Ratcheting Charged Polymers through Symmetric Nanopores Using Pulsed Fields: Designing a Low Pass Filter for Concentrating Polyelectrolytes.

We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation, and pulsed fields. Using Langevin dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses can significantly enhance the device efficiency.

Capture and translocation of a rod-like molecule by a nanopore: orientation, charge distribution and hydrodynamics.

We investigate the translocation of rods with different charge distributions using hybrid Langevin dynamics and lattice Boltzmann (LD-LB) simulations. Electrostatic interactions are added to the system using the PM algorithm to model the electrohydrodynamic interactions (EHI). We first examine the free-solution electrophoretic properties of rods with various charge distributions.

An efficient kinetic Monte Carlo to study analyte capture by a nanopore: transients, boundary conditions and time-dependent fields.

To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically symmetric system onto the 1D biased random walk. Our algorithm recovers the steady-state analytical solution and allows us to study time-dependent processes such as transients. Simulation results show that the steady-state depletion zone near pore is barely larger than the pore radius and narrows at higher field intensities; as a result, the time to reach steady-state is much smaller than the time required to empty a zone of the size of the capture radius λe.

Capture of rod-like molecules by a nanopore: Defining an "orientational capture radius".

Both the translational diffusion coefficient D and the electrophoretic mobility μ of a short rod-like molecule (such as dsDNA) that is being pulled toward a nanopore by an electric field should depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an inhomogeneous electric field, D and μ will change as the molecule approaches the nanopore, and this will impact the capture process. We present a simplified study of this problem using theoretical arguments and Langevin dynamics simulations.

Voltage-driven translocation: Defining a capture radius.

Analyte translocation involves three phases: (i) diffusion in the loading solution, (ii) capture by the pore, and (iii) threading. The capture process remains poorly characterized because it cannot easily be visualized or inferred from indirect measurements. The capture performance of a device is often described by a capture radius generally defined as the radial distance R at which diffusion-dominated dynamics cross over to field-induced drift.

Electrophoretic ratcheting of spherical particles in well/channel microfluidic devices: Making particles move against the net field.

We examine the electrophoresis of spherical particles in microfluidic devices made of alternating wells and narrow channels, including a system previously used to separate DNA molecules. Our computer simulations predict that such systems can be used to separate spherical particles of different sizes that share the same free-solution mobility. Interestingly, the electrophoretic velocity shows an inversion as the field intensity is increased: while small particles have higher velocities at low field, the situation is reversed at high fields with the larger particles then moving faster.

Reducing the variance in the translocation times by prestretching the polymer.

Langevin dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the trans side. Under the influence of stretching forces, the elongated polymer ensemble contains less variations in conformations compared to an unstretched ensemble.

Highly driven polymer translocation from a cylindrical cavity with a finite length.

We present a computer simulation study of polymer translocation in a situation where the chain is initially confined to a closed cylindrical cavity in order to reduce the impact of conformational diversity on the translocation times. In particular, we investigate how the coefficient of variation of the distribution of translocation times can be minimized by optimizing both the volume and the aspect ratio of the cavity. Interestingly, this type of confinement sometimes increases the number and impact of hairpin conformations such that the fluctuations in the translocation process do not follow a power law in time (for instance, these fluctuations can even vary non-monotonically with time).

Langevin dynamcis simulations of driven polymer translocation into a cross-linked gel.

We investigate the dynamics of driving a polyelectrolyte such as DNA through a nanopore and into a cross-linked gel. Placing the gel on the trans-side of the nanopore can increase the translocation time while not negatively affecting the capture rates. Thus, this setup combines the mechanics of gel electrophoresis with nanopore translocation.

Physical confinement signals regulate the organization of stem cells in three dimensions.

During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environment of a blastocyst. Embryonic stem cells (ESCs) are derived from the ICM, and mimicking embryogenesis in vitro, mouse ESCs (mESCs) are often cultured in hanging droplets. This promotes the formation of a spheroid as the cells sediment and aggregate owing to increased physical confinement and cell-cell interactions.

Interfacing solid-state nanopores with gel media to slow DNA translocations.

We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude.

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.

Using a Péclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions.

Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavor to match any particular set of experimental conditions. In this manuscript, we use the concept of a Péclet number for translocation, P(t), to compare the drift-diffusion balance in a typical experiment vs a typical simulation.

Simulating the entropic collapse of coarse-grained chromosomes.

Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres.

Coarse-grained molecular dynamics simulations of depletion-induced interactions for soft matter systems.

Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics (MD) simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (Weeks-Chandler-Andersen (WCA)) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer.

Translocation of a polymer through a nanopore starting from a confining nanotube.

In this manuscript, Langevin Dynamics simulations and Tension-Propagation theory are used to investigate the forced translocation of a polymer from a confining tube through a nanopore situated at one of the tube's ends. The diameter of the tube allows for a control over the polymer conformations: decreasing the tube diameter reduces the number of conformations available to the polymer chain both before and during translocation. As the tube diameter is decreased, the translocation time is observed to increase.

Diffusing diffusivity: a model for anomalous, yet Brownian, diffusion.

Wang et al. [Proc. Natl.

Biomolecule transport across biomembranes in the presence of crowding: polymer translocation driven by concentration and disorder gradients.

The transport of biomolecules across biomembranes occurs in a complex environment where the fluid on both sides of the membrane contains many inclusions. We investigate the translocation of a polymer through a nanopore in such crowded environments via computer simulations. Modeling intracellular and extracellular inclusions as spherical obstacles, the emergence of an entropic driving force is demonstrated for (i) a gradient in the number of obstacles on either side of the pore and (ii) having the obstacles in an ordered arrangement on one side and disordered on the other.

Can gel concentration gradients improve two-dimensional DNA displays?

The abrupt reduction in gel electrophoretic mobility that is observed when a dsDNA fragment is partially denatured has recently been predicted to exhibit a dependence upon the gel pore size. Using theoretical modeling, we demonstrate that this dependence can be exploited and used to improve the performance of 2D display of DNA. We report experimental evidence of this dependence and propose a new separation system in which a gel porosity gradient is utilized in a way analogous to temperature or denaturant gradients in traditional 2D display.

Theory of end-labeled free-solution electrophoresis: is the end effect important?

In the theory of free-solution electrophoresis of a polyelectrolyte (such as the DNA) conjugated with a "drag-tag," the conjugate is divided into segments of equal hydrodynamic friction and its electrophoretic mobility is calculated as a weighted average of the mobilities of individual segments. If all the weights are assumed equal, then for an electrically neutral drag-tag, the elution time t is predicted to depend linearly on the inverse DNA length 1/M. While it is well-known that the equal-weights assumption is approximate and in reality the weights increase toward the ends, this "end effect" has been assumed to be small, since in experiments the t(1/M) dependence seems to be nearly perfectly linear.

Translocation of a polymer through a nanopore across a viscosity gradient.

The translocation of a polymer through a pore in a membrane separating fluids of different viscosities is studied via several computational approaches. Starting with the polymer halfway, we find that as a viscosity difference across the pore is introduced, translocation will predominately occur towards one side of the membrane. These results suggest an intrinsic pumping mechanism for translocation across cell walls which could arise whenever the fluid across the membrane is inhomogeneous.

Field-flow fractionation and hydrodynamic chromatography on a microfluidic chip.

We present gravitational field-flow fractionation and hydrodynamic chromatography of colloids eluting through 18 μm microchannels. Using video microscopy and mesoscopic simulations, we investigate the average retention ratio of colloids with both a large specific weight and neutral buoyancy. We consider the entire range of colloid sizes, including particles that barely fit in the microchannel and nanoscopic particles.

Translocation of a polymer through a nanopore modulated by a sticky site.

Using a one-dimensional model for the translocation of a polymer through a nanopore, the effect of a "sticky site" at which the polymer binds to the pore is explored via exact numerical techniques. Results for the mean translocation time and the probability of translocation on the insertion of the first monomer in the pore are generated across a wide range of driving forces and binding potential strengths (well depths). The balance between the driving force, diffusion, and well depth yields a rich set of dynamics that depend strongly on where the sticky site is located along the polymer.

Structure of polyelectrolyte brushes subject to normal electric fields.

Molecular dynamic simulations of salt-free polyelectrolyte brushes subject to external fields applied normal to the grafting substrate reveal the three-dimensional monomer and counterion distributions. It is found that below a critical electric field, local electroneutrality holds for densely grafted brushes and the brush height remains independent of field intensity. Above this critical field (which scales as 1/3 with grafting density) brush height increases smoothly, and the fraction of condensed counterions decreases.

Translocation of "rod-coil" polymers: probing the structure of single molecules within nanopores.

Using simulation and analytical techniques, we demonstrate that it is possible to extract structural information about biological molecules by monitoring the dynamics as they translocate through nanopores. From Langevin dynamics simulations of polymers exhibiting discrete changes in flexibility (rod-coil polymers), distinct plateaus are observed in the progression towards complete translocation. Characterizing these dynamics via an incremental mean first passage approach, the large steps are shown to correspond to local barriers preventing the passage of the coils while the rods translocate relatively easily.