Physics of DNA. R. Podgornik. Laboratory of Physical and Structural Biology. National Institute of Child Health and Human Development
|
|
- Rosanna Oliver
- 6 years ago
- Views:
Transcription
1 Physics of DNA R. Podgornik Laboratory of Physical and Structural Biology National Institute of Child Health and Human Development National Institutes of Health Bethesda, MD
2 - DNA as a polyelectrolyte - electrostatic interactions - correlation effect - equation of state - fluctuation effect - DNA mesophases - orientational interactions - interactions and order - DNA elasticity - anomalous elastic moduli -DNA collapse
3 DNA helix Structure (B-form) R. Franklin, photo 51. Charge: 2 e 0 / 3.4 Å ~ e 0 / nm 2 grooves discrete charges Polipeptides: 0.6 e o / nm Membranes: e 0 / nm 2 a ~ 1 nm h(dna) = 1.7 Å DNA length from 50 nm to ~ µm DNA is not the proverbial spherical cow, or in this case a cylindrical one. it is a RH double helix it has lots of discrete structural (phosphate) charges (ph > 1) it has lots of room to accommodate small counterions
4 The great electrostatic divide Bjerrum length Coulomb s law and kt Gouy - Chapman length Ratio between the Bjerrum and the Gouy - Chapman lengths. Bulk versus surface interactions. Coupling parameter Weak coupling limit (Poisson - Boltzmann) Ξ 0 Strong coupling limit (Netz - Moreira) Ξ Collective description ( N description) vs. Single particle description ( 1 description) Z
5 The weak coupling limit (collective description) + electrostatic energy ideal gas entropy minimize to get equilibrium Non-equilibrium free energy = (electrostatic energy) - k (ideal gas entropy) Minimization yields the Poisson - Boltzmann equation. Screening. Debye length ~ 3.05 Å / M
6 The strong coupling limit (one particle description) Z + Z + Z + Z Electrostatic energy without mobile counterions Electrostatic energy of a single counterion Electrostatic energy of two counterions Oosawa derives attractive interactions between DNAs (late 60 s) Simulation of DLVO interactions (early 80 s - el. bilayer Torrie and Valleau (1980)) Fundamental paper by Gulbrand, Jonsson, Wennerstrom and Linse (1984) 90 realisation of the correlation effect in DNA quantitative theories of the correlation effect Collective description vs. one particle description. repulsion + 2 X attraction = attraction
7 Simulations A pair of DNAs with poly-counterions: (Gronbech-Jensen et al. 1997) Hexagonal array of DNA poly-counterions: (Lyubartsev and Nordenskiold, 1995)
8 Experiments Osmotic pressure Osmotic stress method (Parsegian & Rand) The Boyle experiment
9 Osmotic stress method Π dv µdn Setting the osmotic pressure and measuring the density of DNA
10
11 Experiment vs. theory monovalent counterions DNA in monovalent (NaCl) salt solution. Osmotic pressure for a 2D hexagonal array. PB does not seem to be working! Osmotically stressed subphase.
12 Polyvalent counterions Co(NH 3 ) mM 8mM Mn 2+ 5 o 20mM 12mM 50 o 35 o Polyvalent counterions + NaCl at 0.25 M: Co(NH 3 ) 6 Cl 3 counterion Co(NH 3 ) 6 3+ (Z = 3) MnCl 2 counterion Mn 2+ (Z = 2) Attraction is obviously there. Quantitative comparison still difficult. Monovalent salt + polyvalent counterions Osmotically stressed subphase. Or condensed.
13 Bjerrum defects screen polarization. (Onsager - Dupuis theory) rescaled charge density Last few Angstroms... HPC schizophyllan Na-DNA Na-Xanthan TMA-DNA (raw) TMA-DNA (rescaled) DDP bilayers log Π [dynes/cm 2 ] Log[Π] [dynes/cm 2 ] Surface separation, [Å] C DNA [M] Commonality of forces among charged, neutral, cylindrical and 2 planar molecules in salt solution and distilled water. Charges: DNA 1e/1.75 Å, xanthan 4 e/ 15 Å, DDP 1e/55 Å (Leikin et al. 1993) Marcelja and Radic, Perturbation of water order parameter. Similar foces in ice.
14 Conformational fluctuations Surprisingly the PB limit for finite salt does not work. What are we missing in this picture? Orientational order L p ~ 50 nm K C = k B T L p DNA is a flexible molecule. E ~ 300 MPa (plexiglass) At room temperature big conformational fluctuations.
15 Conformational fluctuations Elastic energy of the DNA Consequences: bumping into the hard wall of its nearest neighbors. This is the Odijk interaction (1986). Similar to Helfrich interaction between surfaces. Long range interaction (short range thermal undulations long range) Now assume a soft Debye - Hueckel potential: Fluctuation renormalization of interactions! (Podgornik et al. 1989)
16 Conformational fluctuations Electrostatics can only be seen indirectly, as modified by the presence of conformational fluctuations. Renormalized value of λ: λ (r) = 4 λ D. Factor 4 due to elasticity (fourth derivative) as well as the 1D nature of DNA (linear polymer). Liquid disorder! DNA in monovalent (NaCl) salt solution. Paradigmatic behavior for all monovalent salts.
17 DNA Elasticity and mesophases Persistence length of a semiflexible polymer µ tubules 0.1 M NaCl 10 7 TMV 0.1 M NaCl 10 6 F actin 0.1 M NaCl Schizophyllan water 200 Xanthan 0.1 M NaCl 120 ds-dna 0.2 M NaCl 50 Spectrin 0.1 M NaCl 15 ss-dna 0.2 M NaCl 3 Hyaluronic acid 0.2 M NaCl 1 Long Alkanes 0.5 E~300 Mpa (plexiglass) Onsager s argument valid also for polymers. cholesteric Liquid crystalline mesophases. Livolant et al. (97) line hexatic
18 DNA phase diagram A B A B x-ray beam L L L P L c β β β α (Livolant, Leforestier, Rill, Robinson, Strzelecka, Podgornik, Strey )
19 Durand, Doucet, Livolant (1992) J. Physique 2, Pelta, Durand, Doucet, Livolant (1996) Biophys. J., 71,
20 The line hexatic phase (Predicted by Toner, 1983) Long range BO order ~ 0.6 mm Long range nematic order Liquid like positional order, λ PO An anomalous 3D hexatic phase! (Podgornik et al. 1999)
21 Why is this relevant? (D. Nelson. (1995)) E.Coli 630 m long 1 mm thick 25 cm T2 P~100 atm ρ~100 mg/ml (R. Cavenoff (1995)) (Kleinschmidt et al. (1962)) Vortex lines in II sc Tension Non-chiral Magnetic field Temperature London repulsion Bending Chiral density Ionic strength Debye-Huckel repulsion
22 Why orthorhombic phase at high density? Realistic geometric models of DNA.. Kornyshev - Leikin, 1998, 2000, Allahyarov et al., R A R A R Schematics of the orientational effect. Strand opposition. from R= 24 Å out φ 0 = 18 0 and 0 0. explicit DNA structure explicit counterions explicit salt ions different salt concentrations
23 Lattice frustrations due to orientational interactions In a lattice the configurations are frustrated Hexagonal lattice nearest neighbors in optimal config. not all are happy (Lorman, Podgornik, Zeks 2001) Lattice distortions alleviate frustrations: distorted hexatic phase A 1D crystallization (1) 2D crystallization (2a, 2b, 2c) For the non-parallel orientation state a hexatic (hexagonal) phase becomes a distorted (orthorhombic or monoclinic) crystal! (Rosalind Franklin, 1952).
24 Single molecule physics Many chains Single chain
25 Measuring DNA elasticity (Baumann, Smith, Bloomfield, Bustamante 1997) Force curve fit to model (a 4 par fit) elastic constants
26 Bending and stretching bending external force stretching Small force Entropic elasticity Hookeian elasticity Large force Entropic plus enthalpic Hookeian elasticity The experiment gives us both moduli Kc as well as λ (0). ds-dna is not very stretchable, but it is not rigid either.
27 DNA - an Euler-Kirchhoffian filament or not? In classical elasticity (cylindrical Euler - Kirchhoff filament) K C = 1 4 λ R 2 Bending is just local stretching. Landau and Lifshitz, Since variations in ionic strength are involved, we assume that the foul play is due to electrostatics. Lowering the ionic strength increases the measured persistence length, but seems to reduce DNA s elastic stretch modulus, contradicting the elastic rod model. Bustamante et al. (2000).
28 Interactions and elasticity L A constrained fit : L 0, K c, λ(k c ) L Bending rigidity Podgornik et al Rouzina (2002) a a = 6.7 ± 0.7 Å (Manning a = 7.2 Å) L P ~ 48 nm l ~ 1200 pn a Stretching modulus Wenner, Williams, Rouzina and Bloomfield (2002). For ionic strengths: 1000, 500, 250, 100, 53.3, 25, 10, 2.6 mm.
29 Repulsions vs. attractions A reminder of the DNA - DNA interactions. Attraction energies: ~ 0.1 kt/ base pair. Correlation attractions. Hydration attractions. Podgornik et al Monovalent counterions Rau et al., Polyvalent counterions
30 DNA condensation Hud & Downing (2001) Chattoraj et al. (1978). T4 DNA R ~ 1000 nm to 50 nm nm nm 2.4 nm
31 Euler buckling Euler buckling instability: Press on an elastic filament hard enough and it buckles. Kirchhoff kinematic analogy. The role of compressional force is played by diminished (on addition of polyvalent counterions) electrostatic interactions. No correlation effect at that time! (Manning, 1985.)
32 racquet-like Manning buckling with correlation attractions Shape equation of the elastic filament (DNA): V(r-r ) toroidal Euler (elastic) intermediates are clearly seen also in simulations of Schnurr et al. (2002). We understand well only one side of the transition. The destabilization of the persistence length leading to a 1st order transition.
33 DNA condensation simulations Elastic, Euler-like, states are important for DNA collapse. Stiff polymers have a different Collapse pathway (originates in the buckling transition) then flexible polymers. There might be a whole slew of Euler-like intermediate states that lead to DNA collapse. Much more ordered collapsed state than for flexible polymers. Stevens BJ (2001). This collapse is very different from a flexible chain.
34 Organization of ds-dna inside the viral capsid shows nematic or hexatic- like order with ~25 Å separation, similar to toroidal aggregates. Cerritelli et al. (1997). T7 DNA. Osmotic pressure inside the capsid ~ 100 atm (Champagne bottle ~ 5 atm).
35 Harnessing the DNA spring. Evilevitch et al DNA equation of state. PEG equation of state. DNA osmotic pressure insside balanced by PEG osmotic pressure outside. Bacteriophage λ with external PEG8000 solution. External osmotic pressure opposes ejection of viral DNA. Ejection regulation.
36 FINIS
Molecular attractions:
Molecular attractions: a.) van der Waals interactions b.) electrostatic correlation interactions c.) polyelectrolyte bridging interactions Rudi Podgornik Laboratory of Physical and Structural Biology National
More informationElectrostatic Effects in Soft Matter and Biophysics
Electrostatic Effects in Soft Matter and Biophysics R.Podgornik Department of Physics University of Ljubljana, Slovenia and Laboratory of physical and structural biology NIH, Bethesda, MD SOFT CONDENSED
More information8.592J HST.452J: Statistical Physics in Biology
Assignment # 4 8.592J HST.452J: Statistical Physics in Biology Coulomb Interactions 1. Flory Theory: The Coulomb energy of a ball of charge Q and dimension R in d spacial dimensions scales as Q 2 E c.
More informationV = 2ze 2 n. . a. i=1
IITS: Statistical Physics in Biology Assignment # 3 KU Leuven 5/29/2013 Coulomb Interactions & Polymers 1. Flory Theory: The Coulomb energy of a ball of charge Q and dimension R in d spacial dimensions
More informationElectrostatic Interactions in Mixtures of Cationic and Anionic Biomolecules: Bulk Structures and Induced Surface Pattern Formation
Electrostatic Interactions in Mixtures of Cationic and Anionic Biomolecules: Bulk Structures and Induced Surface Pattern Formation Monica Olvera de la Cruz F. J. Solis, P. Gonzalez- Mozuleos (theory) E.
More informationEquation of state for polymer liquid crystals: Theory and experiment
PHYSICAL REVIEW E VOLUME 59, NUMBER 1 JANUARY 1999 Equation of state for polymer liquid crystals: Theory and experiment H. H. Strey, * V. A. Parsegian, and R. Podgornik National Institutes of Health, National
More informationMolecular attractions:
Molecular attractions: a.) van der Waals interactions b.) electrostatic correlation interactions c.) polyelectrolyte bridging interactions Rudi Podgornik Laboratory of Physical and Structural Biology National
More informationINTERMOLECULAR AND SURFACE FORCES
INTERMOLECULAR AND SURFACE FORCES SECOND EDITION JACOB N. ISRAELACHVILI Department of Chemical & Nuclear Engineering and Materials Department University of California, Santa Barbara California, USA ACADEMIC
More informationMolecular attractions:
Molecular attractions: a.) van der Waals interactions b.) electrostatic correlation interactions c.) polyelectrolyte bridging interactions Rudi Podgornik Laboratory of Physical and Structural Biology National
More informationBond Orientational Order, Molecular Motion arxiv:chem-ph/ v1 25 Aug and Free Energy of High Density DNA Mesophases
Bond Orientational Order, Molecular Motion arxiv:chem-ph/9508004v1 25 Aug 1995 and Free Energy of High Density DNA Mesophases R. Podgornik, H.H. Strey, K. Gawrisch, D.C. Rau, A. Rupprecht and V.A. Parsegian
More informationGrand-canonical simulation of DNA condensation with two salts, effect of divalent counterion size
Grand-canonical simulation of DNA condensation with two salts, effect of divalent counterion size Toan T. Nguyen 1,2 1 Faculty of Physics, Hanoi University of Science, Vietnam National University, 334
More informationDNA Condensation. Matej Marin Advisor: prof. Rudi Podgornik. 4th April 2002
DNA Condensation Matej Marin Advisor: prof. Rudi Podgornik 4th April 2002 Abstract Recent studies of DNA condensation are reviewed. First, dierent intrachain interactions (based on DNA - DNA interactions
More informationInteractions in Macromolecular Complexes Used as Nonviral Vectors for Gene Delivery
21 Interactions in Macromolecular Complexes Used as Nonviral Vectors for Gene Delivery Rudolf Podgornik, D. Harries, J. DeRouchey, H. H. Strey, and V. A. Parsegian CONTENTS 21.1 Introduction...444 21.2
More informationdration properties of the molecular surface and consequently change the strength of the hydration force. To the extent that
962 Biophysical Journal olume 66 April 1994 962-971 Parametrization of Direct and Soft Steric-Undulatory Forces Between DNA Double Helical Polyelectrolytes in Solutions of Several Different Anions and
More informationSimple Simulations of DNA Condensation
130 Biophysical Journal Volume 80 January 2001 130 139 Simple Simulations of DNA Condensation Mark J. Stevens Sandia National Laboratory, P.O. Box 5800, MS 1111, Albuquerque, New Mexico 87185 USA ABSTRACT
More informationarxiv: v1 [cond-mat.soft] 11 Oct 2012
Europhysics Letters PREPRINT arxiv:1210.3228v1 [cond-mat.soft] 11 Oct 2012 Confined chiral polymer nematics: ordering and spontaneous condensation Daniel Svenšek 1 and Rudolf Podgornik 1,2,3 1 Dept. of
More informationCharge inversion accompanies DNA condensation. by multivalent ions. Construction, mechanics, and electronics. 11 May 2008.
Charge inversion accompanies DNA condensation by multivalent ions DNA-based nanotechnology: Construction, mechanics, and electronics 11 May 2008 Serge Lemay Kavli Institute of Nanoscience Delft University
More informationExchange of Counterions in DNA Condensation. Abstract
Exchange of Counterions in DNA Condensation Yoshihiro Murayama and Masaki Sano Department of Physics, University of Tokyo, Tokyo 113-0033, Japan Abstract We measured the fluorescence intensity of DNA-bound
More informationGeneralizations for the Potential of Mean Force between Two Isolated Colloidal Particles from Monte Carlo Simulations
Journal of Colloid and Interface Science 252, 326 330 (2002) doi:10.1006/jcis.2002.8497 Generalizations for the Potential of Mean Force between Two Isolated Colloidal Particles from Monte Carlo Simulations
More informationPHASE TRANSITIONS IN SOFT MATTER SYSTEMS
OUTLINE: Topic D. PHASE TRANSITIONS IN SOFT MATTER SYSTEMS Definition of a phase Classification of phase transitions Thermodynamics of mixing (gases, polymers, etc.) Mean-field approaches in the spirit
More informationSoft Matter - Theoretical and Industrial Challenges Celebrating the Pioneering Work of Sir Sam Edwards
Soft Matter - Theoretical and Industrial Challenges Celebrating the Pioneering Work of Sir Sam Edwards One Hundred Years of Electrified Interfaces: The Poisson-Boltzmann theory and some recent developments
More information2 Structure. 2.1 Coulomb interactions
2 Structure 2.1 Coulomb interactions While the information needed for reproduction of living systems is chiefly maintained in the sequence of macromolecules, any practical use of this information must
More informationand Matej Praprotnik SI-1001 Ljubljana, Slovenia Jadranska 19, SI-1000 Ljubljana, Slovenia Slovenia
Supplementary Information: Order and interactions in DNA arrays: Multiscale molecular dynamics simulation Julija Zavadlav, 1, 2, a) Rudolf Podgornik, 2, 3, b) 1, 2, c) and Matej Praprotnik 1) Department
More informationMultimedia : Fibronectin and Titin unfolding simulation movies.
I LECTURE 21: SINGLE CHAIN ELASTICITY OF BIOMACROMOLECULES: THE GIANT PROTEIN TITIN AND DNA Outline : REVIEW LECTURE #2 : EXTENSIBLE FJC AND WLC... 2 STRUCTURE OF MUSCLE AND TITIN... 3 SINGLE MOLECULE
More informationEXAM I COURSE TFY4310 MOLECULAR BIOPHYSICS December Suggested resolution
page 1 of 7 EXAM I COURSE TFY4310 MOLECULAR BIOPHYSICS December 2013 Suggested resolution Exercise 1. [total: 25 p] a) [t: 5 p] Describe the bonding [1.5 p] and the molecular orbitals [1.5 p] of the ethylene
More informationElasticity of the human red blood cell skeleton
Biorheology 40 (2003) 247 251 247 IOS Press Elasticity of the human red blood cell skeleton G. Lenormand, S. Hénon, A. Richert, J. Siméon and F. Gallet Laboratoire de Biorhéologie et d Hydrodynamique Physico-Chimique,
More informationLecture 3 Charged interfaces
Lecture 3 Charged interfaces rigin of Surface Charge Immersion of some materials in an electrolyte solution. Two mechanisms can operate. (1) Dissociation of surface sites. H H H H H M M M +H () Adsorption
More informationElectrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte
THE JOURNAL OF CHEMICAL PHYSICS 122, 044903 2005 Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte Zhi-Jie Tan and Shi-Jie Chen a) Department of Physics and
More informationBchem 675 Lecture 9 Electrostatics-Lecture 2 Debye-Hückel: Continued Counter ion condensation
Bchem 675 Lecture 9 Electrostatics-Lecture 2 Debye-Hückel: Continued Counter ion condensation Ion:ion interactions What is the free energy of ion:ion interactions ΔG i-i? Consider an ion in a solution
More informationElectrostatics of membrane adhesion
Electrostatics of membrane adhesion S. Marcelja Department of Applied Mathematics, Research School of Physical Sciences and Engineering, The Australian National University, Canberra ACT 6, Australia ABSTRACT
More informationHelix-Specific Interactions Induce Condensation of Guanosine Four-Stranded Helices in Concentrated Salt Solutions
430 Biophysical Journal Volume 74 January 1998 430 435 Helix-Specific Interactions Induce Condensation of Guanosine Four-Stranded Helices in Concentrated Salt Solutions Paolo Mariani, Federica Ciuchi,
More informationElectrostatic interaction between long, rigid helical macromolecules at all interaxial angles
PHYSICAL REVIEW E VOLUME 6, NUMBER AUGUST Electrostatic interaction between long, rigid helical macromolecules at all interaxial angles A. A. Kornyshev* Institute for Theoretical Physics, University of
More informationSec. 2.1 Filaments in the cell 21 PART I - RODS AND ROPES
Sec. 2.1 Filaments in the cell 21 PART I - RODS AND ROPES Sec. 2.1 Filaments in the cell 22 CHAPTER 2 - POLYMERS The structural elements of the cell can be broadly classified as filaments or sheets, where
More information3 Biopolymers Uncorrelated chains - Freely jointed chain model
3.4 Entropy When we talk about biopolymers, it is important to realize that the free energy of a biopolymer in thermal equilibrium is not constant. Unlike solids, biopolymers are characterized through
More informationBrownian Dynamics Simulation of DNA Condensation
1858 Biophysical Journal Volume 77 October 1999 1858 1870 Brownian Dynamics Simulation of DNA Condensation Pierre-Edouard Sottas, Eric Larquet, Andrzej Stasiak, and Jacques Dubochet Laboratoire d Analyse
More informationChapter 10: Liquids and Solids
Chapter 10: Liquids and Solids Chapter 10: Liquids and Solids *Liquids and solids show many similarities and are strikingly different from their gaseous state. 10.1 Intermolecular Forces Intermolecular
More informationFlexible Polymer-Induced Condensation and Bundle Formation of DNA and F-Actin Filaments
1186 Biophysical Journal Volume 80 March 2001 1186 1194 Flexible Polymer-Induced Condensation and Bundle Formation of DNA and F-Actin Filaments Renko de Vries Laboratory of Physical Chemistry and Colloid
More informationA FIELD THEORETIC APPROACH TO THE ELECTRIC INTERFACIAL LAYER. MIXTURE OF TRIVALENT ROD-LIKE AND MONOVALENT POINT-LIKE IONS BETWEEN CHARGED WALLS.
Modern Physics Letters B c World Scientific Publishing Company A FIELD THEORETIC APPROACH TO THE ELECTRIC INTERFACIAL LAYER. MIXTURE OF TRIVALENT ROD-LIKE AND MONOVALENT POINT-LIKE IONS BETWEEN CHARGED
More informationarxiv: v1 [q-bio.bm] 6 Apr 2016
Multi-shell model of ion-induced nucleic acid condensation Igor S. Tolokh Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA Aleksander Drozdetski Department of Physics, Virginia
More informationNanomechanical Forces Generated by Surface Grafted DNA
J. Phys. Chem. B 2002, 106, 10163-10173 10163 Nanomechanical Forces Generated by Surface Grafted DNA Michael F. Hagan,, Arun Majumdar,, and Arup K. Chakraborty*,,,, Department of Chemical Engineering,
More informationCorrelated and decorrelated positional and orientational order in the nucleosomal core particle mesophases
EUROPHYSICS LETTERS 5 March 2005 Europhys. Lett., 69 (6), pp. 07 023 (2005) DOI: 0.209/epl/i2004-0437-5 Correlated and decorrelated positional and orientational order in the nucleosomal core particle mesophases
More informationProteins polymer molecules, folded in complex structures. Konstantin Popov Department of Biochemistry and Biophysics
Proteins polymer molecules, folded in complex structures Konstantin Popov Department of Biochemistry and Biophysics Outline General aspects of polymer theory Size and persistent length of ideal linear
More informationChiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity
http://www.aimspress.com/ AIMS Biophysics, 2(4): 666-694. DOI: 10.3934/biophy.2015.4.666 Received date 28 August 2015, Accepted date 29 October 2015, Published date 06 November 2015 Research article Chiral
More informationIon Competition in Condensed DNA Arrays in the Attractive Regime
984 Biophysical Journal Volume 105 August 2013 984 992 Ion Competition in Condensed DNA Arrays in the Attractive Regime Xiangyun Qiu, * John Giannini, Steven C. Howell, Qi Xia, Fuyou Ke, and Kurt Andresen
More informationSoft Matter and Biological Physics
Dr. Ulrich F. Keyser - ufk20 (at) cam.ac.uk Soft Matter and Biological Physics Question Sheet Michaelmas 2011 Version: November 2, 2011 Question 0: Sedimentation Initially consider identical small particles
More informationForce-Induced Melting of the DNA Double Helix. 2. Effect of Solution Conditions*
894 Biophysical Journal Volume 80 February 2001 894 900 Force-Induced Melting of the DNA Double Helix. 2. Effect of Solution Conditions* Ioulia Rouzina and Victor A. Bloomfield Department of Biochemistry,
More information*blood and bones contain colloids. *milk is a good example of a colloidal dispersion.
Chap. 3. Colloids 3.1. Introduction - Simple definition of a colloid: a macroscopically heterogeneous system where one component has dimensions in between molecules and macroscopic particles like sand
More informationContents. Preface XI Symbols and Abbreviations XIII. 1 Introduction 1
V Contents Preface XI Symbols and Abbreviations XIII 1 Introduction 1 2 Van der Waals Forces 5 2.1 Van der Waals Forces Between Molecules 5 2.1.1 Coulomb Interaction 5 2.1.2 Monopole Dipole Interaction
More informationCHARGED POLYMERS THE STORY SO FAR
CHARGED POLYMERS THE STORY SO FAR Andrey V Dobrynin Institute of Materials Science &Department of Physics University of Connecticut What are polyelectrolytes? Poly(styrene sulfonate) CH-CH 2 SO Na Poly(methacrylic
More informationSwelling and Collapse of Single Polymer Molecules and Gels.
Swelling and Collapse of Single Polymer Molecules and Gels. Coil-Globule Transition in Single Polymer Molecules. the coil-globule transition If polymer chains are not ideal, interactions of non-neighboring
More informationRoland R. Netz Max-Planck Institute for Colloids and Interfaces, Potsdam, Germany
282 2 Electrochemical Double Layers 2.7 Polyelectrolytes in Solution and at Surfaces Roland R. Netz Max-Planck Institute for Colloids and Interfaces, Potsdam, Germany David Andelman School of Physics and
More informationEffective interaction between helical bio-molecules
Effective interaction between helical bio-molecules E.Allahyarov 1,2, H.Löwen 1 1 Institut für Theoretische Physik II, Heinrich-Heine-Universität Düsseldorf, D-4225 Düsseldorf, Germany 2 Institute for
More informationEffect of Counterion Condensation on Rigidity of Semiflexible Polyelectrolytes
Macromolecules 006, 39, 9519-957 9519 Effect of Counterion Condensation on Rigidity of Semiflexible Polyelectrolytes Andrey V. Dobrynin Polymer Program, Institute of Materials Science and Department of
More informationInteractions and conformational fluctuations in DNA arrays
1 Interactions and conformational fluctuations in DNA arrays Rudolf Podgornik Laboratory of Physical and Structural Biology National Institute of Child Health and Human Development National Institutes
More informationMultimedia : Boundary Lubrication Podcast, Briscoe, et al. Nature , ( )
3.05 Nanomechanics of Materials and Biomaterials Thursday 04/05/07 Prof. C. Ortiz, MITDMSE I LECTURE 14: TE ELECTRICAL DOUBLE LAYER (EDL) Outline : REVIEW LECTURE #11 : INTRODUCTION TO TE ELECTRICAL DOUBLE
More informationXI. NANOMECHANICS OF GRAPHENE
XI. NANOMECHANICS OF GRAPHENE Carbon is an element of extraordinary properties. The carbon-carbon bond possesses large magnitude cohesive strength through its covalent bonds. Elemental carbon appears in
More informationMolecular Driving Forces
Molecular Driving Forces Statistical Thermodynamics in Chemistry and Biology SUBGfittingen 7 At 216 513 073 / / Ken A. Dill Sarina Bromberg With the assistance of Dirk Stigter on the Electrostatics chapters
More informationThe existence of distinct states of DNA compaction is vital to
DNA condensation in two dimensions Ilya Koltover, Kathrin Wagner, and Cyrus R. Safinya Materials Department, Physics Department, and Biochemistry and Molecular Biology Program, University of California,
More informationEffects of Solvent Mediated Interactions on Electrolytes and Related Electrostatic Systems
Effects of Solvent Mediated Interactions on Electrolytes and Related Electrostatic Systems Thesis submitted towards the degree Doctor of Philosophy by Yoram Burak Submitted to the Senate of Tel Aviv University
More informationLiquids and Solids Chapter 10
Liquids and Solids Chapter 10 Nov 15 9:56 AM Types of Solids Crystalline solids: Solids with highly regular arrangement of their components Amorphous solids: Solids with considerable disorder in their
More informationElectrostatics of rigid polyelectrolytes
Current Opinion in Colloid & Interface Science 11 (2006) 310 315 www.elsevier.com/locate/cocis Electrostatics of rigid polyelectrolytes Gerard C.L. Wong Materials Science and Engineering Dept., Physics
More informationMagnetic tweezers and its application to DNA mechanics
Biotechnological Center Research group DNA motors (Seidel group) Handout for Practical Course Magnetic tweezers and its application to DNA mechanics When: 9.00 am Where: Biotec, 3 rd Level, Room 317 Tutors:
More information1924 Biophysical Journal Volume 107 October
194 Biophysical Journal Volume 107 October 014 194 199 Article Ejecting Phage DNA against Cellular Turgor Pressure Sanjin Marion 1, * and Antonio Siber 1 1 Institute of Physics, Zagreb, Croatia ABSTRACT
More informationThe effect of surface dipoles and of the field generated by a polarization gradient on the repulsive force
Journal of Colloid and Interface Science 263 (2003) 156 161 www.elsevier.com/locate/jcis The effect of surface dipoles and of the field generated by a polarization gradient on the repulsive force Haohao
More informationREVIEW : INTRODUCTION TO THE MOLECULAR ORIGINS OF MECHANICAL PROPERTIES QUANTITATIVE TREATMENT OF INTERATOMIC BONDING : THE LENNARD-JONES POTENTIAL
LECTURE #19 : 3.11 MECANICS OF MATERIALS F3 INSTRUCTOR : Professor Christine Ortiz OFFICE : 13-422 PONE : 452-384 WWW : http://web.mit.edu/cortiz/www REVIEW : INTRODUCTION TO TE MOLECULAR ORIGINS OF MECANICAL
More informationElectrostatic contribution to DNA condensation application of energy minimization in a simple model in strong Coulomb coupling regime.
lectrostatic contribution to DNA condensation application of energy minimization in a simple model in strong Coulomb coupling regime. Arup K. Mukherjee Department of Physics, Chancellor College, Box 80,
More informationAn Introduction to namic Light Scattering by Macromole cules
An Introduction to namic Light Scattering by Macromole cules Kenneth S. Schmitz Department of Chemistry University of Missouri-Kansas Kansas City, Missouri City ACADEMIC PRESS, INC. Harcourt Brace Jovanovich,
More informationSelf-Assembly. Self-Assembly of Colloids.
Self-Assembly Lecture 5-6 Self-Assembly of Colloids. Liquid crystallinity Colloidal Stability and Phases The range of forces attractive and repelling forces exists between the colloidal particles van der
More informationPolyelectrolyte and polyampholyte. effects in synthetic and biological
arxiv:1103.1908v1 [cond-mat.soft] 9 Mar 2011 Chapter 4 Polyelectrolyte and polyampholyte effects in synthetic and biological macromolecules Ngo Minh Toan, Bae-Yeun Ha and D. Thirumalai 1 2 CHAPTER 4. PE
More informationCharge fluctuations and counterion condensation
PHYSICAL REVIEW E, VOLUME 65, 0550 Charge fluctuations and counterion condensation A. W. C. Lau, D. B. Lukatsky, P. Pincus, 3 and S. A. Safran Department of Physics and Astronomy, University of Pennsylvania,
More informationCurrent Opinion in Colloid & Interface Science
Current Opinion in Colloid & Interface Science 13 (2008) 376 388 Contents lists available at ScienceDirect Current Opinion in Colloid & Interface Science journal homepage: www.elsevier.com/locate/cocis
More informationConfigurations of confined nematic polymers
SEMINAR 1 1 st YEAR, SECOND CYCLE DEGREE Configurations of confined nematic polymers Author: Danijel Vidaković Mentor: Daniel Svenšek Ljubljana, March 2018 Abstract In this seminar, I present the construction
More informationFree Energy and Thermal Fluctuations of Neutral Lipid Bilayers
Langmuir 001, 17, 455-463 455 Free Energy and Thermal Fluctuations of Neutral Lipid Bilayers Marian Manciu and Eli Ruckenstein* Department of Chemical Engineering, State University of New York at Buffalo,
More informationInvestigation of dsdna Stretching Meso-Mechanics Using LS-DYNA
8 th International LS-DYNA Users Conference Simulation echnology (3) Investigation of dsdna Stretching Meso-Mechanics Using LS-DYNA C. A. Yuan and K. N. Chiang Department of Power Mechanical Engineering,
More informationLong-range many-body polyelectrolyte bridging interactions
THE JOURNAL OF CHEMICAL PHYSICS 122, 204902 2005 Long-range many-body polyelectrolyte bridging interactions Rudi Podgornik a Department of Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana,
More informationCH676 Physical Chemistry: Principles and Applications. CH676 Physical Chemistry: Principles and Applications
CH676 Physical Chemistry: Principles and Applications History of Nanotechnology: Time Line Democritus in ancient Greece: concept of atom 1900 : Rutherford : discovery of atomic nucleus The first TEM was
More informationSurfactant/Polymer Assemblies. 2. Polyelectrolyte Properties
2966 Macromolecules 1998, 31, 2966-2971 Surfactant/Polymer Assemblies. 2. Polyelectrolyte Properties Edson Minatti, David P. Norwood, and Wayne F. Reed* Department of Physics, Tulane University, New Orleans,
More informationLipid Demixing and Protein-Protein Interactions in the Adsorption of Charged Proteins on Mixed Membranes
Biophysical Journal Volume 79 October 2000 1747 1760 1747 Lipid Demixing and Protein-Protein Interactions in the Adsorption of Charged Proteins on Mixed Membranes Sylvio May,* Daniel Harries, and Avinoam
More informationMetal Ion-Induced Lateral Aggregation of Filamentous Viruses fd and M13
University of Pennsylvania ScholarlyCommons Institute for Medicine and Engineering Papers Institute for Medicine and Engineering July 2002 Metal Ion-Induced Lateral Aggregation of Filamentous Viruses fd
More informationChapter 11. Liquids and Intermolecular Forces
Chapter 11. Liquids and Intermolecular Forces 11.1 A Molecular Comparison of Gases, Liquids, and Solids Gases are highly compressible and assume the shape and volume of their container. Gas molecules are
More informationIntroduction to polymer physics Lecture 1
Introduction to polymer physics Lecture 1 Boulder Summer School July August 3, 2012 A.Grosberg New York University Lecture 1: Ideal chains Course outline: Ideal chains (Grosberg) Real chains (Rubinstein)
More informationarxiv:cond-mat/ v2 [cond-mat.soft] 6 Aug 2002
Radial Distribution Function of Rod-like Polyelelctrolytes Roya Zandi Department of Chemistry and Biochemistry, UCLA, Box 95569, Los Angeles, California, 995-569 arxiv:cond-mat/7v [cond-mat.soft] 6 Aug
More informationChapter 11. Intermolecular Forces and Liquids & Solids
Chapter 11 Intermolecular Forces and Liquids & Solids The Kinetic Molecular Theory of Liquids & Solids Gases vs. Liquids & Solids difference is distance between molecules Liquids Molecules close together;
More informationCHEM Principles of Chemistry II Chapter 10 - Liquids and Solids
CHEM 1212 - Principles of Chemistry II Chapter 10 - Liquids and Solids 10.1 Intermolecular Forces recall intramolecular (within the molecule) bonding whereby atoms can form stable units called molecules
More informationIntermolecular and Surface Forces
Intermolecular and Surface Forces ThirH FHitinn '' I I 111 \J& LM* КтЛ I Km I W I 1 Jacob N. Israelachvili UNIVERSITY OF CALIFORNIA SANTA BARBARA, CALIFORNIA, USA AMSTERDAM BOSTON HEIDELBERG LONDON NEW
More informationCytoskeleton dynamics simulation of the red blood cell
1 Cytoskeleton dynamics simulation of the red blood cell Ju Li Collaborators: Subra Suresh, Ming Dao, George Lykotrafitis, Chwee-Teck Lim Optical tweezers stretching of healthy human red blood cell 2 Malaria
More informationSolving the Poisson Boltzmann equation to obtain interaction energies between confined, like-charged cylinders
JOURNAL OF CHEMICAL PHYSICS VOLUME 109, NUMBER 20 22 NOVEMBER 1998 Solving the Poisson Boltzmann equation to obtain interaction energies between confined, like-charged cylinders Mark Ospeck a) and Seth
More informationLocal molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions
Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions Yng-Gwei Chen and John D. Weeks Departments of Physics and Chemistry and
More informationTunable Nanoparticle Arrays at Charged Interfaces
Tunable Nanoparticle Arrays at Charged Interfaces Supporting Material Sunita Srivastava 1, Dmytro Nykypanchuk 1, Masafumi Fukuto 2 and Oleg Gang 1* 1 Center for Functional Nanomaterials, Brookhaven National
More information- intermolecular forces forces that exist between molecules
Chapter 11: Intermolecular Forces, Liquids, and Solids - intermolecular forces forces that exist between molecules 11.1 A Molecular Comparison of Liquids and Solids - gases - average kinetic energy of
More informationChapter 12. Insert picture from First page of chapter. Intermolecular Forces and the Physical Properties of Liquids and Solids
Chapter 12 Insert picture from First page of chapter Intermolecular Forces and the Physical Properties of Liquids and Solids Copyright McGraw-Hill 2009 1 12.1 Intermolecular Forces Intermolecular forces
More informationREVIEW : INTERATOMIC BONDING : THE LENNARD-JONES POTENTIAL & RUBBER ELASTICITY I DERIVATION OF STRESS VERSUS STRAIN LAWS FOR RUBBER ELASTICITY
LECTURE #3 : 3.11 MECHANICS O MATERIALS 03 INSTRUCTOR : Professor Christine Ortiz OICE : 13-40 PHONE : 45-3084 WWW : http://web.mit.edu/cortiz/www REVIEW : INTERATOMIC BONDING : THE LENNARD-JONES POTENTIAL
More informationTorsional Deformation of Double Helix in Interaction and Aggregation of DNA
6508 J. Phys. Chem. B 2004, 108, 6508-6518 Torsional Deformation of Double Helix in Interaction and Aggregation of DNA A. G. Cherstvy,, A. A. Kornyshev, and S. eikin*, Institut für Festkörperforschung
More informationBiological Polyelectrolytes and Biological Complexes
Biological Polyelectrolytes and Biological Complexes Monica Olvera de la Cruz Francisco Solis Pedro Gonzalez-Mozuelos Eric Raspaud Jean Louis Sikorav Michel Delsanti Luc Belloni Alexander Ermoshkin Alexander
More informationNonlinear elasticity of single collapsed polyelectrolytes
Nonlinear elasticity of single collapsed polyelectrolytes Hirofumi Wada,* Yoshihiro Murayama, and Masaki Sano Department of Physics, University of Tokyo, Hongo, Tokyo, 113-0033, Japan Received 6 January
More informationOrigin of the Electrophoretic Force on DNA in Nanopores. Biological and Soft Systems - Cavendish Laboratory
Origin of the Electrophoretic Force on DNA in Nanopores Ulrich F. Keyser Biological and Soft Systems - Cavendish Laboratory Acknowledgements Delft Cees Dekker, Nynke H. Dekker, Serge G. Lemay R. Smeets,
More informationRandomly Triangulated Surfaces as Models for Fluid and Crystalline Membranes. G. Gompper Institut für Festkörperforschung, Forschungszentrum Jülich
Randomly Triangulated Surfaces as Models for Fluid and Crystalline Membranes G. Gompper Institut für Festkörperforschung, Forschungszentrum Jülich Motivation: Endo- and Exocytosis Membrane transport of
More informationOne- and two-particle microrheology in solutions of actin, fd-virus and inorganic rods
Microrheology of Biopolymers (ITP Complex Fluids Program 3/05/02) One- and two-particle microrheology in solutions of actin, fd-virus and inorganic rods Christoph Schmidt Vrije Universiteit Amsterdam Collaborators:
More information5. STRUCTURES AND DEFECTS IN AMORPHOUS SOLIDS
62 5. STRUCTURES AND DEFECTS IN AMORPHOUS SOLIDS 5.1 Review/Background: In Chapter 4, we discussed the origin of crystal structures and Bravais lattices based on Euler relationship. In this chapter, we
More informationMolecular Dynamics Simulation of High Density DNA Arrays
Review Molecular Dynamics Simulation of High Density DNA Arrays Rudolf Podgornik 1,2 ID, Julija Zavadlav 3 and Matej Praprotnik 4, * ID 1 Department of Physics, Faculty of Mathematics and Physics, University
More information