Simultaneous action of electric fields and nonelectric forces on a polyelectrolyte: Motion and deformation

Deformation Response of Catenated DNA Networks in a Planar Elongational Field

A kinetoplast is a complex catenated DNA network that bears resemblance to a two-dimensional polymeric system. In this work, we use single-molecule experiments to study the transient and steady-state deformation of kinetoplasts in a planar elongational field. We demonstrate that kinetoplasts deform in a stagewise manner and undergo transient deformation at large strains, due to conformational rearrangements from an intermediate metastable state. Kinetoplasts in an elongational field achieve a steady-state deformation that depends on strain rate, akin to the deformation of linear polymers. We do not observe an abrupt transition between the nondeformed and deformed states of a kinetoplast, in contrast to the coil-stretch transition for a linear polymer.

Local and global force balance for diffusiophoretic transport

Electro- and diffusio- phoresis of particles correspond respectively to the transport of particles under electric field and solute concentration gradients. Such interfacial transport phenomena take their origin in a diffuse layer close to the particle surface, and the motion of the particle is force-free. In the case of electrophoresis, it is further expected that the stress acting on the moving particle vanishes locally as a consequence of local electroneutrality. But the argument does not apply to diffusiophoresis, which takes its origin in solute concentration gradients. In this paper we investigate further the local and global force balance on a particle undergoing diffusiophoresis. We calculate the local tension applied on the particle surface and show that, counter-intuitively, the local force on the particle does not vanish for diffusiophoresis, in spite of the global force being zero as expected. Incidentally, our description allows to clarify the osmotic balance in diffusiophoresis, which has been a source of debates in the recent years. We explore various cases, including hard and soft interactions, as well as porous particles, and provide analytic predictions for the local force balance in these various systems. The existence of local stresses may induce deformation of soft particles undergoing diffusiophoresis, hence suggesting applications in terms of particle separation based on capillary diffusiophoresis.

Coarse-grained molecular dynamics study of wettability influence on protein translocation through solid nanopores

Protein translocation through nanopores is widely involved in molecular sensing and analyzing devices, whereby nanopore surface properties are crucial. However, fundamental understanding of how these properties affect protein motion inside nanopores remains lacking. In this work, we study the influence of nanopore surface wettability on voltage-driven protein translocation through nanopores with coarse-grained molecular dynamics simulations. The results show that the electrophoretic mobility of protein translocation increases as the contact angle of nanopore surface increases from 0° to 90°, but becomes almost constant as the contact angle is above 90°. This observation can be attributed to the variation of the friction coefficient of protein translocation through the nanopores with different nanopore contact angles. We further show that the interaction between nanopore and water, rather than that between the nanopore and protein, dominates the protein transport in nanopores. These findings provide new insights into protein translocation dynamics across nanopores and will be beneficial to the design of high-efficiency nanopore devices for single molecule protein sensing.

Conformation and Dynamics of Long-Chain End-Tethered Polymers in Microchannels

Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, considering that deoxyribonucleic acid (DNA) molecules are polyelectrolytes. This review summarizes the single-molecule experimental and molecular dynamics simulation-based studies of end-tethered polyelectrolytes, especially addressing their relaxation dynamics and deformation characteristics under various external forces in micro-confined environments. In most of these studies, DNA is considered as a model polyelectrolyte. Apart from summarizing the results obtained in that area, the most important experimental and simulation techniques are explained.

Osmosis, from molecular insights to large-scale applications

Osmosis is a universal phenomenon occurring in a broad variety of processes and fields. It is the archetype of entropic forces, both trivial in its fundamental expression - the van 't Hoff perfect gas law - and highly subtle in its physical roots. While osmosis is intimately linked with transport across membranes, it also manifests itself as an interfacial transport phenomenon: the so-called diffusio-osmosis and -phoresis, whose consequences are presently actively explored for example for the manipulation of colloidal suspensions or the development of active colloidal swimmers. Here we give a global and unifying view of the phenomenon of osmosis and its consequences with a multi-disciplinary perspective. Pushing the fundamental understanding of osmosis allows one to propose new perspectives for different fields and we highlight a number of examples along these lines, for example introducing the concepts of osmotic diodes, active separation and far from equilibrium osmosis, raising in turn fundamental questions in the thermodynamics of separation. The applications of osmosis are also obviously considerable and span very diverse fields. Here we discuss a selection of phenomena and applications where osmosis shows great promises: osmotic phenomena in membrane science (with recent developments in separation, desalination, reverse osmosis for water purification thanks in particular to the emergence of new nanomaterials); applications in biology and health (in particular discussing the kidney filtration process); osmosis and energy harvesting (in particular, osmotic power and blue energy as well as capacitive mixing); applications in detergency and cleaning, as well as for oil recovery in porous media.

DNA capture into the ClyA nanopore: diffusion-limited versus reaction-limited processes

The capture and translocation of biomolecules through nanometer-scale pores are processes with a potentially large number of applications, and hence they have been intensively studied in recent years. The aim of this paper is to review existing models of the capture process by a nanopore, together with some recent experimental data of short single- and double-stranded DNA captured by the Cytolysin A (ClyA) nanopore. ClyA is a transmembrane protein of bacterial origin which has been recently engineered through site-specific mutations, to allow the translocation of double- and single-stranded DNA. A comparison between theoretical estimations and experiments suggests that for both cases the capture is a reaction-limited process. This is corroborated by the observed salt dependence of the capture rate, which we find to be in quantitative agreement with the theoretical predictions.

Entropic trap purification of long DNA

Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.

Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels

The ability to precisely control the transport of single DNA molecules through a nanoscale channel is critical to DNA sequencing and mapping technologies that are currently under development. Here we show how the electrokinetically driven introduction of DNA molecules into a nanochannel is facilitated by incorporating a three-dimensional nanofunnel at the nanochannel entrance. Individual DNA molecules are imaged as they attempt to overcome the entropic barrier to nanochannel entry through nanofunnels with various shapes. Theoretical modeling of this behavior reveals the pushing and pulling forces that result in up to a 30-fold reduction in the threshold electric field needed to initiate nanochannel entry. In some cases, DNA molecules are stably trapped and axially positioned within a nanofunnel at sub-threshold electric field strengths, suggesting the utility of nanofunnels as force spectroscopy tools. These applications illustrate the benefit of finely tuning nanoscale conduit geometries, which can be designed using the theoretical model developed here.Forcing a DNA molecule into a nanoscale channel requires overcoming the free energy barrier associated with confinement. Here, the authors show that DNA injected through a funnel-shaped entrance more efficiently enters the nanochannel, thanks to facilitating forces generated by the nanofunnel geometry.

Electric-field-induced stretching of surface-tethered polyelectrolytes in a microchannel

We study the stretching of a surface-tethered polyelectrolyte confined between parallel surfaces under the application of a dc electric field. We explore the influence of the electric-field strength, the length of the polyelectrolyte, and the degree of confinement on the conformation of the polyelectrolyte by single-molecule experiments and coarse-grained coupled lattice-Boltzmann molecular-dynamics simulations. The fractional extension of the polyelectrolyte is found to be a universal function of the product of the applied electric field and the molecular contour length, which is explained by simple scaling arguments. The degree of confinement does not have any significant influence on the stretching. We also confirm that an electrohydrodynamic equivalence principle relating the stretching in an electric field to that in a flow field is applicable.

DNA dielectrophoresis: Theory and applications a review

Dielectrophoresis is the migration of an electrically polarizable particle in an inhomogeneous electric field. This migration can be exploited for several applications with (bio)molecules or cells. Dielectrophoresis is a noninvasive technique; therefore, it is very convenient for (selective) manipulation of (bio)molecules or cells. In this review, we will focus on DNA dielectrophoresis as this technique offers several advantages in trapping and immobilization, separation and purification, and analysis of DNA molecules. We present and discuss the underlying theory of the most important forces that have to be considered for applications with dielectrophoresis. Moreover, a review of DNA dielectrophoresis applications is provided to present the state-of-the-art and to offer the reader a perspective of the advances and current limitations of DNA dielectrophoresis.

A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential

A new feature of the popular software DelPhi is developed and reported, allowing for computing the surface averaged electrostatic potential (SAEP) of macromolecules. The user is given the option to specify the distance from the van der Waals surface where the electrostatic potential will be outputted. In conjunction with DelPhiPKa and the BION server, the user can adjust the charges of titratable groups according to specific pH values, and add explicit ions bound to the macromolecular surface. This approach is applied to a set of four proteins with "experimentally" delivered zeta (ζ)-potentials at different pH values and salt concentrations. It has been demonstrated that the protocol is capable of predicting ζ-potentials in the case of proteins with relatively large net charges. This protocol has been less successful for proteins with low net charges. The work demonstrates that in the case of proteins with large net charges, the electrostatic potential should be collected at distances about 4 Å away from the vdW surface and explicit ions should be added at a binding energy cutoff larger than 1-2kT, in order to accurately predict ζ-potentials. The low salt conditions substantiate this effect of ions on SAEP.

Communication: Charge, diffusion, and mobility of proteins through nanopores

Implementation of Einstein's law connecting charge, diffusion coefficient, and mobility to interpret experimental data on proteins from single molecule electrophoresis through nanopores faces serious difficulties. The protein charge and diffusion coefficient, inferred with the Einstein law, can be orders of magnitude smaller than their bare values depending on the electrolyte concentration, pore diameter, chemical nature of the pore wall, and the externally applied voltage. The main contributors to the discrepancies are the coupled dynamics of the protein and its counterion cloud, confinement effects inside the pore, and the protein-pore-surface interaction. We have addressed these ingredients by harking on classical theories of electrophoresis of macroions and hydrodynamics inside pores, and deriving new results for pore-protein interactions. Putting together various components, we present approximate analytical formulas for the effective charge, diffusion coefficient, and mobility of a protein in the context of single molecule electrophoresis experiments. For the omnipresent pore-protein interactions, nonlinear dependence of the velocity of protein on voltage sets in readily and analytical formulas for this effect are presented. The derived formulas enable the determination of the bare charge and size of a protein from the experimentally measured apparent values.

Electrophoretic Mobility of Polyelectrolytes within a Confining Well

We present a numerical study of polyelectrolytes electrophoresing in free solution while squeezed by an axisymmetric confinement force transverse to their net displacement. Hybrid multiparticle collision dynamics and molecular dynamics simulations with mean-field finite Debye layers show that even though the polyelectrolyte chains remain "free-draining" their electrophoretic mobility increases with confinement in nanoconfining potential wells. The primary mechanism leading to the increase in mobility above the free-solution value, despite long-range hydrodynamic screening by counterion layers, is the orientation of polymer segments within Debye layers. The observed length dependence of the electrophoretic mobility arises due to secondary effects of counterion condensation related to confinement compactification.

Influence of nanopore surface charge and magnesium ion on polyadenosine translocation

We investigate the influence of a nanopore surface state and the addition of Mg(2+) on poly-adenosine translocation. To do so, two kinds of nanopores with a low aspect ratio (diameter ∼3-5 nm, length 30 nm) were tailored: the first one with a negative charge surface and the second one uncharged. It was shown that the velocity and the energy barrier strongly depend on the nanopore surface. Typically if the nanopore and polyA exhibit a similar charge, the macromolecule velocity increases and its global energy barrier of entrance in the nanopore decreases, as opposed to the non-charged nanopore. Moreover, the addition of a divalent chelating cation induces an increase of energy barrier of entrance, as expected. However, for a negative nanopore, this effect is counterbalanced by the inversion of the surface charge induced by the adsorption of divalent cations.

Close encounters with DNA

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Computing the electrophoretic mobility of large spherical colloids by combining explicit ion simulations with the standard electrokinetic model

The electrophoretic mobility of large spherical colloids in different salt solutions of varying valency and concentration is studied via a combination approach of numerically solving the standard electrokinetic model with a ζ potential that has been obtained from explicit ion simulations of the restricted primitive model, thus going beyond the standard mean-field treatment. We compare our theoretical mobility curves to two distinct sets of experimental results and obtain good agreement for monovalent and divalent salt solutions. For the case of the trivalent La(3+) salt, the experimentally obtained mobility reversal at high ionic strengths can be obtained only by adding an additional attractive interaction of 4k(B)T to the potential between the colloid and La(3+), hinting at the presence of a nonelectrostatic binding term for this ion. It is also shown that, contrary to intuition, charge inversion does not necessarily result in mobility reversal.

DNA interactions in crowded nanopores

The motion of DNA in crowded environments is a common theme in physics and biology. Examples include gel electrophoresis and the self-interaction of DNA within cells and viral capsids. Here we study the interaction of multiple DNA molecules within a nanopore by tethering the DNA to a bead held in a laser optical trap to produce a "molecular tug-of-war". We measure this tether force as a function of the number of DNA molecules in the pore and show that the force per molecule decreases with the number of molecules. A simple scaling argument based on a mean field theory of the hydrodynamic interactions between multiple DNA strands explains our observations. At high salt concentrations, when the Debye length approaches the size of the counterions, the force per molecule becomes essentially independent of the number of molecules. We attribute this to a sharp decrease in electroosmotic flow which makes the hydrodynamic interactions ineffective.

Electrophoretic mobility reversal of polyampholytes induced by strong electric fields or confinement

We investigate the mobility of polyampholytes consisting of both negatively and positively charged sections. The simulations are carried out using molecular dynamics simulations with electrohydrodynamical effects taken into account via a simple coupling scheme to a lattice-Boltzmann fluid. Our results show a previously predicted mobility reversal of the polyampholytes as the applied electric field is increased due to stretching of the polyampholytes. Further, we show that a similar mobility reversal can be induced due to confinement between parallel plates. At high electric field strengths, the polyampholytes' electrophoretic mobility is a non-monotonic function of the distance between the plates. These results help to clarify the role of deformation and confinement on the electrophoretic mobility of polyampholytes.

Electrophoresis of a DNA coil near a nanopore

Motivated by DNA electrophoresis near a nanopore, we consider the flow field around an "elongated jet," a long thin source which injects momentum into a liquid. This solution qualitatively describes the electro-osmotic flow around a long rigid polymer, where due to electrohydrodynamic coupling, the solvent receives momentum from the electric field. Based on the qualitative behavior of the elongated jet solution, we develop a coarse-grained scheme which reproduces the known theoretical results regarding the electrophoretic behavior of a long rigid polymer and a polymer coil in a uniform field, which we then exploit to analyze the electrophoresis of a polymer coil in the nonuniform field near a nanopore.

Electrophoretic capture of a DNA chain into a nanopore

Based on our formulation of the DNA electrophoresis near a pore [Rowghanian and Grosberg, Phys. Rev. E (to be published)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption to a sink placed on top of an energy barrier. Reproducing the previously observed diffusion-limited and barrier-limited regimes as two different limits of the particle absorption process and matching the data, our model suggests a slower growth of the capture rate with the DNA length for very large DNA molecules than the previous model, motivating more experiments beyond the current range of electric field and DNA length. At moderately weak electric fields, our model predicts a different effect, stating that the DNA length dependence of the capture rate first disappears as the field is reduced and eventually reverses to a decreasing trend with N.

Electrophoresis of deformable polyelectrolytes in a nanofluidic channel

The influence of the shape of a polyelectrolyte (PE) on its electrophoretic behavior in a nanofluidic channel is investigated by considering the translocation of a deformable ellipsoidal PE along the axis of a cylindrical nanochannel. A continuum model comprising a Poisson equation for the electric potential, Nernst-Planck equations for the ionic concentrations, and modified Stokes equations for the flow field is adopted. The effects of the PE shape, boundary, bulk ionic concentration, counterion condensation, electroosmotic retardation flow, and electroosmotic flow (EOF) on the PE mobility are discussed. Several interesting behaviors are observed. For example, if the nanochannel is uncharged and the double layer is thick, then the PE mobility increases (decreases) with increasing double-layer thickness for a smaller (larger) boundary, which has not been reported previously. If the nanochannel is negatively charged and the double layer is thick, then a negatively charged PE moves in the direction of the applied electric field. The results gathered provide necessary information for both the interpretation of experimental data and the design of nanochannel-based sensing devices.

Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol

Nanopore-based technologies have attracted much attention recently for their promising use in low-cost and high-throughput genome sequencing. To achieve single-base resolution of DNA sequencing, it is critical to slow and control the translocation of DNA, which has been achieved in a protein nanopore but not yet in a solid-state nanopore. Using all-atom molecular dynamics simulations, we investigated the dynamics of a single-stranded DNA (ssDNA) molecule in an aqueous glycerol solution confined in a SiO(2) nanopore. The friction coefficient ξ of the ssDNA molecule is found to be approximately 18 times larger in glycerol than in water, which can dramatically slow the motion of ssDNA. The electrophoretic mobility μ of ssDNA in glycerol, however, decreases by almost the same factor, yielding the effective charge (ξμ) of ssDNA being roughly the same as in water. This is counterintuitive since the ssDNA effective charge predicted from the counterion condensation theory varies with the dielectric constant of a solvent. Due to the larger friction coefficient of ssDNA in glycerol, we further show that glycerol can improve trapping of ssDNA in the DNA transistor, a nanodevice that can be used to control the motion of ssDNA in a solid-state nanopore. Simulation results of slowing ssDNA translocation were confirmed in our nanopore experiment.

Electric-field-induced friction reduction and control

Friction is always present when surfaces in contact are set in motion. In this work I describe how a precise, active control of the global friction is possible by adjusting the local molecular conformation of a polyelectrolyte coating via the application of an alternating electric field. The intensity of the applied field determines the degree of interpenetration between polymer brushes in contact, regulating chain stretching while sliding, which is the process at the origin of the global friction. The dynamics of the problem is controlled by the relaxation times of the polyelectrolyte.

Simulations of free-solution electrophoresis of polyelectrolytes with a finite Debye length using the Debye-Hückel approximation

We introduce a mesoscale simulation method based on multiparticle collision dynamics (MPCD) for the electrohydrodynamics of polyelectrolytes with finite Debye lengths. By applying the Debye-Hückel approximation to assign an effective charge to MPCD particles near charged monomers, our simulations are able to reproduce the rapid rise in the electrophoretic mobility with respect to the degree of polymerization for the shortest polymer lengths followed by a small decrease for longer polymers due to charge condensation. Moreover, these simulations demonstrate the importance of a finite Debye length in accurately determining the mobility of uniformly charged polyelectrolytes and net neutral polyampholytes.

Nanopores: A journey towards DNA sequencing

Much more than ever, nucleic acids are recognized as key building blocks in many of life's processes, and the science of studying these molecular wonders at the single-molecule level is thriving. A new method of doing so has been introduced in the mid 1990's. This method is exceedingly simple: a nanoscale pore that spans across an impermeable thin membrane is placed between two chambers that contain an electrolyte, and voltage is applied across the membrane using two electrodes. These conditions lead to a steady stream of ion flow across the pore. Nucleic acid molecules in solution can be driven through the pore, and structural features of the biomolecules are observed as measurable changes in the trans-membrane ion current. In essence, a nanopore is a high-throughput ion microscope and a single-molecule force apparatus. Nanopores are taking center stage as a tool that promises to read a DNA sequence, and this promise has resulted in overwhelming academic, industrial, and national interest. Regardless of the fate of future nanopore applications, in the process of this 16-year-long exploration, many studies have validated the indispensability of nanopores in the toolkit of single-molecule biophysics. This review surveys past and current studies related to nucleic acid biophysics, and will hopefully provoke a discussion of immediate and future prospects for the field.

Hydrodynamic manipulation of DNA in nanopost arrays: unhooking dynamics and size separation

Micro- or nanofabricated obstacle arrays are widely used as model matrices to perform fast DNA separations by electrophoresis. In this report, a gallery of obstacles of radii spanning from 40 to 250 nm are used to investigate the dynamics of hydrodynamic-field-driven DNA-nanopost collisions at the single-molecule level. The data shows that DNA disengagement dynamics are reasonably well described by conventional electrophoretic models in the limit of a large spacing between obstacles and for moderate migration velocities. It is also demonstrated that the use of hydrodynamic flow fields to convey DNA molecules is associated with changes in the configurational space of hooking events, and to altered relaxation dynamics between consecutive collisions. This study defines experimental conditions for the efficient separation of DNA fragments of tens of base pairs, and provides a complete framework by which to understand the behavior of DNA in the course of hydrodynamic-driven migrations through nanopost arrays.

Charge inversion, condensation and decondensation of DNA and polystyrene sulfonate by polyethylenimine

We study the formation and structure of stable electrostatic complexes between polyanions (DNA and poly(styrene-sulfonate)) and linear polyethylenimine. The charge ratio x of the mixture is tuned by varying the concentration of the polycation at constant concentration of polyanion. In agreement with recent theories, dynamic light scattering and electrophoretic mobility measurements show two distinct regimes of weak and strong complexation. At low polycation concentration, negatively charged small complexes involving a few polyanion chains are observed first. By further increasing x, these small complexes condense at a precise charge ratio x(c) < 1 to form large anionic aggregates. The inversion of the charge of the condensed complexes coincides with the maximum of complexation and precedes the dissolution of the aggregates which occurs at a well-defined decondensation threshold x(d) > 1. Above x(d), positively charged complexes containing again a few overcharged polyanion chains are observed. The macroscopic phase diagram is qualitatively well corroborated by AFM observation of the complexes. The influence of entropic effects is probed by varying parameters like concentration, polycation molecular weight and ionic strength. Structure of stable negatively charged complexes is investigated at higher concentration using Small Angle Neutron Scattering. In the condensed regime, we observe large soluble bundles with sharp interfaces where the local structure of the polyanions is preserved.

Nanopore translocation dynamics of a single DNA-bound protein

We study the translocation dynamics of a single protein molecule attached to a double-stranded DNA that is threaded through a solid-state nanopore by optical tweezers and an electric field (nanopore force spectroscopy). We find distinct asymmetric and retarded force signals that depend on the protein charge, the DNA elasticity and its counterionic screening in the buffer. A theoretical model where an isolated charge on an elastic, polyelectrolyte strand is experiencing an anharmonic nanopore potential was developed. Its results compare very well with the measured force curves and explain the experimental findings that the force depends linearly on the applied electric field and exhibits a small hysteresis during back and forth translocation cycles. Moreover, the translocation dynamics reflects the stochastic nature of the thermally activated hopping between two adjacent states in the nanopore that can be adequately described by Kramers rate theory.

Separation of DNA Using Ferrofluid Array Electrophoresis

We present a new method for electrophoretic separation of DNA, Ferro fluid Array Electrophoresis (FAE). The method uses a stabilized suspension of an hydrophobic ferrofluid in aqueous buffer as the separating medium. When this suspension is placed in a slab cell and submitted to a magnetic field perpendicular to the slab plane, it organizes into a regular array of columns with micron-sized spacing. DNA migrating in this maze leads to size-fractionation. Resolution of lambda phage (48.5 kbp) and T4 (140 kbp) DNA molecules in 30 mn is achieved. The motion of individual DNA molecules during FAE is observed using fluorescence videomicroscopy, and the molecular mechanisms responsible for separation are discussed in the light of recent computer simulations. During migration, large DNA molecules temporarily wrap around the impenetrable ferrofluid columns. They disengage by slippage, like a rope on a pulley, and the dependence of the disengagement time upon DNA size is responsible for the size-fractionation.

Implicit method for simulating electrohydrodynamics of polyelectrolytes

We introduce a novel method to couple Lennard-Jones beads to a lattice-Boltzmann fluid by adding a term which represents the slip within the Debye layer with respect to the surrounding fluid. The method produces realistic electrophoretic dynamics of charged free chains, as well as the correct stall force in the limit of a thin Debye layer. Our simulations also demonstrate how a net-neutral polyampholyte can have a nonzero net force due to hydrodynamic interactions. This method represents an efficient way to simulate a wide variety of complex problems in electrohydrodynamics.

Exploiting lattice potentials for sorting chiral particles

Several ways are demonstrated of how periodic potentials can be exploited for sorting molecules or other small objects which only differ by their chirality. With the help of a static bias force, the two chiral partners can be made to move along orthogonal directions. Time-periodic external forces even lead to motion into exactly opposite directions.

Theory of capture rate in polymer translocation

The translocation of macromolecules through a nanopore requires the impingement of the molecules at the pore followed by threading through the pore. While most of the discussion on the translocation phenomenon focused so far on the threading process, the phenomenology on the frequency of encounters between the polymer and the pore exhibits diverse features in terms of polymer length, solution conditions, driving force, and pore geometry. We derive a general theory for the capture rate of polyelectrolyte molecules and the probability of successful translocation through a nanopore, under an externally imposed electric field. By considering the roles of entropic barrier at the pore entrance and drift of the polyelectrolyte under the electric field, we delineate two regimes: (a) entropic barrier regime and (b) drift regime. In the first regime dominated by the entropic barrier for the polyelectrolyte, the capture rate is an increasing nonlinear function in the electric field and chain length. In the drift regime, where the electric field dwarfs the role of entropic barriers, the capture rate is independent of chain length and linear in electric field. An analytical formula is derived for the crossover behavior between these regimes, and the general results are consistent with various experimentally observed trends.

Deciphering ionic current signatures of DNA transport through a nanopore

Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single-molecule manipulation and analysis. In a typical setup, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through a single nanopore, across an otherwise impermeable membrane. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide makeup of a DNA strand. Despite great success, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. Such a relationship can be determined using molecular dynamics-a computational method that can accurately predict the time evolution of a molecular system starting from a given microscopic state. This article describes recent applications of this method to the process of DNA transport through biological and synthetic nanopores.