Biopolymer filtration in corrugated nanochannels

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. In a previous publication, we discovered a hairpin unraveling mechanism, namely, the pulley effect, in a pressure-driven translocation system. In this paper, we further investigate the pulley effect in the presence of pressure-driven fluid flow and an opposing force provided by an electrostatic field as an approach to increase single-file capture probability. A hydrodynamic flow is used to move the polymer forward, and two oppositely charged electrostatic square loops are used to create an opposing force. By optimizing the balance between forces, we show that the single-file capture can be amplified from about 50% to almost 95%. The force location, force strength, and flow rate are used as the optimizing variables.

Parallel computing for mobilities in periodic geometries

We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.

The journey of a single polymer chain to a nanopore

For a polymer to successfully thread through a nanopore, it must first find the nanopore. This so-called capture process is typically considered as a two-stage operation consisting of the chain being delivered at the entrance of the nanopore and then insertion of one of the ends. Studying molecular dynamics-lattice Boltzmann simulations of the capture of a single polymer chain under pressure driven hydrodynamic flow, we observe that the insertion can be essentially automatic with no delay for the ends searching for the nanopore. The deformation of the chain within the converging flow area and also, the interplay between the chain elastic forces and the hydrodynamic drag play an important role in the capture of the chain by the nanopore. Along the journey to the nanopore, the chain may form folded shapes. The competition between the elastic and hydrodynamic forces results in unraveling of the folded conformations (hairpins) as the chain approaches the nanopore. Although the ends are not the only monomers that can thread into the nanopore, the unraveling process can result in much higher probability of threading by the ends.

Anomalous interplay of slip, shear and wettability in nanoconfined water

Slip of liquid over nanometer scales is traditionally believed to be augmented with interfacial shear. In sharp contrast to this intuitive paradigm, here we show that a reverse of this phenomenon may also be possible, by exploiting a rich and non-trivial interplay between interfacial wettability and shear distribution in nano-confined water. This may be attributed to the complex overlapping effect of the local hydrodynamic fields imposed by the opposing boundaries, in the case of highly confined water molecules. The net effect culminates in the form of intriguing molecular layering that can by no means be intuitively estimated, as unveiled from the present molecular dynamics simulations. The consequent complex nature of the interfacial friction is observed to depend not only on the chemical and physical signature of the interface but also on the distribution of the shear rate. We also provide a simple continuum-based theory, in an effort to capture the essential aspects of the underlying physico-chemical interactions. These results are likely to open up new windows for control of slippery and sticky flows in nanofluidic channels.

Propulsion and controlled steering of magnetic nanohelices

Externally controlled motion of micro and nanomotors in a fluid environment constitutes a promising tool in biosensing, targeted delivery and environmental remediation. In particular, recent experiments have demonstrated that fuel-free propulsion can be achieved through the application of external magnetic fields on magnetic helically shaped structures. The magnetic interaction between helices and the rotating field induces a torque that rotates and propels them via the coupled rotational-translational motion. Recent works have shown that there exist certain optimal geometries of helical shapes for propulsion. However, experiments show that controlled motion remains a challenge at the nanoscale due to Brownian motion that interferes with the deterministic motion and makes it difficult to achieve controlled steering. In the present work we employ quantitatively accurate simulation methodology to design a setup for which magnetic nanohelices of 30 nm in radius and 180 nm in length (corresponding to previously determined optimal length to radius ratio of 6), with and without cargo, can be accurately propelled and steered in the presence of thermal fluctuations. In particular, we demonstrate fast transport of such nanomotors and devise protocols in manipulating external fields to achieve directionally controlled steering at biologically relevant temperatures.

Polymer margination in uniform shear flows

We address the issue of polymer margination (migration towards surfaces) in uniform shear flows through extensive LBMD (lattice-Boltzmann molecular dynamics) simulations. In particular we consider the effect of monomer size, a on the chain's overall margination tendency for chains of length N = 16, 32 monomers in flows at multiple shear rates [small gamma, Greek, dot above]. We observed higher margination of chains with larger radii monomers in comparison to smaller radii monomer chains of the same length N. We quantify this effect by considering various measures such as the distribution of the maximum extent of the chain into the channel bulk, zm, distribution of its center of mass in the direction normal to the surface, zc and the distributions of the chain's radius of gyration in directions parallel and perpendicular to the surface i.e. Rx, Ry and Rz respectively.

Flow Behavior of Chain and Star Polymers and Their Mixtures

Star-shaped polymers show a continuous change of properties from flexible linear chains to soft colloids, as the number of arms is increased. To investigate the effect of macromolecular architecture on the flow properties, we employ computer simulations of single chain and star polymers as well as of their mixtures under Poiseuille flow. Hydrodynamic interactions are incorporated through the multi-particle collision dynamics (MPCD) technique, while a bead-spring model is used to describe the polymers. For the ultradilute systems at rest, the polymers are distributed uniformly in the slit channel, with a weak dependence on their number of arms. Once flow is applied, however, we find that the stars migrate much more strongly towards the channel center as the number of arms is increased. In the star-chain mixtures, we find a flow-induced separation between stars and chains, with the stars located in the channel center and the chains closer to the walls. In order to identify the origin of this flow-induced partitioning, we conduct additional simulations without hydrodynamic interactions, and find that the observed cross-stream migration originates from a combination of wall-induced hydrodynamic lift forces and viscoelastic effects. The results from our study give valuable insights for designing microfluidic devices for separating polymers based on their architecture.

Simulations of microscopic propulsion of soft elastic bodies

Using simulations that realistically model both hydrodynamic and elastic behavior, we study the motion of a microscopic, driven elastic sphere immersed in water. We first confirm the "jittery" relaxation recently predicted theoretically for an externally driven elastic sphere. The sphere is then divided in two and each section is driven internally with the two sections 180^° out of phase. With periodic and perfectly symmetric driving, the elastic sphere spontaneously breaks symmetry and can attain macroscopic average swimming velocities to the right or left, the direction depending only on the initial state. With asymmetric driving the elastic sphere swims in one direction and the maximum speed is obtained with a 1/3:2/3 split. At high drive frequencies close to elastic resonances of the sphere, the motion can be quite efficient. At low drive frequencies the propulsion speed becomes independent of the elastic constants of the sphere and less efficient, but still substantial. Inertia is found to be an important driver of the behavior despite the small size of the spheres. As we model the full three-dimensional elasticity and compressible hydrodynamics, our simulations give not just qualitative indications but quantitative predictions for the motion.

Topology-Sensitive Microfluidic Filter for Polymers of Varying Stiffness

The separation of polymers based on their size, rigidity, and topology is an essential but also highly challenging task for nanoscience and engineering. Using hybrid molecular dynamics simulations that correctly take into account hydrodynamics, we have designed microfluidic channels for separating linear from ring polymers in dilute solutions. We establish that the transport velocity of the polymers is independent of their topology and rigidity when the channel walls are smooth and repulsive. However, when the walls are decorated with attractive spots arranged on lines parallel to the flow, ring polymers exhibit an order of magnitude higher transport velocity compared to linear chains. The spots induce a homeotropic-like reorientation of ring polymers close to walls leading to a tank treading motion along them, whereas linear chains are immobilized upon adsorption. This mechanism becomes more enhanced with increasing polymer rigidity. The presented technique holds thus promise for reliably separating nanoparticles based on their topology.

Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers

We investigate with experiments and computer simulations the nonequilibrium dynamics of DNA polymers crossing arrays of entropic barriers in nanofluidic devices in a pressure-driven flow. With increasing driving pressure, the effective diffusivity of DNA rises and then peaks at a value that is many times higher than the equilibrium diffusivity. This is an entropic manifestation of "giant acceleration of diffusion." The phenomenon is sensitive to the effective energy landscape; thus, it offers a unique probe of entropic barriers in a system driven away from equilibrium.

Sorting ring polymers by knot type with modulated nanochannels

In this theoretical study we discuss a novel method for sorting ring polymers according to their topological, knotted state. The proposed approach harnesses the rich dynamical behaviour of polymers confined inside spatially-modulated nanochannels. The longitudinal mobility of the rings is shown to have two key properties that are ideally suited for knot sorting. First, at fixed topology, the mobility has an intriguing oscillatory dependence on chain length. Second, the mobility ranking of different knot types is inverted upon increasing the chain length. We show that this complex interplay of channel geometry, chain length and topology can be rationalised within a simple theoretical framework based on Fick-Jacobs's diffusive theory. The results and the interpretative scheme ought to be useful for designing microfluidic devices with optimal topological sorting capabilities.

Mesoscopic simulation of single DNA dynamics in rotational flows

In this numerical study, the transport and dynamics of an isolated DNA in rotational flow generated in a microchannel have been investigated using dissipative particle dynamics. Often, inertial flow through microchannels with a sudden change in surface structure facilitates a re-circulation or vortex region. The conformation and mobility of the bio-polymer under the influence of such rotating fluid inside a square cavity of the microchannel is analyzed. The flexible polymer chain is found to migrate towards the rotating region and follows the vortex streamline. The orientation, size and tumbling period of polymer strands are affected by the strength of the microvortex. At elevated flow rates, the macromolecule prefers to remain inside the vortex and a hydrodynamic trap is formed. Moreover, residence time of the single molecule in the microcavity is significantly influenced by the chain length and flow strength. Further, it has been demonstrated that, such entrapment duration can be strategically altered by modifying the hydrophobicity of the microchannel.

Stretching of DNA confined in nanochannels with charged walls

There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.

Driven polymer transport through a periodically patterned channel

We study the driven transport of polymers in a periodically patterned channel using Langevin dynamics simulations in two dimensions. The channel walls are patterned with periodically alternating patches of attractive and non-attractive particles that act as trapping sites for the polymer. We find that the system shows rich dynamical behavior, observing giant diffusion, negative differential mobility, and several different transition mechanisms between the attractive patches. We also show that the channel can act as an efficient high-pass filter for polymers longer than a threshold length Nthr, which can be tuned by adjusting the length of the attractive patches and the driving force. Our findings suggest the possibility of fabricating polymer filtration devices based on patterned nanochannels.