to high values of reflected intensity below the phase transition. As mentioned in the previous chapter it may be that this has the effect of masking the peak in reflection at the phase transition that is seen for cells with lower reflected intensity in the nematic phase. The reflected intensities from the arrays as they are cooled are reproduced from Chapter 8 for ease of comparison and are shown in Figure

207 Normalised Intensity (Arbitrary Units) Temperature ( o C) a Normalised Intensity (Arbitrary Units) Temperature (oc) b Normalised Intensity (Arbitrary Units) Temperature ( o C) c Normalised Intensity (Arbitrary Units) Temperature ( o C) Figure 9.3 Reflected intensity from a cell filled with 5CB on cooling through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. d It is interesting that the intensities on cooling have very similar profiles to the intensities seen on heating. This is not observed for the other liquid crystals shown below. 07

208 9. E7 Images of a cell with an average thickness of 8.9µm (±0.6µm) filled with E7 are shown in Figure 9.4. The phase sequence for E7 is nematic-60.5 C-isotopic; 1 the width of the biphasic region is ~ C. a b c Figure 9.4 Optical microscopy images of a cell ~9µm thick filled with E7 and an acid terminated SAM over an array of 8µm gold spots separated by 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. d 00µm As for 5CB, the gold spots show up brightly in the nematic phase, with a significant planar component to the alignment that allowed the angle of maximum intensity to be identified for reflection measurements. The rest of the cell (away from the arrays) exhibits homeotropic alignment which was verified conoscopically. On heating through the phase transition, the gold spots show up significantly more brightly. The apparent darkness of some regions of the array is a result of the automatic exposure imposed by the camera. The rest of the cell 08

209 remains dark in contrast. On cooling, bright cross defects appear to nucleate semirandomly. Those that form seem to be positioned in the space between a square of four spots but not every four spots support a defect. Images of the transition for the four arrays can be seen in Figure 9.5. It is possible that cross defects are forming on the gold spots but that they cannot be seen due to the automatic exposure of the camera. The bright circles correspond directly to the position of the gold spots beneath, they have the same periodicity and their position can be matched to the spots in images of the arrays without crossed polarisers. a b c d 00µm Figure 9.5 Polarising microscopy images of a cell ~9µm thick filled with E7 and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. Each array shows qualitatively similar behaviour on heating. The intensities reflected from these textures are shown in Figure

210 Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) c Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) Temperature ( o C) Figure 9.6 Reflected intensity from a cell filled with E7 on heating through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. b d The continuous increases in intensity of reflection in the nematic phase shows that the apparent darkness of some gold spots seen in Figure 9.5 is an effect of the imaging contrast and not an effect of changing alignment. This is probably caused by changes in the birefringence with temperature and possibly also changes in the tilt of the partially planar alignment of the liquid crystal on the gold spots. Steeper gradients of the intensity profiles can be seen for the arrays shown in Figure 9.6 (a) and (c) than for the two arrays shown in Figure 9.7 (b) and (d). This may be a result of slightly different alignment orientation on the gold spots. As the planar component of the orientation does not appear to be uniform across different spots in the arrays, different numbers of spots aligned in different direction would produce different average alignment over the whole array. 10

211 Images of the same arrays as the liquid crystal is cooled through the phase transition are shown in Figure 9.7. a b c Figure 9.7 Polarising microscopy images of a cell ~9µm thick filled with E7 and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. d 00µm Similar to 5CB, defects nucleate over the array of spots as the cell is cooled. There appears to be a spatial correlation between the defects and the spots but not uniformly across the array. The cross defects appear to be anchored in the spaces between squares of four spots. Where these defects are located near the gold spots, the gold shows up brightly. The reflected intensities from the arrays on cooling are shown in Figure

212 Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) Temperature ( o C) a b Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) Temperature ( o C) c d Figure 9.8 Reflected intensity from a cell filled with E7 on cooling through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The dotted lines represent the width of the biphasic temperature range. The intensity profiles are different in form from those seen for 5CB. This is partially because E7 is a multi-component material and has a biphasic temperature range where the nematic and isotropic phases both exist stably. The widths of the peaks, from approximately C, correspond to the temperature range of the biphasic region for E7. This range is slightly smaller than the biphasic range recorded in Chapter 5, Table 5.1. This is because, where the nematic portion of the biphasic range is very small, at temperatures close to the isotropic phase, the reflected intensity is too small to be distinguished from the isotropic background. The reflected intensity is only detectable after the nematic phase can be distinguished optically. The temperature difference between these thresholds is different for each array but was observed to be up to ~0.5 C. The reflected intensity measured in the nematic phase, below 60 C, increases and decreases for all four arrays as the temperature changes. This is separate from the 1

213 peak seen at the phase transition, above 60 C, and is likely to be a result of the change in birefringence as a function of temperature. As the intensity of light transmitted through a birefringent sample is dependent on sin (πd. n eff /λ 0 ) (see Chapter 3) a change in birefringence may increase or decrease the reflected intensity. n eff is the effective birefringence, which is dependent on the polar tilt of the liquid crystal director from the optic axis. The peaks in the biphasic region for different arrays show similar variation in height to that seen for 5CB and may be due to the irregular manner in which defects form on cooling. The temperature profiles as a whole show a clear difference in form between the heating and cooling regimes. They vary particularly in two manners, the temperature at which the apparent phase transitions occur and the general shape of the profiles. The temperature differences are attributable to two effects. The nematic to isotropic phase transition is of first order and as such is affected by a degree of hysteresis. Also, at a heating and cooling rate of 1 C.min -1, there can be an appreciable thermal lag ( C) between the temperature of the hotstage and the temperature of the liquid crystal. The shape of the profiles can also be attributed to multiple physical effects. The manner in which the nematic phase nucleates on cooling is different from the way is melts on heating. The domain boundaries of new nematic regions have an effect on the liquid crystal alignment and affect the reflected intensity. Also, on cooling, optical textures larger than the gold spots can be seen. In addition to this it has been shown in the literature the density of biomolecules on a surface can affect the time for a nematic liquid crystal to adopt long range surface induced orientational order. If time as well as temperature affects the formation of nematic alignment on cooling, this explains the difference in the gradient of the reflected intensity at temperatures immediately below the biphasic region for heating and cooling. 13

214 Near the phase transition, a component of the reflected intensity may be dependent on light scattering from the liquid crystal. Because liquid crystals are birefringent, changes in the director orientation, due to defects or thermal fluctuations, cause rapid changes in the apparent refractive index of the system for polarised light. 3 This will scatter the incident laser light in all directions. This will be particularly strong for biphasic materials such as E7. In the biphasic temperature range, droplets of nematic and isotropic phases exist stably. At the domain wall between these regions, the director orientation of the liquid crystal changes very quickly and will induce scattering. The possible impact of scattering on the reflected intensity is discussed later. 9.3 ZLI 1695 Images of a cell of average thickness 9.µm (±0.7µm) filled with ZLI 1695 are shown in Figure 9.9. The phase sequence for ZLI 1695 is nematic-7.0 Cisotropic; 1 the biphasic region is ~0.5 C wide. 14

215 a b c Figure 9.9 Optical microscopy images of a cell ~9µm thick filled with ZLI 1695 and an acid terminated SAM over Array 3 of 8µm gold spots separated by 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. d 00µm The images here are of Array 3. This is because Array 1 on this substrate was formed with significant errors during the photolithography process and was not suitable for measurements. In addition to this, Array is optically dark in the nematic phase. For Arrays 3 and 4, the gold spots show up relatively brightly in the nematic phase, Figure 9.9 (b), though even in this case the array is much closer to homeotropic alignment than any observed for 5CB or E7. On heating through the phase transition, the gold spots show more brightly than in the nematic phase and cross defects can be seen on the gold spots, Figure 9.9 (c). On cooling the nematic phase appears to nucleate in circular domains with a diameter of approximately 0µm, Figure 9.9 (d). Within these areas, the alignment is not homeotropic and the gold spots can be seen clearly. These regions are clearly distinct from the black 15

216 isotropic domains. Images of the phase transition for the three arrays can be seen in Figure a b 00µm c Figure 9.10 Polarising microscopy images of a cell ~9µm thick filled with ZLI 1695 and an acid terminated SAM over three different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array. (b) Array 3. (c) Array 4. Array is totally dark in the nematic phase and on heating, Figure 9.10 (a), it appears very faintly green and the gold spots can be made out. It is not clear whether this is an effect of the gold spots or a change in alignment across the whole of the array, gold and silicon together. Array 3 appears patchily bright in the nematic phase, and on heating, Figure 9.10 (b), the gold spots shine more brightly before cross defects can be seen. Array 4 has very faint bright spots in the nematic phase, but on heating, Figure 9.10 (c), cross defects can be seen as clearly as for Array 3. 16

217 Images of the optical textures that form on cooling over the three arrays can be seen in Figure a b 00µm c Figure 9.11 Polarising microscopy images of a cell ~9µm thick filled with ZLI 1695 and an acid terminated SAM over three different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array. (b) Array 3. (c) Array 4. Qualitatively similar behaviour is shown for each of the three arrays. It is interesting to note that the array that is homeotropically dark (verified conoscopically) in the nematic phase (Array ) appears noticeably darker at the phase transition. The reflected intensities are shown in Figure

218 0. 0. Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) b 0. Normalised Intensity (Arbitrary Units) Temperature ( o C) c Figure 9.1 Reflected intensity from a cell filled with ZLI 1695 on cooling through the nematic to isotropic phase transition. (a) Array. (b) Array 3. (c) Array 4. The dotted lines represent the width of the biphasic temperature range. For Array, shown Figure 9.1 (a), the angle of maximum intensity was determined by repeated measurements of the reflected intensity as a function of temperature over a range of angles of rotation. For Arrays 3 and 4, shown in Figure 9.1 (b) and (c), enough intensity was measured in the nematic phase to determine the angle without changes in temperature. The peaks in intensity for the arrays shown in Figure 9.1 (a) and (b) are much lower than for 5CB and E7 and for the array shown in Figure 9.1 (c) no peak was observed. Part of this effect may be due to the fact that the birefringence of ZLI 1695 is approximately half that of the other liquid crystals close to the phase transition (0.03 compared with 0.06). However the lack of a peak seen for one array suggests that the director orientation here undergoes a different change from the other arrays on the cell. It is also apparent from these intensity profiles that even the apparently bright gold spots of 18

219 Arrays 3 and 4 are closer to homeotropic alignment that the arrays in the 5CB and E7 cells. The possible effects of birefringence are discussed in detail later. 9.4 ZLI 113 Images of a cell of average thickness 10µm (±1µm) filled with ZLI 113 are shown in Figure The phase sequence for ZLI 113 is nematic-71.0 Cisotropic; the biphasic region is ~ C wide. 1 a b c Figure 9.13 Optical microscopy images of a cell ~10µm thick filled with ZLI 113 and an acid terminated SAM over Array 1 of 8µm gold spots separated by 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. d 00µm Some of the gold spots for the array show up brightly in the nematic phase while others do not, Figure 9.13 (b). This indicates a regional change in alignment over these spots that is not accounted for by the SAM or by the intended surface topography. The bright to dark change on the spots is consistent on rotation which 19

220 indicates that the dark spots are not tilted in alignment but rather have a uniform homeotropic alignment. Arrays 1 and 4 have bright areas in the nematic phase while Arrays and 3 do not. The cross defects seen for 5CB are also observed here as the cell is heated, Figure 9.13 (c). This kind of defect is seen for all spots, those that are both light and dark in the nematic phase. Therefore, the formation of these defects is not directly linked to the initial orientation of the liquid crystal on the gold at temperatures below the phase transition. On cooling, the nematic phase nucleates in circular domains similar to those seen for ZLI 1695, Figure 9.13 (d). However, unlike for ZLI 1695, some of the gold spots within these regions show up significantly more brightly than others and the silicon areas remain dark. The position of the brighter spots also does not appear to be linked to the bright spots in the nematic phase. 0

221 Images of the four identical arrays taken as the cell is heated through the phase transition can be seen in Figure a b c Figure 9.14 Polarising microscopy images of a cell ~10µm thick filled with ZLI 113 and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. d 00µm As the cell is heated, the brightness over some of the gold spots moves out of the frame in bands. This is consistent with a minor temperature gradient (less than ±0.1 C) across the cell, with the brightness following isothermal contours. Once it is gone, the change in contrast allows the formation of cross defects above the gold spots to be seen for Arrays 1, and 3 shown in Figure 9.14 (a), (b), and (c). They are not clear on Array 4 shown in Figure 9.14 (d) but it is possible that this is the result of a slightly different optical exposure of the camera. For the Array, Figure 9.14 (b), the defects can be seen to merge with their neighbours, in some cases producing a different texture where larger defects appear to be pinned within a 1

222 square of gold spots instead of on top of each spot. The intensities of reflected light from these arrays are shown in Figure Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) Temperature ( o C) a b Normalised Intensity (Arbitrary Units) Temperature ( o C) Normalised Intensity (Arbitrary Units) Temperature ( o C) c d Figure 9.15 Reflected intensity from a cell filled with ZLI 113 on heating through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The apparent temperature difference between the clearing point of Arrays 1 and 4, Figure 9.15 (a) and (d) can be attributed to imperfect thermal contact between those areas of the substrate and the hot-stage. The presence of the gold anchored cross defects does not necessarily have a significant effect on the reflected intensity. Cross defects are clearly seen for Array, (Figure 9.14 (b)) that does not correlate to a significant reflection in Figure 9.15 (b). In contrast, the cross defects observed for Array 1, Figure 9.14 (a), are accompanied by a band of very bright gold spots that passes across the cell as the nematic phase retreats. This matches a very high reflected intensity in Figure 9.15 (a) and this suggests that the reflected intensity on heating is more dependent on

223 the brightness of the gold spots in the nematic phase than on the formation of defects at the phase transition. Images of the four arrays as the cell is cooled through the phase transition can be seen in Figure a b c Figure 9.16 Polarising microscopy images of a cell ~10µm thick filled with ZLI 113 and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. d 00µm As the nematic phase nucleates some of the gold spots show up brightly and some remain dark. The degree to which this happens between different areas appears to be different for the each array. The reflected intensities from these arrays are shown in Figure

224 0.4 Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) b Normalised Intensity (Arbitrary Units) Temperature (C) Normalised Intensity (Arbitrary Units) Temperature ( o C) c d Figure 9.17 Reflected intensity from a cell filled with ZLI 113 on cooling through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The dotted lines represent the width of the biphasic temperature range. The intensity profiles show significantly dissimilar results for each of the four arrays. Arrays 1 and 4 have bright gold areas in the nematic phase and this corresponds to high reflected intensity at low temperatures, Figure 9.17 (a) and (d). Arrays and 3 do not have bright areas of gold in the nematic phase and reflected intensities near zero are correspondingly measured, Figure 9.17 (b) and (c). It is also interesting that peaks in the reflected intensity are only recorded for Arrays 1 and though qualitatively similar optical textures can be seen for all four arrays. Similar to the heating profiles, this suggests that for this material the reflected intensity at the phase transition is greatly affected by the brightness of the gold spots in the nematic phase. 4

225 In the nematic, phase ZLI 113 has a clearly tilted alignment on some clearly defined areas of Arrays 1 and 4, the rest of the arrays are homeotropically dark. This suggests that the physical parameters of this cell are very close to a critical anchoring transition between planar and homeotropic on the gold spots. Possible causes of this are discussed later. 9.5 MDA Images of a cell of average thickness 8µm (±0.8µm) filled with MDA are shown in Figure The phase sequence for MDA is nematic Cisotropic, the biphasic region is ~1.5 C wide. 4 5

226 a b c Figure 9.18 Optical microscopy images of a cell ~8µm thick filled with MDA and an acid terminated SAM over Array 1 of 8µm gold spots separated by 0µm. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c) Crossed polarisers on heating through the nematic to isotropic phase transition at 1 C.min -1. (d) Crossed polarisers on cooling through the isotropic to nematic phase transition at 1 C.min -1. d 00µm As for ZLI 113, some of the gold spots show up brightly in the nematic phase but not all. This effect is reproducible over many heating and cooling cycles. However, this is not observed for all of the four arrays measured. Arrays 1 and 4 have bright areas while Arrays and 3 are uniformly dark in the nematic phase. As the cell is heated, cross defects form on the gold spots as seen for 5CB, ZLI 1695 and ZLI 113. On cooling, the growth of nematic domains is clear and distinct from the isotropic melt and the gold and silicon show up brightly. As the nematic area grows, all gold spots within can be seen, both those that are bright and dark at lower temperatures. Images of the four arrays as the cell is heated through the phase transition can be seen in Figure

227 a b c Figure 9.19 Polarising microscopy images of a cell ~8µm thick filled with MDA and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is heated through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. d 00µm The distinct cross defects that can be seen on Array 1, Figure 9.19 (a) are present but are much less clear on Array 3 seen in Figure 9.19 (c). These are not seen for the other two arrays over repeated heating cycles. The nucleation of the cross defects on the gold spots does not appear to be linked to the brightness of gold spots in the nematic phase. The reflected intensities from these arrays are shown in Figure

228 Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) a Temperature ( o C) b Normalised Intensity (Arbitrary Units) Temperature (C) Normalised Intensity (Arbitrary Units) Temperature ( o C) c d Figure 9.0 Reflected intensity from a cell filled with MDA on heating through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The high reflected intensities measured below the phase transition seen for in Figure 9.0 (a) and (d) correspond to the Arrays 1 and 4 which show bright gold spots in the nematic phase. The growth of the cross defects for Array 1, Figure 9.0 (a), does not appear to have an effect on the reflected intensity, as no cross defects are observed for Array 4, Figure 9.0 (b), and the two arrays have very similar intensity profiles. The very faint crosses seen for Array 3, Figure 9.0 (c), also do not appear to affect the reflected intensity and the profile of the array appears flat, similar that shown for the uniformly dark Array 4, Figure 9.0 (d). These results are qualitatively similar to those recorded for ZLI 113 and suggest that the physical properties of this cell are close to a critical anchoring transition between planar and homeotropic alignment on the gold spots. 8

229 Images of the four arrays as the cell is cooled can be seen in Figure 9.1. a b c Figure 9.1 Polarising microscopy images of a cell ~8µm thick filled with MDA and an acid terminated SAM over four different arrays of 8µm gold spots separated by 0µm. The cell is cooled through the isotropic to nematic transition at a rate of 1 C.min -1. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. d 00µm Qualitatively similar optical responses can be seen for each of the four arrays as the nematic phase nucleates. The reflected intensities from the arrays are shown in Figure 9.. 9

230 Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) Temperature ( o C) a b Normalised Intensity (Arbitrary Units) Normalised Intensity (Arbitrary Units) Temperature ( o C) Temperature ( o C) c d Figure 9. Reflected intensity from a cell filled with MDA on cooling through the nematic to isotropic phase transition. (a) Array 1. (b) Array. (c) Array 3. (d) Array 4. The dotted lines represent the width of the biphasic temperature range. The non-zero reflected intensities measured below the phase transition for Array 1 and Array 4 correspond to the bright spots seen in the nematic phase for these arrays. The height of the intensity peaks do not appear to correspond to this brightness. 30

231 9.6 Discussion A summary of the optical textures and reflected intensities of the liquid crystals is detailed in Table 9.1. Optical Responses of the Different Liquid Crystals Nematic phase texture Textures on heating Textures on cooling Reflected intensity peak on heating (Arbitrary Units) Reflected intensity peak on cooling (Arbitrary Units) 5CB, cell thickness 9.0µm±0.5 E7, cell thickness 8.9µm±0.6 ZLI 1695, cell thickness 9.µm±0.7 Bright gold Bright gold Array : dark Array 3: bright gold Array 4: faint gold Cross defects on the spots Random planar texture (one array shows defect nucleation on gold spots) Gold show up very brightly (possible cross defects lost in contrast) Random planar texture Cross defects on the bright Arrays 3 and 4, nothing on Array Bright circular nematic domains in which gold can be seen ZLI 113, cell thickness 10.0µm±1 Patches of arrays dark and bright Bright gold and cross defects Dark circular nematic domains in which gold can be seen MDA 01-01, cell thickness 8.0µm±0.8 Some arrays dark, some arrays have bright areas Some arrays show cross defects, others dark Large bright nematic domains in which gold can be seen 0.3± ± ± ± ± ±0.38* 0.03±0.03* 0.068±0.1* 0.615±0.4* Table 9.1 A summary of the optical response observed on heating and cooling through the nematic to isotropic phase transition of the different liquid crystals. *Intensity profiles with a distinct peak at the isotropic to nematic phase transition. Measurements of the reflected intensity peaks are averages between the four arrays on each cell. The listed uncertainties are approximations of the variation of the data between the arrays. Where a distinct peak was not visible in the intensity profile, the intensity at the temperature of the phase transition was recorded. The variation of peak height between repeated measurements of a single array was found to be approximately 5%. Similar to the results given in Chapter 8 these are not true errors but serve to give an impression of the spread of the data. Despite the textures observed optically for ZLI 1695 on heating, no reflected intensity changes above background noise could be detected and a value of zero was recorded. 31

232 9.6.1 Optical textures in the nematic phase It is not surprising that different liquid crystals exhibit different alignments on the gold spots in the nematic phase. The different chemical structures of the liquid crystals will interact with the acid terminated SAMs in different manners. Because of the similarities between the components of 5CB and E7, the similarity of their textures in the nematic phase is not unexpected. However, the disparity between arrays for the liquid crystals ZLI 1695, ZLI 113 and MDA is interesting. On some arrays the gold spots show up brightly but on other arrays they do not. Indeed, in some cases, a dividing line between bright and dark spots can be observed within a single array, Figure 9.13 (b) and Figure 9.18 (b). These effects have been observed to be consistent over repeated heating and cooling cycles and are not affected by azimuthal rotation of the substrates. It was shown in Chapter 8 that small changes in thickness (approximately 3µm) can correspond to changes in the appearance of gold spots in the nematic phase and that a cell 10µm thick had different nematic textures on the gold spots from cells 7.5µm and 1.7µm thick, see Table 8.1. This suggests that 10µm might be close to some critical thickness for 5CB. For these different liquid crystals, the cell thicknesses vary by approximately µm from cell to cell. However, the variation in thickness between the areas of the same cell is never greater than 1µm and the variation in thickness between areas of an individual array is not more than 0.1µm. Unless the dependence of alignment in the nematic phase on cell thickness is extremely sensitive, it is unlikely that it could cause the effect seen. Barbero and Barberi 5 showed that, in a cell with hybrid alignment, a critical thickness can exist. Below this thickness, no deformation in the director profile will be observed. This is dependent on the anchoring energies at the aligning surfaces and the elastic constants of the liquid crystal and could explain why an anchoring transition across an array can be seen for some liquid crystals but not others. It does not by itself explain the dark-bright-dark nematic alignment on the gold spots for 5CB for cell thicknesses of µm. Another explanation is that the SAM at the surface of the gold is not completely uniform. If the SAM did not form properly due to surface contamination in the cell construction process, the surface anchoring at different areas of the gold would be 3

233 different. This could also occur if the SAM is disrupted after the construction. However, since the sulfur group of the thiols is known to covalently bond to the gold surface this is less likely. The interaction between the SAM and the gold spots themselves could also be responsible for the anchoring transitions observed. It has been reported in the literature that, for the case of a planar alignment inducing substrate and a homeotropic SAM, the tilt angle of the liquid crystal at the surface will be dependent on the thickness and quality of the SAM. 6 It is reasonable to assume the same for a gold surface with a slight anisotropy covered in a planar aligning SAM (as used in this thesis). In the case of the arrays with both black and bright areas of gold, minor difference in the SAM could cause an anchoring transition. However, it is unlikely that minor SAM differences would follow sharp lines and explain the sharp bright-dark change seen for some arrays. If the properties of the SAM can have a critical affect on alignment, then it follows that variations in the surface anisotropy of the gold spots could have a similar effect. Skaife and Abbott 7 quantified the effect on anchoring energy of obliquely evaporated gold films onto glass substrates. 10nm thick layers of gold on substrates with orthogonally orientated angles of deposition were shown to induce a twist deformation in 5CB in a cell ~10µm thick. For the substrates used in this thesis, gold was evaporated from a single point and a range of tilt angles can be seen to be induced by the gold from array to array. This can be seen in the patchy bright gold spots in Figure 9.4 (b). It is possible that a change in surface anisotropy, caused by the gradual change in angle of gold deposition across an array, crosses some critical threshold for some liquid crystals and induces a sharp planar to homeotropic anchoring transition. Surfaces with gold supported SAMs have been observed by Alkhairalla et al. 8 to be very close to homeotropic-planar anchoring transitions for 5CB and 9CB. The same surfaces induced uniform alignment in other ncb liquid crystals. The interaction of gold surface anisotropy, SAM formation and cell thickness together could explain the differences in liquid crystal alignment seen for different arrays here and in Chapter 8. Future work investigating this is needed to make 33

234 definitive statements about the effect of these cell properties on nematic alignment and how this affects possible biosensors Optical textures on heating and cooling The formation of cross defects at the gold spots as the cells are heated through the nematic to isotropic phase transition appears to be much more consistent than the alignment in the nematic phase. These defects are observed for all five liquid crystals for at least some of the arrays measured. It is particularly clear in Figure 9.13 (b) and (c) that cross defects form on gold spots that are both dark and bright in the nematic phase. If the difference in alignment in the nematic phase is a result of the interaction of cell thickness, surface chemistry, and gold anisotropy, then the nucleation of the anchored cross defects may be induced by the surface topography of the 50nm thick gold spots, as this does not change across an array. However, similar cross defects have been shown to form on substrates patterned with circular spots of different surface chemistry by Bramble et al. 9 They showed that 10µm circles of planar aligning COOH terminated SAMs induced circular cross defects in the nematic liquid crystal 9CB. This was shown in the nematic phase. It is possible that for the system of raised gold spots, a similar liquid crystal alignment is only seen close to the phase transition, where the values of the elastic constants of the liquid crystals are lower. However, this would imply that there would be a correlation between the presence of the cross defects and the elastic constants of the liquid crystals at the phase transition and this is not seen. This is discussed below. As the cells are cooled, no cross defect nucleation can be spatially linked to the gold spots. Instead, cross defects can be seen to form in the spaces between the spots but only for 5CB and E7. However, where the nematic phase forms from the isotropic melt the gold spots shine extremely brightly for all liquid crystals, even in areas of the arrays that are dark at lower temperatures. The formation of defects and the propagation of director distortion into the liquid crystal bulk is also discussed with reference to the values of the elastic constants of the liquid crystals below. 34

235 9.6.3 The relationship between peak height and birefringence Measurements of the birefringence of the liquid crystals for temperatures approaching the clearing point were presented in Chapter 6. To within experimental errors, the liquid crystals 5CB, E7, ZLI 113 and MDA all have the same birefringence at the phase transition. Only ZLI 1695 has a significantly different birefringence. In order to analyse the possible implications of this, the reflected intensities at the phase transition were plotted against sin (πd. n/λ 0 ) for the reasons described in Chapter 8. This assumes that the effective birefringence of the sample n e -n o (which is dependent on director tilt) is equal to the absolute birefringence of the liquid crystal, n (which is independent of director orientation). This is a reasonable approximation for the case of a single liquid crystal with a changing cell thickness in Chapter 8 but is a less good approximation of the reflected intensity for the case of different liquid crystals. This is because it assumes that the director orientation distribution throughout the liquid crystal sample and that the tilt angle at the gold and silicon surface are the same for the different systems considered. In the case of different liquid crystals, the anchoring energy at the surface is likely to be different for each material and the different elastic constants will cause the director distribution in the liquid crystal bulk to be different. However, the fact that four of the materials studied have the same value of birefringence but clearly different surface and bulk conditions enables the relative importance of those factors to be assessed. Graphs of the reflected intensity of the different liquid crystals as they are heated and cooled through the phase transition plotted against retardance can be seen in Figure

236 Normalised Intensity Peak Height (Arbitrary Units) sin (πd n/λ 0 ) 5CB E7 ZLI 1695 ZLI 113 MDA Normalised Intensity Peak Height (Arbitrary Units) sin (πd n/λ 0 ) 5CB E7 ZLI 1695 ZLI 113 MDA a b Figure 9.3 Graphs of peak height on (a) heating and (b) cooling plotted against the retardance of the liquid crystals at the phase transition. The lines above and below each point are representative of the uncertainty in the peak height as described in Table 9.1. As previously mentioned, the value of the birefringence at the phase transition for 5CB, E7, ZLI 113 and MDA are the same. Variations in the x-axis position of these materials are therefore solely a function of the difference in thickness of these cells. Due to the large effective errors in the measurement of the peak height, it is difficult to make definitive statements about the effect of birefringence. However, it was shown in Chapter 8 that the effect of thickness induced retardance on the reflected intensity for small changes in thickness (<µm) is small compared to the variation between measurements of different arrays of identical thicknesses. As was mentioned earlier, it is possible that there is a significant contribution to the reflected intensity from scattering of the incident light. Scattering is caused by changes in refractive index of the scattering medium over a small area. Thus the effect of scattering will be proportional to the absolute birefringence of the liquid crystal material. Graphs of peak height plotted against birefringence can be seen in Figure

237 Normalised Intensity Peak Height (Arbitrary Units) CB E7 ZLI 1695 ZLI 113 MDA Birefringence (at phase transition) Normalised Intensity Peak Height (Arbitrary Units) CB E7 ZLI 1695 ZLI 113 MDA Birefringence (at phase transition) a b Figure 9.4 Graphs of peak height on (a) heating and (b) cooling plotted against the birefringence of the liquid crystals at the phase transition. The values of birefringence for 5CB, E7, ZLI 113 and MDA were measured to be the same at the phase transition. They are separated by a nominal amount in the x axes of these graphs for clarity. The spread of measurements for each liquid crystal is large compared to the spread of measurements between different liquid crystals. The effect of scattering might be expected to be greater in biphasic materials where domain walls between phases cause a sharp change in refractive index. However, the single component material 5CB can be seen to have a comparable reflected intensity to those of the other biphasic materials. Thus it can be assumed that the result of scattering on the reflected intensity on heating and cooling is small compared to the influence of other physical effects The relationship between peak height and elasticity In a liquid crystal cell with planar anchoring at one surface and homeotropic anchoring at the other, the elastic constants K 11 and K 33 will be important in describing the director orientation and therefore the intensity of light transmitted by the cell. 10 Measurements of the elastic constants K 11 and K 33 of the liquid crystals at temperatures approaching the nematic to isotropic phase transition were also presented in Chapter 6. Graphs of the reflected intensity of the different liquid crystals as they are heated and cooled through the phase transition plotted against K 11 can be seen in Figure

238 Normalised Intensity Peak Height (Arbitrary Units) K11 (pn) 5CB E7 ZLI 1695 ZLI 113 MDA Normalised Intensity Peak Height (Arbitrary Units) K11 (pn) 5CB E7 ZLI 1695 ZLI 113 MDA a b Figure 9.5 Graphs of peak height on (a) heating and (b) cooling plotted against the elastic constant K 11 of the liquid crystals at the phase transition. The lines above and below each point are representative of the variation in measurements of the peak height between different arrays for each liquid crystal as described above. The large variation in the data makes it difficult to determine a conclusive relationship between reflected intensity on heating and the elastic constant K 11. Given the apparent lack of correlation between reflected intensity and the formation of cross defects (see Figure 9.14 and Figure 9.15 and Figure 9.19 and Figure 9.0) this is not surprising. The measurement technique does not appear able to reliably detect the light reflected from the cross defects, particularly when other brighter optical textures are present. On cooling, a trend can be seen for the reflected intensity as K 11 changes. In general, lower values of K 11 correspond with higher values of intensity. The large variation of the intensity for individual liquid crystals makes this less certain but it matches what has been reported in the literature. It has been shown in the literature that director distortions propagate further from a disrupting surface or particle for lower values of the elastic constants in the one constant approximation. 11 The observed trend could be caused by a tilted anchoring profile at the gold surfaces that propagates further into the homeotropically aligned liquid crystal bulk for lower values of K 11. A larger the portion of the liquid crystal bulk with a tilted orientation relative to the polariser and analyser would increase the intensity of light reflected from the surface. 38

239 Graphs of the reflected intensity of the different liquid crystals as they are heated and cooled through the phase transition plotted against K 33 can be seen in Figure 9.6. Normalised Intensity Peak Height (Arbitrary Units) K33 (pn) 5CB E7 ZLI 1695 ZLI 113 MDA Normalised Intensity Peak Height (Arbitrary Units) K33 (pn) 5CB E7 ZLI 1695 ZLI 113 MDA Figure 9.6 a b Graphs of peak height on (a) heating and (b) cooling plotted against the elastic constant K 33 of the liquid crystals at the phase transition. No clear quantitative relationship for the reflected intensity on heating can be seen but the same relationship observed for K 11 on cooling is present here. This also matches literature predictions of a deformation dependent on both K 11 and K 33 in a cell with different directions of planar alignment. 1 For changes in alignment between two differently orientated tilt angles, the ratio K 33 /K 11 has been shown to be important. 13 It has been reported that smaller values of the ratio cause a liquid crystal to be more easily reoriented by an electric field (in an electro-optic cell) to allow light to pass through a cell. Graphs of the reflected intensity of the different liquid crystals as they are heated and cooled through the phase transition plotted against K 33 /K 11 can be seen in Figure

240 Normalised Intensity Peak Height (Arbitrary Units) K33/K11 5CB E7 ZLI 1695 ZLI 113 MDA Normalised Intensity Peak Height (Arbitrary Units) K33/K11 5CB E7 ZLI 1695 ZLI 113 MDA Figure 9.7 a b Peak height on (a) heating and (b) cooling plotted against the ratio of the elastic constants of the liquid crystals at the phase transition K 33 / K 11. This also shows a trend of increased intensity for decreasing values of K 33 /K 11. More recent work by Atherton and Sambles 14 has modelled the case of alternating homeotropic and planar aligning stripes at a surface and found that the bulk free energy difference between the areas was proportional to (K /K 11 ), though this assumes K 11 =K 33. This suggests that measurements of the values of K for the liquid crystals at the phase transition could be useful for a more complete analysis of the effect of elasticity. The large variation in the reflected intensities of the arrays for each liquid crystal makes it difficult to make definitive conclusions. A large source of this variation appears to be the difference in peak height for arrays with different anchoring in the nematic phase. It is reasonable to assume that the difference between measurements of arrays that are intended to be identical is a result of changes in the anchoring energies at the surfaces. Possible reasons for these differences have been discussed above. This is the most important factor affecting the system and its potential for biosensor applications that has not been directly addressed in this chapter. It has been shown in Figure 9.15 and Figure 9.0 that the difference between arrays with areas of bright gold and those with only dark gold is particularly apparent in the reflected intensity on heating through the phase transition. A more careful approach to the construction and testing of the SAMs, more uniform gold 40

241 deposition and a closer analysis of the orientation of the liquid crystal at the surfaces would be very important in understanding the mechanics of the system. However, this may be a very important result for the design of a potential biosensor. Arrays close to an anchoring transition in the nematic phase show very different reflected intensities as they are cooled through the phase transition. This may be a way of optically detecting very small surface changes where they affect some critical parameter. 9.7 Summary All five liquid crystals have displayed some degree of sensitivity to the presence of the gold spots. On heating, the presence of cross defects anchored to the spots has been reported in almost every case. Unfortunately this effect does not appear to be clearly distinguished from the brightness of gold in the nematic phase by the reflected intensity technique. On cooling, cross defects appear to nucleate in the space between squares of four spots for 5CB and E7. However, the gold spots have been seen to shine brightly at the phase transition despite unreliable brightness deeper in the nematic phase for every liquid crystal. The effect of birefringence and thickness induced retardance on the intensity of light transmitted at the phase transmission has been shown to be smaller than the effects of elasticity and surface anchoring. This means that the large differences in peak heights for the materials 5CB, E7, ZLI 113 and MDA are the effect of different elastic constants and surface anchoring. That elasticity and surface anchoring have a greater effect on the reflected intensity than birefringence is an important conclusion for the design of a liquid crystal based biosensor. It would be more important to design a liquid crystal with the desired elastic constants and a surface with the desired anchoring interaction than to obtain a liquid crystal with a specific value of n. The reflected intensity on cooling appears to be repeatedly higher for smaller values of K 11, K 33 and K 33 / K 11. This is consistent with the propagation of a surface induced director distortion into the liquid crystal bulk as predicted by the literature. It suggests that a liquid crystal optical biosensor would be more sensitive to the presence of surface defects if it were tuned to have small values of elasticity. 41

242 The next chapter will investigate the effect of changing the size and separation of the gold spots on the optical textures and reflected intensity observed. 1 Merk Data Sheet, Merck KGaA, Darmstadt, Germany. Clare, B.H. and Abbott, N.L. (005), Langmuir 1, Heiderich, A., Maynard, R. and van Tigglen, B.A. (1997), J. Phys. II France 7, Strömer, J.F, Raynes, E.P. and Brown, C.V. (006) APL 88, Barbero, G. And Barberi, R. (1983), J. Physique 44, Lee, Y.J., Gwag, J.S., Kim, Y.K., Jo, S.I., Kang, S.G., Park, Y.R. and Kim, J.H. (009), Appl. Phys. Lett. 94, Skaife, J.J. and Abbott, N.L. (1999), Chem. Mater. 11, Alkhairalla, B., Allinson, H., Boden., N., Evans, S.D. and Henderson, J.R. (1999), Phys. Rev. E 59, no 3, Bramble, J.P., Evans, S.D., Henderson, J.R., Anquetil, C. Cleaver, D.J. and Smith, N.J. (007), Liq. Cryst. 34, no 9, Sparavigna, A., Komitov, L. and Strigazzi, A. (199), Physica Scripta. 43, Ruhwandl, R.W. and Terentjev, E.M. (1997), Phys. Rev. E 55 (3), Batalioto, F., Bechtold, I. H., Oliveira, E. A. and Evangelista, L. R. (005), Phys. Rev. E, 7, Kuo, C.L., Miyashia, T., Suzuki, M. and Uchida, T. (1996), Appl. Phys. Lett. 68, no 11, Atherton, T.J. and Sambles, J.R. (006), Phys. Rev. E 74,

243 Chapter 10 The Effects of Spot Size and Separation, Array Properties In this chapter, the effects of the size and separation of the raised gold spots on the optical textures and intensity of reflected light observed for a liquid crystal cell are investigated. It is important to understand the sensitivity of a liquid crystal based system to the size and concentration of topographical surface defects to assess its potential as a biosensor. An acid terminated SAM, homeotropic aligning cover slips and 5µm spacer beads were used for consistency with the measurements in the previous two chapters, the cell constructed was measured to be approximately 10µm thick (more specific measurements are given in Figure 10.14). The liquid crystal 5CB was chosen because it is a single component material with no biphasic temperature region and it may be less sensitive to imperfect thermal contact between different areas of the cell. The similarity of the measurements of its reflected intensity on heating and cooling (see Figure 9. and 9.3) increase the likelihood of meaningful data being recorded for both kinds of temperature change. In addition to this, no anchoring transitions were observed across a single array for 5CB. Thus, the cell properties are less likely to be close to a critical parameter and they array s responses are less likely to be influenced by uncontrolled surface and thickness effects. The effects of two different parameters are considered. The size of the gold spots is varied for a constant percentage of gold surface coverage, and spot separation is varied for a constant spot size. For varying spot size, the array properties were: µm diameter spots with 5µm array pitch (these arrays were labelled s5p), 4µm spots with 10µm array pitch (4s10p), 8µm spots with 0µm array pitch (8s0p, which were used in the previous two chapters) and 16µm spots with a 40µm array pitch (16s40p). Arrays with 1µm spots and.5µm array pitch were included in the design of the substrates but it was not possible to reliably develop this size of spot in the photolithography process. For varying spot separation, the arrays used were: 4µm spots with 7µm array pitch (4s7p), 4µm spots with 10µm array pitch (4s10p), 4µm spots with 0µm array pitch (4s0p) and 4µm spots with 40µm array pitch (4s40p). 4µm spot diameter was used because it allowed a large range of separations to be 43

244 considered, whilst maintaining good construction reproducibility. As described in Chapter 8, two sets of arrays (Array Series 1 and ) were included on each substrate, this enabled two duplicate arrays for each set of array properties to be measured for a single cell. Similar to the results presented in Chapters 7, 8 and 9, the liquid crystal cell was heated and cooled at a rate of ±1 C.min -1. Due to the nature of the results, white light optical microscopy images of each array are presented in order of increasing spot size and spot separation. This allows clear comparison of the relative optical textures observed. The images show a sample array without crossed polarisers and the same array with crossed polarisers in the nematic phase. Images of the nematic to isotropic transition on heating and cooling with crossed polarises are then shown for both of the duplicated arrays from Array Series 1 and. These are followed by measurements of the reflected intensity of monochromatic light (670nm) as they are heated and cooled through the phase transition from each array in turn. The results are then summarised and discussed µm spot diameter, 5µm array pitch Images of the optical textures that form on an array of µm spots with a separation of 5µm can be seen in Figure The gold spots are small enough that they are hard to see without crossed polarisers (Figure 10.1 (a)), and do not appear to disrupt the homeotropic alignment in the nematic phase (Figure 10.1 (b)), this was conoscopically verified, On heating, random flashes of light make the spots briefly visible, (Figure 10.1 (c) and (e)), though not in a regular manner across the arrays. On cooling, the cell shows bright planar alignment over a small temperature range (<0.1 C) and the gold spots can more clearly seen. 44

245 a b c d e f 00µm Figure 10.1 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. µm diameter spots, 5µm array pitch (s5p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. 45

246 10. 4µm spot diameter, 7µm array pitch Images of the optical textures that form on an array of 4µm spots with a separation of 7µm can be seen in Figure 10.. No deviation from homeotropic alignment can be seen in the nematic phase, Figure 10. (b). As the cell is heated through the phase transition, bright circles can be seen over some of the gold spots (Figure 10. (c) and (e)). Other less bright gold spots can also be seen. In the case of the array from Array Series, some evidence of defects centred on the gold spots can be seen, (Figure 10. (e)). On cooling, the gold spots show up brightly and some evidence of a square grid of defects is visible (Figure 10. (d) and (f)). 46

247 a b c d e f 00µm Figure 10. Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 4µm diameter spots, 7µm array pitch (4s7p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. 47

248 10.3 4µm spot diameter, 10µm array pitch Images of the optical textures that form on an array of 4µm spots with a separation of 10µm can be seen in Figure In the nematic phase, the gold spots of Array Series 1 show up brightly (Figure 10.3 (b)) but those of Array Series do not, this suggests an anchoring transition occurs due to other physical parameters between the substrates positions of the two arrays. As the cell is heated, the gold spots of Array Series 1 show up more brightly, following isothermal contours consistent with a very small temperature gradient (<0.1ºC) across the array (Figure 10.3 (c)). It is possible that cross defects are present on the gold spots but cannot be seen due to the contrast of the image. Mirroring the nematic textures, the gold spots of Array Series are much darker at the phase transition but appear to induce very dim cross defects anchored to the spots (Figure 10.3 (e)). On cooling,- the arrays of Array Series 1 and Array Series show the same behaviour (Figure 10.3 (d) and (f)). Areas of the arrays show up brightly and within these the gold spots can be seen clearly. There is also significantly more evidence of a square lattice of defects than could be seen for the 4µm spots with a separation of 7µm (Figure 10. (d) and (f)). 48

249 a b c d e f 00µm Figure 10.3 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 4µm diameter spots, 10µm array pitch (4s10p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. 49

250 10.4 4µm spot diameter, 0µm array pitch Images of the optical textures that form on an array of 4µm spots with a separation of 0µm can be seen in Figure Bright circles show over the gold spots in the nematic phase (Figure 10.4 (b)) but this is slightly patchy and suggests a non uniform tilt angle from spot to spot across the array. The gold spots are faintly visible for Array Series 1 on heating through the phase transition but no significant textures are seen (Figure 10.4 (c)). On heating, Array Series shows dark circles around the gold spots in a very regular pattern (Figure 10.4 (e)). It is possible that this is the nucleation of the isotropic phase as the surrounding areas are slightly coloured, consistent with a tilted nematic orientation. On cooling, a square checkerboard lattice of defects can clearly be seen for both arrays. This is much more distinct than for either the 4s7p or 4s10p arrays. This suggests that the distance between the gold spots affects the formation of possible defects. 50

251 a b c d e f 00µm Figure 10.4 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 4µm diameter spots, 0µm array pitch (4s0p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. 51

252 10.5 4µm spot diameter, 40µm array pitch Images of the optical textures that form on an array of 4µm spots with a separation of 40µm can be seen in Figure In the nematic phase, the gold spots show up brightly (Figure 10.5 (b)). On heating through the phase transition, both of the two arrays show very little brightness and the isotropic phase appears to nucleate in random patches (Figure 10.5 (c) and (e)). On cooling, many cross defects can be seen but there does not appear to be any consistent spatial correlation to the gold spots (Figure 10.5 (d) and (f)). Instead, each spot seems to be the centre of a uniformly dark domain, which could be the remnant of the isotropic phase in the area immediately around the gold spots. However, as 5CB is not biphasic and this is unlikely unless there is a significant temperature difference (>0.1 C) between the gold spots and the silicon. This is not observed for any of the other arrays. Another possibility is that there is homeotropic alignment directly around the gold spots at the phase transition. The small size and transient nature of this observation makes verification of either of these theories difficult. 5

253 a b c d e f 00µm Figure 10.5 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 4µm diameter spots, 40µm array pitch (4s40p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1 for Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1 for Array Series 1 and. 53

254 10.6 8µm spot diameter, 0µm array pitch Images of the optical textures that form on an array of 8µm spots with a separation of 0µm can be seen in Figure Four arrays with these properties are present on each substrate. The optical response of these arrays has been discussed in detail in Chapters 8 and 9. As described in Chapter 8, the gold spots shine in the nematic phase with a patchy difference in intensity across the array. This suggests a non uniform angle of tilt at the gold surface from spot to spot (Figure 10.6 (b)). Cross defects can be seen to be anchored to the gold spots on heating (Figure 10.6 (c) and (e)). Of the four arrays observed, three display a semi-random distribution of defects as shown in Figure 10.6 (d). One array shows a very clear series of cross defects that form in the spaces between groups of four spots (Figure 10.7 (f)). 54

255 a b c d e f 00µm Figure 10.6 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 8µm diameter spots, 0µm array pitch (8s0p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1, Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1, Array Series 1 and. 55

256 µm spot diameter, 40µ array pitch Images of the optical textures that form on an array of 16µm spots with a separation of 40µm can be seen in Figure In the nematic phase, the gold spots are distinct but dim for both arrays (Figure 10.7 (b)). On heating through the phase transition, the spots remain dark but very bright cross defects can be seen on every spot (Figure 10.7 (c) and (e)). On cooling, cross defects on each spot are also seen but here they extend past the boundary of the spot. Additional cross defects can be seen pinned in the spaces between groups of four spots as the defects merge Figure 10.7 (d) and (f). 56

257 a b c d e f 00µm Figure 10.7 Microscopic images of a ~10µm thick cell filled with 5CB and an acid terminated SAM. 16µm diameter spots, 40µm array pitch (16s40p), Array Series 1. (a) No polariser. (b) Crossed polarisers in the nematic phase. (c+e) Heating through the nematic to isotropic phase transition at 1 C.min -1, Array Series 1 and. (d+f) Cooling through the isotropic to nematic phase transition at 1 C.min -1, Array Series 1 and. 57