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.

Dispersion and orientation patterns in nanorod-infused polymer melts.

Introducing nanorods into a polymeric matrix can enhance the physical and mechanical properties of the resulting material. In this paper, we focus on understanding the dispersion and orientation patterns of nanorods in an unentangled polymer melt, particularly as a function of nanorod concentration, using molecular dynamics simulations. The system is comprised of flexible polymer chains and multi-thread nanorods that are equilibrated in the NPT ensemble. All interactions are purely repulsive except for those between polymers and rods. Results with attractive vs repulsive polymer-rod interactions are compared and contrasted. The concentration of rods has a direct impact on the phase behavior of the system. At lower concentrations, rods phase separate into nematic clusters, whereas at higher concentrations more isotropic and less structured rod configurations are observed. A detailed examination of the conformation of the polymer chains near the rod surface shows extension of the chains along the director of the rods (especially within clusters). The dispersion and orientation of the nanorods are a result of the competition between depletion entropic forces responsible for the formation of rod clusters, the enthalpic effects that improve mixing of rods and polymer, and entropic losses of polymers interpenetrating rod clusters.

Effects of structural inhomogeneity on equilibration processes in Langevin dynamics.

In recent decades, computer experiments have led to an accurate and fundamental understanding of atomic and molecular mechanisms in fluids, such as different kinds of relaxation processes toward steady physical states. In this paper, we investigate how exactly the configuration of initial states in a molecular-dynamics simulation can affect the rates of decay toward equilibrium for the widely known Langevin canonical ensemble. For this purpose, we derive an original expression relating the system relaxation time τ_{sys} and the radial distribution function g(r) in the near-zero and high-density limit. We found that, for an initial state which is slightly marginally inhomogeneous in the number density of atoms, the system relaxation time τ_{sys} is much longer than that for the homogeneous case and an increasing function of the Langevin coupling constant, γ. We also found, during structural equilibration, g(r) at large distances approaches 1 from above for the inhomogeneous case and from below for the macroscopically homogeneous one.

Modeling of a two-stage polymerization considering glass fibre sizing using molecular dynamics.

Fibre reinforced polymers are an important class of materials due to their light weight, high strength, and stiffness. However, there is a lack of knowledge about the interaction of fibre surface, sizing (fibre coating), and resin. Often only idealised academic systems are studied, and only rarely realistic systems that are used in an industrial context. Therefore, methods for studying the behaviour of complex sizing are highly desirable, especially as they play a crucial role in the performance of fibre reinforced polymers. Here, a simplified, yet industrially used resin system is extended using molecular dynamics simulations by adding a fibre surface and sizing layers. Furthermore, a common coupling agent was selected, and several additional assumptions were made about the structure of the sizing. Based on this, a systematic procedure for the development of a final cured system is introduced: a condensation reaction to form oligomers from coupling agent monomers is conducted. Subsequently, a two stage reaction, a polyurethane reaction and a radical polymerisation, is modelled based on an established approach. Using the final cured system, evaluations of averaged quantities during the reactions are carried out. Moreover, the system is evaluated along the normal direction of the fibre surface, which proves a spatial analysis of the fibre-sizing-resin interface.

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.

Stability of binary colloidal crystals immersed in a cholesteric liquid crystal.

In this paper, we model a number of both closed-packed and non-closed-packed crystals inside a cholesteric liquid crystal (LC) with different pitch values and nematic LC through the Landau-de Gennes free-energy method. We used binary boundary conditions (normal and planar anchoring) applied on the surface of colloids as we are interested in investigating the stability of binary crystals. The results indicate that body-centered-cubic (BCC) crystals have a lower-energy lattice defect structure than the diamond crystal, and the most energetically favorable BCC lattice can be formed in a cholesteric liquid crystal with a pitch value commensurate with the lattice spacing. Furthermore, it is shown that a pair of binary colloids can be self-assemble into a stable face-centered-cubic lattice structure inside a nematic LC, as it has the lowest energy comparing to diamond and BCC crystals.

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.

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.

Heterogeneous colloidal particles immersed in a liquid crystal.

In this paper, we explore anisotropic interactions between particles with heterogeneous boundary conditions inside both nematic and cholesteric liquid crystals. The results show that when particles are put at different distances and angles with respect to each other, new types of defect structures are produced, depending on the relative distances and directions. In a cholesteric liquid crystal, the value of the pitch affects the defect structures and induced forces. Moreover, it was observed that it is energetically favorable for the particles to remain in a plane parallel to the far-field director in a nematic liquid crystal, while for particles immersed in a cholesteric there are multiple energy minima not all located in the same plane.

Photonic band structure of diamond colloidal crystals in a cholesteric liquid crystal.

In this paper, we demonstrate the presence of a photonic band gap for a diamond lattice structure made of particles with normal anchoring inside a cholesteric liquid crystal. As is typical for liquid crystals (LCs), there is considerable contrast between the dielectric constant parallel ε_{∥} and perpendicular ε_{⊥} to the director, with ε_{∥}/ε_{⊥}∼4 here. It is shown that the size of the photonic band gap is directly related to the size of colloidal particles and the contrast between the dielectric constant in the particles and the extreme values of ε in the LC medium (one needs either ε in the particle much smaller than ε_{⊥} or much bigger than ε_{∥}). No opening is seen in the band diagrams for small particles. For larger particles a partial gap opens when the particles are composed of very low dielectric material but never a complete gap. On the other hand, a complete gap starts to be revealed when the size of the colloidal particles is increased and when a high dielectric constant is used for filling inside the particles. The maximum size of the gap is observed when the particles are large enough so that their surfaces overlap.

Dynamics of disk pairs in a nematic liquid crystal.

We use a hybrid lattice Boltzmann method to study the behavior of sets of ferromagnetic colloidal disks in a nematic liquid crystal. When a weak rotating magnetic field acts on the system, the disks rotate following the magnetic field. This leads to a distortion in the liquid crystal that drives translational motion of the disks. If the concentration of disks is high, disks get locked together: a stable chain configuration is created, where each disk lays on the nearest neighbor. For intermediate concentrations of disks, a different behavior is observed. When disks are rotated by the magnetic field by more than 90^{∘} from their initial orientation, the distortion in the liquid crystal leads to a simultaneous flip of both disks. The final disk positions depends only weakly on the initial configuration. Consecutive rotations of magnetic field push disks towards an equidistant configuration. Periodicity of the systems studied and analysis of the flipping motion of a single disk imply that one can use weak rotating magnetic fields to create stable crystal structures of disks.

Dynamics of a disc in a nematic liquid crystal.

We use lattice Boltzmann simulations to study the dynamics of a disc immersed in a nematic liquid crystal. In the absence of external torques, discs with homeotropic anchoring align with their surface normal parallel to the director of the nematic liquid crystal. In the presence of a weak magnetic field a ferromagnetic disc will rotate to equilibrate the elastic torque due to the distortion of the nematic director and the magnetic torque. When the magnetic field rotates the disc so that the angle θ between normal to the surface of the disc â and director of the liquid crystal n[combining circumflex] becomes greater than π/2, the disc flips around the axis perpendicular to the rotation axis so that â sweeps through π radians. An analysis of this behaviour was performed. In particular, we look at the impact of the disc thickness and edges on defect creation and the flipping transition. We also analyse the importance of backflow.

Biopolymer filtration in corrugated nanochannels.

We examine pressure-driven nonequilibrium transport of linear, circular, and star polymers through a nanochannel containing a rectangular pit with full hydrodynamic interactions and thermal fluctuations. We demonstrate that with sufficiently small pressure differences, there is contour length-dependent entropic trapping of the polymer in the pit when the pit and the polymer sizes are compatible. This is due to competition between flow and chain relaxation in the pit, which leads to a nonmonotonic dependence of the polymer mobility on its size and should aid in the design of nanofiltration devices based on the polymer size and shape.

One- and two-particle dynamics in microfluidic T-junctions.

Advances in precise focusing of colloidal particles in microfluidic systems open up the possibility of using microfluidic junctions for particle separation and filtering applications. We present a comprehensive numerical study of the dynamics of solid and porous microparticles in T-shaped junctions. Good agreement with experimental data is obtained on the location of particle-separating streamlines for single solid particles with realistic parameters corresponding to the experiments. We quantify the changes in the position of the separating line for porous, partially penetrable colloids. A prediction of the full phase diagram for particle separation is presented in the case of two successive particles entering a T-junction. Our results suggest the intriguing possibility of using the one- and two-particle T-junctions as logic gates.

Fluctuating lattice-Boltzmann model for complex fluids.

We develop and test numerically a lattice-Boltzmann (LB) model for nonideal fluids that incorporates thermal fluctuations. The fluid model is a momentum-conserving thermostat, for which we demonstrate how the temperature can be made equal at all length scales present in the system by having noise both locally in the stress tensor and by shaking the whole system in accord with the local temperature. The validity of the model is extended to a broad range of sound velocities. Our model features a consistent coupling scheme between the fluid and solid molecular dynamics objects, allowing us to use the LB fluid as a heat bath for solutes evolving in time without external Langevin noise added to the solute. This property expands the applicability of LB models to dense, strongly correlated systems with thermal fluctuations and potentially nonideal equations of state. Tests on the fluid itself and on static and dynamic properties of a coarse-grained polymer chain under strong hydrodynamic interactions are used to benchmark the model. The model produces results for single-chain diffusion that are in quantitative agreement with theory.

Constitutive relations in dense granular flows.

We use simulations to investigate constitutive relations in dry granular flow. Our system is comprised of polydisperse sets of spherical grains falling down a vertical chute under the influence of gravity. Three phases or states of granular matter are observed: a free-fall dilute granular gas region at the top of the chute, a granular fluid in the middle and then a glassy region at the bottom. We examine a complete closed set of constitutive relations capable of describing the local stresses, heat flow, and dissipation in the different regions. While the pressure can be reasonably described by hard sphere gas models, the transport coefficients cannot. Transport coefficients such as viscosity and heat conductivity increase with decreasing temperature in the fluid and glassy phases. The glass exhibits signs of a finite yield stress and we show that the static sand pile is a limit of our glassy state.

Non-bonded force field for the interaction between metals and organic molecules: a case study of olefins on aluminum.

In this work, we parameterize an empirical potential for the interaction between organic molecules and metal surfaces via force matching. This is done by pursuing a self-consistent approach similar to the ones used for equilibrium simulations; however, special attention is paid to the suitability of the resulting potential for tribological (non-equilibrium) situations. Specifically, we study olefin molecules confined between two aluminum surfaces under realistic pressures and shear rates. We find that the Buckingham potential produces better agreement with the first principle data than other force fields. While our training set only contains hexene molecules, we find that the standard error in the fitted olefin-aluminum interaction increases only by a factor of 1.15 when the force field is applied to butene, octene, and decene. Including mirror charges into the treatment only marginally improves fits. While olefins on aluminum is merely a special case, the proposed methodology can be used to parameterize any other interaction between polymers and metal surfaces for use in tribological simulations.

Velocity fluctuations in dense granular flows.

We use simulations to investigate velocity fluctuations in dry granular flow. Our system is comprised of mono- and polydisperse sets of spherical grains falling down a vertical chute under the influence of gravity. We find three different classes of velocity distributions depending on factors such as the local density. The class of the velocity distribution depends on whether the grains are in a free-fall, fluid, or glassy state. The analytic form of the distributions match those that have been found by other authors in fairly diverse systems. Here, we have all three present in a single system in steady state. Power-law tails that match recent experiments are also found but in a transition area suggesting they may be an artifact of crossover from one class of velocity distribution to another. We find evidence that the transition from one class to another may correspond to a second order dynamical phase transition in the limit that the vertical flow speed goes to zero.

General continuum boundary conditions for miscible binary fluids from molecular dynamics simulations.

Molecular dynamics simulations are used to explore the flow behavior and diffusion of miscible fluids near solid surfaces. The solid produces deviations from bulk fluid behavior that decay over a distance of the order of the fluid correlation length. Atomistic results are mapped onto two types of continuum model: Mesoscopic models that follow this decay and conventional sharp interface boundary conditions for the stress and velocity. The atomistic results, and mesoscopic models derived from them, are consistent with the conventional Marangoni stress boundary condition. However, there are deviations from the conventional Navier boundary condition that states that the slip velocity between wall and fluid is proportional to the strain rate. A general slip boundary condition is derived from the mesoscopic model that contains additional terms associated with the Marangoni stress and diffusion, and is shown to describe the atomistic simulations. The additional terms lead to strong flows when there is a concentration gradient. The potential for using this effect to make a nanomotor or pump is evaluated.

On the orientation of lamellar block copolymer phases under shear.

Self-assembled lamellar structures composed of block copolymers are simulated by molecular dynamics. The response of a bulk system to external shear is investigated, in particular, the average energy, the entropy production, and the stability of the lamellae's orientation. We distinguish two orientations, a parallel orientation in which the normal to the lamellae sheets lies in the direction of the shear gradient, and a perpendicular orientation in which the normal lies perpendicular to the shear gradient and shear direction. The perpendicular phase is stable throughout all shear rates. The parallel phase has higher internal energy and larger entropy production than the perpendicular phase and moreover becomes unstable at relatively small shear rates. The perpendicular orientation should therefore be more stable at any finite shear rate. Surface effects are probably responsible for the stability of the parallel phase observed experimentally at small shear rates.