Stochastic kinetic theory applied to coarse-grained polymer model.

A stochastic field theory approach is applied to a coarse-grained polymer model that will enable studies of polymer behavior under non-equilibrium conditions. This article is focused on the validation of the new model in comparison with explicit Langevin equation simulations under conditions with analytical solutions. The polymers are modeled as Hookean dumbbells in one dimension, without including hydrodynamic interactions and polymer-polymer interactions.

Continuous transition of colloidal crystals through stable random orders.

Randomly stacked 2D hexagonal close-packed (RHCP) layer structures are frequently observed in colloids and other material systems but are considered metastable. We report a stable RHCP phase domain of poly(butadiene--ethylene oxide) (PB-PEO) diblock copolymer micellar colloids in water. The stable RHCP colloidal crystals emerge in the middle of a continuously transiting phase domain of close-packed PB-PEO colloids from a face-centered cubic (FCC) polytype to a HCP polytype.

Application of a Simple Short-Range Attraction and Long-Range Repulsion Colloidal Model toward Predicting the Viscosity of Protein Solutions.

Some hard-sphere colloidal models have been criticized for inaccurately predicting the solution viscosity of complex biological molecules like proteins. Competing short-range attractions and long-range repulsions, also known as short-range attraction and long-range repulsion (SALR) interactions, have been thought to affect the microstructure of a protein solution at low to moderate ionic strength. However, such interactions have been implicated primarily in causing phase transition, protein gelation, or reversible cluster formation, and their effect on protein solution viscosity change is not fully understood.

Mesoscale simulation approach for assembly of small deformable objects.

We adapt Vertex models to understand the physical origin of the formation of long-range ordered structures in repulsive soft particles. The model incorporates contributions from the volume and surface area of each particle. Sampling using Monte Carlo simulations allows the system to naturally select preferred structures.

Dumbbell kinetic theory for polymers in a combination of flow and external electric field.

Combining Poiseuille flow with an external electric field is a demonstrated method to drive transverse migration in capillary electrophoresis. Despite both computational and experimental studies, a number of questions about how to best model polymers under these conditions remains. Attempts have been made to develop a kinetic theory for a bead-spring dumbbell model, but these have only been accurate at low electric field strength and have not captured the nonmonotonic relationship between migration and electric field strength.

Predicting Steady Shear Rheology of Condensed-Phase Monomolecular Films at the Air-Water Interface.

Predicting the non-Newtonian shear response of soft interfaces in biophysical systems and engineered products has been compromised by the use of linear (Newtonian) constitutive equations. We present a generalized constitutive equation, with tractable material properties, governing the response of Newtonian and non-Newtonian interfaces subjected to a wide range of steady shear. With experiments spanning six decades of shear rate, we capture and unify divergent reports of shear-thinning behavior of monomolecular films of the lipid dipalmitoylphosphatidylcholine, the primary constituent of mammalian cell walls and lung surfactant, at near-physiological packing densities.

Examination of the Statistical Effects Associated with Tracking Propulsive Particles.

Particle tracking of active colloidal particles can be used to compute mean-squared displacements that are fit to extract properties of the particles including the propulsive speed. Statistical errors in the mean-squared displacement leads to errors in the extracted properties especially for more weakly propelling particles. Brownian dynamics simulations in which the particle parameters are prescribed were used to examine the statistics of tracking self-propelling objects.

Passive trapping of rigid rods due to conformation-dependent electrophoretic mobility.

We present computer simulations of a rigid rod in a combination of an extensional fluid flow and extensional electric field. The electrophoretic mobility of the rod is different parallel or perpendicular to the rod. The dependence of the mobility on the conformation (orientation) leads to a new phenomenon where the rods can be passively trapped in all directions at the stagnation point.

Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics.

The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model.

Influence of shear on globule formation in dilute solutions of flexible polymers.

Polyelectrolytes, polymers in poor solvents, polymers mixed with particles, and other systems with attractions and repulsions show formation of globules/structures in equilibrium or in flow. To study the flow behavior of such systems, we developed a simple coarse-grained model with short ranged attractions and repulsions. Polymers are represented as charged bead-spring chains and they interact with oppositely charged colloids.

Impact of external flow on the dynamics of swimming microorganisms near surfaces.

Swimming microorganisms have been previously observed to accumulate along walls in confined systems both experimentally and in computer simulations. Here, we use computer simulations of dilute populations for a simplified model of an organism to calculate the dynamics of swimmers between two walls with an external fluid flow. Simulations with and without hydrodynamic interactions (HIs) are used to quantify their influence on surface accumulation.

Fluctuations in the coil-stretch transition of flexible polymers in good solvents: a peak due to nonlinear force relation.

Long flexible polymers undergo a coil to stretch transition (CST) in an elongational flow. Near the CST, a peak can be observed in the fluctuations of the size of a molecule (|R|). Solvent effects on the fluctuations are studied using Brownian dynamics simulations of a nonlinear spring force relation that can represent real molecules.

Effect of viscoelasticity on the collective behavior of swimming microorganisms.

Hydrodynamic interactions of swimming microorganisms can lead to coordinated behaviors of large groups. Using a mean-field theory and the Oldroyd-B constitutive equation, we show how linear viscoelasticity of the suspending fluid alters the hydrodynamic interactions and therefore the ability of the group to coordinate. We quantify the ability to coordinate by the initial growth rate of a small disturbance from the uniform isotropic state.

Dynamics of confined suspensions of swimming particles.

Low Reynolds number direct simulations of large populations of hydrodynamically interacting swimming particles confined between planar walls are performed. The results of simulations are compared with a theory that describes dilute suspensions of swimmers. The theory yields scalings with concentration for diffusivities and velocity fluctuations as well as a prediction of the fluid velocity spatial autocorrelation function.

Diffusion and spatial correlations in suspensions of swimming particles.

Populations of swimming micro-organisms produce fluid motions that lead to dramatically enhanced diffusion of tracer particles. Using simulations of suspensions of swimming particles in a periodic domain, we capture this effect and show that it depends qualitatively on the mode of swimming: swimmers "pushed" from behind by their flagella show greater enhancement than swimmers that are "pulled" from the front. The difference is manifested by an increase, that only occurs for pushers, of the diffusivity of passive tracers and the velocity correlation length with the size of the periodic domain.

DNA stretch during electrophoresis due to a step change in mobility.

We investigate DNA stretching during electrophoresis when the mobility abruptly changes. This is a simplified geometry that produces a nonhomogeneous strain rate over the scale of a single molecule. An effective Weissenberg number (Wi) and Deborah number were identified, and the degree of stretching was examined as a function of these two parameters.