PHYchip Corporation. SCU Nanotechnology Course presentation. Dhaval Brahmbhatt President & CEO. Friday, June 3 rd, 2005

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1 SCU Nanotechnology Course presentation Dhaval Brahmbhatt President & CEO Friday, June 3 rd, 2005, San Jose, CA

2 Course Books (1) Primary Book: Introduction to Nanoscale Science and Technology Edited by Massimiliano Di Ventra, Stephane Evoy and James R. Heflin, Jr. Kulver Academic Publishers (2) Other Books: Nanosystems. Molecular Machinery, Manufacturing and Computation Author: K. Eric Drexler Wiley Interscience Publication (3) NANOTECHNOLOGY & HOMELAND SECURITY. New weapons for new wars. Authors: Daniel Ratner & Mark A. Ratner. Forwarded by James Murday, Office of Naval Research ADDISON-WESLEY PROFESSIONAL PRENTICE HALL PTR 2

3 23. Nanofluidics INTRODUCTION Lab-on-a-chip or the Micro Total Analysis System concept has generated a renewed interest in micro/nanofluidic technologies Micro Total Analysis Systems have many advantages such as; lower power consumption, smaller reagent consumption, smaller overall size, lower cost, portability, and disposability Miniaturization allows higher speed and better separation resolution per scaling laws of separation resolution Most microfluidic systems demonstrated have dimensions of um still larger than most biological particles or organelles, in contrast Nanofluidic systems provide unique capability in biomolecule analysis and control, it is now possible to fabricate REGULAR nanostructures of dimensions ranging from 10 nm to 1,000 nm (figure 23.1c) At nano size scale, fluids have distinct properties that cannot be found at the macro or micro fluidic size scale, these properties can be exploited to for new concepts such as electrokinetic pumping Size of many organelles or many components in cells fall in this range such as; lysosome (200~500 nm), mitochondria (~500 nm), secretary vesicles (50~200 nm), ribosome (~30 nm), virus particles (~50nm), and DNA (11nm) 3

4 Nanofluidics Introduction contd. In nanofluidic system the interaction between the inner surface of the fluidic device and molecules play a dominant role over the interaction between the molecules and surrounding solvent, this provides opportunities to control these bio-molecules by carefully designed nanofluidic devices or structures Two key drivers for nanofluidics are; possibility of advanced molecular control and novel nanofluidic properties Regular, micromachined nanofluidic structures have a clear advantage over traditional random nanoporous materials in the fact that one can carefully design and control the fluidic motion and molecular motion within the structure 4

5 Fluidics at micro and nano scale Within micro or nano fluidic channels, fluids behave quite differently than in larger channels or pipes because relevant forces scale differently with size At small scale, inertia of fluid becomes negligible while the (viscous) friction force & surface tension become dominant forces, there is no turbulence In fluid mechanics the Reynolds number determines the relative importance of inertia compared to frictional force due to viscosity, expressed as: N R = inertial force/friction (viscous) force N R for a typical microfluidic system is between 10exp-3 to 10exp-5, anything less than 10exp-2 is regarded in low Reynolds number regime Following the Navier-Stokes equation for the low N R, the equation is timeindependent, the fluid therefore only reacts to the external forces (such as electric forces or hydraulic forces), when this external force is reversed the fluid motion is also reversed without any mixing or irreversible change, this turbulence free fluidic environment is ideal for studying and manipulating fragile polymeric biomolecules such as chromosomal DNA On the other hand, it is not trivial to design a fluid mixer in a microfluidic system, lack of turbulence means that diffusion is the only means to mix Approx diffusion time of a fluid molecule ~ (distance) 2 /(diffusion constant), this means that diffusion is very efficient at short length scale 5

6 Figure 23.1: Comparison between microfluidic and nanofluidic biomolecule separation. (a) In microfluidic device, friction between liquid and the molecule determines the molecular mobility. (b) In nanoporous material such as gel, molecules are filtered or sieved by random nanostructures. (c) In nanofluidic devices, the molecular sieve structure is well defined and regular. 6

7 Figure 23.2: High and Low Reynolds number fluidics. When the Reynolds number is low, viscous interaction between the wall and the fluid is strong, and there is no turbulences PHYchip or Corporation vortices. 7

8 Effect of Surface Charge & Debye Layer The high surface to volume ratio means dominance of surface effects on fluidic motion, most surfaces have some surface charges when in contact with an electrolyte solution because the surface chemical group can be protonated or unprotonated depending on the ph of the electrolyte e.g. The surface of silicon dioxide or glass is mostly terminated by silanol groups (-Si-OH), they can be unprotonated at ph higher than 2, therefore at most ph conditions the surface of glass contains negative surface charges and the +ve ions in solution develop a charge screening layer called Debye layer (fig. 23.4) Within the Debye layer, electroneutrality is not satisfied and the electric potential is not zero, this screening charge density decays exponentially from the surface, the characteristic length is called Debye length, as the ionic strength of the electrolyte increases the Debye length decreases At low buffer concentrations and with nanofluidic channels, Debye layer thickness can be comparable to the channel dimension, this could change fluid or biomolecule motion qualitatively in the nanofluidic channel 8

9 Figure 23.4: Charge screening and Debye length. The surface charges are screened by the counterions in the aqueous solution, and the screened charge layer contains mobile, net charges. These mobile charges can drift under the influence of external electric field. 9

10 Electroosmosis & Streaming Potential Electroosmosis consists in the motion of liquids in a porous structure under applied electric field, driven by motion of Debye layer charges, electroosmosis flow can easily be generated by applying electric potential across nanofluidic channel and is the main flow generating mechanism in these devices Electroneutrality of the bulk does not hold at the walls of the porous structure or microchannel, given that the charges within the Debye layer are mobile, they can be driven by applying electric field In the case of ve surface charges (glass), the fluid within the Debye layer will be driven to the cathode under an electric field, the entire fluid column can then be dragged by this layer due to viscous interaction, resulting in a net fluid flow through the channel Streaming Potential is the potential generated when a fluid is forced to flow through a channel or porous material, a reversal of electroosmosis, fluid flow drages and accumulates mobile layer charges resulting in potential difference, the use of streaming potential is limited by the high pressure necessary to force liquids through nanoporous devices or structures Electroosmotic flow velocity v depends on; applied electric field, viscocity of the fluid, and the surface potential due to surface charge density, it does not depend on the size or shape of the channel 10

11 Electroosmotic flow contd. Electroosmotic flow has a flat shaped profile while pressure driven flow has a parabolic profile Measuring electroosmotic flow is also a simple way to measure the surface potential or charge in micro and nanofluidic channels Increased buffer concentration or ionic strength will decrease the electroosmotic flow velocity, since it will decrease the thickness of the Debye layer and the number of mobile screening charges that is responsible for electroosmosis Through an appropriate coating method, it is possible to change the polarity of the surface charge, therefore reversing the electroosmotic flow direction In addition to coating techniques, it is possible to alter the surface potential by applying external electric potential to the channel surface The above two bullets show a way to suppress or change the direction of electroosmotic flow, very useful in some applications 11

12 Figure 23.3: Hydrodynamic focusing of a liquid stream in a microfluidic channel. Fluid containing fluorescent molecules is driven from the inlet to meet with two other non-fluorescent liquid streams from the side channels. The width of the liquid stream can be controlled by changing the pressures applied to side and inlet channels. In the microchannel, only diffusional mixing can occur, and by narrowing down inlet stream width (wf) one can achieve fast diffusional mixing. (Adapted from Ref. 11 by permission of the American Physical Society.) 12

13 Figure 23.5: Pressure-driven flow vs. Electroosmotic flow. These images were taken by caged dye techniques. At t=0, an initial flat fluorescent line is generated in microchannel by pulse-exposing and breaking the caged dye, rendering them fluorescent. These dyes were transported by the fluid flow generated by pressure-driven flow (left column) or electroosmotic flow (right column), showing the flow profile. (Adapted from P. H. Paul, M. G. Garguilo, and D. J. Rakestraw, Anal. Chem. 70, 2459 (1998) by permission of the American Chemical Society.) 13

14 Biomolecule Sieving There is great need in modern biology for a technology that can analyze and separate biomolecules quickly, inexpensively, and accurately Biomolecules in aqueous solutions carry charges, or can be coated with charged molecules such as sodium dodecyl sulfate (SDS), while applied electric field will induce their drift in solution, their interaction with either surrounding fluid or nanoporous structures will result in different drift velocities for different molecules Such motion of charged molecules in an electric field known as electrophoresis is of great interest due to it s widespread use in molecular analysis When the molecular dimension is much larger than the pore dimension, the behavior of the molecules changes drastically, for the example of a long polymer where the width of the polymer is less than the pore size while the extended length is much bigger than the pore a reptation model was developed that assumes the DNA structure is that of a random coil and works well for relatively short DNA molecules and at a moderate electric field For high fields, the DNA aligns in the direction of the field, this makes DNA mobility length independent, so separation of long DNA done with pulsed field 14

15 Figure 23.6: Ogston Sieving model. Gel is modeled as a random distribution of fibers in space. 15

16 Figure 23.7: Reptation of long polymer (DNA) in gel. (a) Two dimensional schematics of reptation dynamics. Due to the constriction imposed by the gel fibers, the polymer (DNA in this case) can only move along the line of its backbone. (b) Experimental demonstration of reptation-like motion PHYchip of DNA Corporation by Perkins et al. (From Ref. 25 by permission of the 16 American Association for the Advancement of Science.)

17 FABRICATION Controlled polymerization process offers great potential for the fabrication of random nanoporous materials with engineered chemical and physical properties, by carefully controlling the sol-gel transition process during polymerization one can produce a random nanoporous material with desired chemical and physical properties (Fig. 23.9) For regular engineered nanofluidic devices, electron beam lithography has been used to pattern ~50 nm pillar array as a DNA sieve structure (Turner et al.), another approach was taken by Park et al., where colloidal block copolymer was used to define regular hexagonal nanostructures 17

18 Figure 23.9: Scanning electron micrograph of a polymer nanoporous material. The scale bar below is 10 mm. (From Ref. 53 by permission of Wiley Periodicals, Inc.) 18

19 Applications of Nanofluidics - I NANOFLUIDIC BIOMOLECULAR SIEVING & SORTING Molecular sieves or filters with nanometer sized pores are repeatedly used in biomolecular separation process When we try to use nanofluidic devices with regular nanostructure or sieve, several issues impede such development; first it is not easy to fabricate nano structures with comparable pore size (1-10 nm) for molecular sieving, second interaction between nanostructures and biomolecules is not well understood Regular nanofluidic channels can still be quite useful in many applications, specially for large molecules or particles, separation of large DNA molecules is a good potential application for nanofluidic applications Since pore shapes in nanofluidic devices can be designed and characterized precisely, they provide a good model system for studying complex dynamic problems, Turner et al. studied entropic recoil froce of long DNA molecule within nanofluidic channel, Nykypanchuk et al. studied hindered Browninan dynamics of a long DNA molecule, Olgica et al. studied dynamics of DNA molecule in a thin nanofluidic channel 19

20 Figure 23.11: Pulsed field electrophoresis of long DNA in artificial system. (a) Principles of operation, presented over the optical micrograph of the actual device used. Electric field is switched in direction by 120 degree as shown in the figure. While shorter DNA strand can progress forward, longer DNA strand gets stuck for longer amount of time. After many repetition of this cycle, DNA molecules with different lengths are separated. (b) Separation of two DNA (166kbp and 48kbp) within the system. (From Ref. 69 by permission of the American Chemical Society.) 20

21 Figure 23.12: Entropic trap DNA separation. (a) Schematic diagram of entropic trap DNA separation system. (b) Separation result of long DNA molecules. (From Ref. 40 by permission of the American Association for the Advancement of Science.) 21

22 Applications of Nanofluidics - II NANOPORE MOLECULAR SCANNER/DETECTORS At moderate concentrations, transport of molecules through nanofluidic channels can be discrete allowing detection of individual particles, this provides a unique opportunity for a new kind of biosensor in which molecules are detected individually as they sieve through nanopores Fig shows a nanofluidic particle counter, since the particle size is comparable to the pore dimension, it s passage would disrupt the electrical property of the channel as it passes through the pore, by measuring the current between the two reservoirs the authors detected single crossing events and also the size of the particles Fig shows a similar approach to scan and sequence single stranded DNA molecule using a membrane pore protein that has 2.6 nm pore, the molecular crossing event occurs in less than a millisecond therefore requiring fast detection capabilities 22

23 Figure 23.13: Nanofluidic Coulter counter for submicrometer particles. (a) Scanning Electron Micrograph of the nanofluidic channel. (b) Detected signal during the passage of several submicrometer particles (bead). (From Ref. 72 by permission of the American Institute of Physics.) 23

24 Figure 23.14: Nanopore DNA sequencing. DNA molecules are forced to pass through the nanopore membrane protein, and the current between the two reservoir is monitored. (From Ref. 79 by permission of the Biophysical Society.) 24

25 Applications of Nanofluidics - III SINGLE MOLECULE DETECTION SINGLE MOLECULE DETECTION Optical florescence is very sensitive technique to visualize molecules in a liquid, and now it is possible to detect signal from a single fluorophore Experiments involving detection of individual molecules allow the investigation of molecular properties without the need of averaging over a large number of molecules Single molecule detection achieved by localizing the excitation light in to a small confocal volume, so only a few fluorophores can be found at a given time, the florescence signal from this small volume would represent the characteristic of molecules in that volume Most widely used technique is confocal (or two photon) fluorescence correlation spectroscopy (FCS), where a laser light is focused in to a diffraction limited volume and the fluorescence signal coming out of that volume is detected If only a small number of molecules are in that volume, the relative fluctuation of the signal is significant, higher concentration degrades signal to noise ratio Can use this technique for molecular sensing and analysis, such as a novel DNA sequencing technique 25

26 Applications of Nanofluidics - IV ELECTRO KINETIC FLUID CONTROL Electroosmosis - the flow speed does not depend on the size of the channel, it only depends on the surface properties and applied potential It takes huge pressure to drive liquid through nanofluidic channels, this means that in a reverse manner Electroosmosis can be used to generate very high pressures, Paul et al. used a glass capillary with micron size silica bead to generate electroosmotic flow, which in turn generated very high pressures up to 8000 psi Electroosmotic flow depends on the surface potential of the micro/nano fluidic channels, this surface potential can be controlled by applying external field Schasfoort et al. used external potential to control the surface potential of the microfluidic channel (fig ) this is similar to FET hence called flow FET By applying external voltage, Schasfoort et al. were able to change the sign and magnitude of the electroosmotic flow, extension of this concept could lead to the development of more complex flow controlling circuit which can then control a complex chemical or biochemical reaction in a micro channel 26

27 Figure 23.15: Control of electroosmotic flow by external electric field (gate voltage). By applying external potential to the outside surface of a fluidic channel, one can control the electroosmotic flow just as one can control the charge inversion region conductances by controlling gate voltage in MOSFET. (a) normal state. (b) applying negative potential to increase the electroosmotic flow. (c) applying positive potential to decrease or reverse the electroosmotic flow. (From Ref. 18 by permission of the American Association for the Advancement of Science.) 27

28 Figure 23.16: FlowFET device fabricated by Schasfoort et al. (a) Schematic diagram of the FlowFET device. The channel wall was 390nm silicon nitride membrane (equivalent to the gate oxide in MOSFET), and external potentials were applied to the gate. (b) Change of electroosmotic flow versus the gate voltage. (From Ref. 18 by permission of the American Association for the Advancement of Science.) 28

29 22. Biomolecular Motors Biomolecular motors are proteins that produce or consume mechanical energy, working in concert they can exert forces exceeding kilonewtons, enabling massive animals such as whales and elephants to move They can exert piconewton forces individually to ferry cargo between different points in a cell, transport ions across membranes, or generate biochemical fuel necessary for other cellular activities Molecular motors are necessary for vital cell functions and life processes, transporting essential solutes and organelles when diffusion is insufficient Various motor proteins can act as rotary motors, linear steppers, and screws Motors range in size from 5nm to hundreds of nm and can operate over a large range of speeds, e.g. subtypes of Myosin move from.06 to 60 um/sec Efficiencies of some of these natural molecular motors are close to 100% Assembly of protein based devices can take place in a test tube or Petri dish, rendering most aspects of device production feasible and economical, MEMS and NEMS are no match to their speed, functions, and manufacture However, MEMS are superior in certain aspects of operation and manufacturing, best of both worlds may result from hybrid combinations of both biological (at fundamental size limits) and inorganic components (macroscopic level for control) 29

30 MEMS & Biomolecular Motors Motor proteins are more attractive compared to MEMS because of their smaller size (hundreds of times smaller), high speeds, high efficiencies and ease of mass production The possibility of incorporating biological components in to hybrid devices offers functions/functionalities superior to purely inorganic devices 3-D geometry and diverse energy requirements facilitate assembly of compact structures While the motor proteins are not self replicating, the biological machinery that makes them is self replicating, leading to low economic and time costs However the precise placement and attachment of biological molecules in complex devices is problematic, additionally the external interfacing and control of such devices is difficult and not currently achievable with complex biological processes 30

31 Operation & Function of Motor Proteins Many proteins act as enzymes and therefore have affinities for the biochemicals involved in the reactions they catalyze, this affinity manifests itself as a strong and exclusive binding of the protein to a biochemical substrate, which is accompanied by a change in the shape of the protein In some instances, this change of shape is incidental to the operation of the protein, in others like the motor proteins - it is essential to it s function, as it causes motion to occur and force to be exerted The coupling of motor proteins shape change to substrate binding and release their enzymatic function catalyzing biomolecular synthesis and hydrolysis highlight the importance of energy and entropy, a thermodynamic analysis of motor proteins illustrates much of their operation Most widely used motor proteins are; Kinesin, Myosin, and F 1 -ATPase 31

32 Biotechnology of Motor Proteins The natural protein manufacturing process occurs through the transcription of DNA to RNA and the translation of RNA to protein Once the protein is made, it folds in to a functional form, ready to work To engineer a selected motor protein, it can either be purified from it s natural form (long process with often low yield), or the gene encoding it can be copied in to a protein expression system these are capable of producing the protein at high efficiency, in large quantities, and with less stringent conditions Once the gene isolating the protein has been identified and sequenced, the protein can be genetically engineered and the amino acid sequence of the protein altered, these changes can alter functional groups, change the folded shape of the protein, or aid in purifying the protein After production, these proteins must be extracted and purified, separating them from thousands of other proteins present in host cells 32

33 Science & Engg of Molecular Motors As the engineering work is quite recent, what we have is mostly science and beginning engineering Bulk and single molecule studies indicate the mechanisms by which some of these motors achieve motion From these experiments we can determine stalling force, speed versus load, and other necessary parameters to design such a device Initial engineering efforts have consisted of proof of concept demonstrations, no useful devices using molecular motors have been made to this date Linear and rotary biomotor systems are being engineered and controlled Progress has also been made toward the manufacture of self sustaining power sources for these systems 33