A unifying theoretical framework for analyzing stochastic data from single-particle tracking (SPT) in viscoelastic materials is presented. A generalization of the bead-spring model for linear polymers is developed from a molecular point of view and from the standpoint of phenomenological linear viscoelasticity. The hydrodynamic interaction in the former is identiied as the dashpots in the latte...

Circular Brownian motion models of random matrices were introduced by Dyson and describe the parametric eigenparameter correlations of unitary random matrices. For symmetric unitary, self-dual quaternion unitary and an analogue of antisymmetric hermitian matrix initial conditions, Brownian dynamics toward the unitary symmetry is analyzed. The dynamical correlation functions of arbitrary number ...

The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoro...

A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular ...

A reaction probability is required to calculate the rate constant of a diffusion-dominated reaction. Due to the complicated geometry and potentially high dimension of the reaction probability problem, it is usually solved by a Brownian dynamics simulation, also known as a random walk or path integral method, instead of solving the equivalent partial differential equation by a discretization met...

FAST ALGORITHMS FOR BROWNIAN DYNAMICS SIMULATION WITH HYDRODYNAMIC INTERACTIONS

Protein association events are ubiquitous in biological systems. Some protein associations and subsequent responses are diffusion controlled in vivo. Hence, it is important to be able to compute bimolecular diffusional association rates for proteins. The Brownian dynamics simulation methodology may be used to simulate protein-protein encounter, compute association rates, and examine their depen...

Using Brownian Dynamics (BD) simulations we investigate non-equilibrium transitions of sheared colloidal films under controlled shear stress σxz. In our approach the shear rate [small gamma, Greek, dot above] is a dynamical variable, which relaxes on a time scale τc such that the instantaneous, configuration-dependent stress σxz(t) approaches a pre-imposed value. Investigating the dynamics unde...

The behavior of a heavy tagged intruder immersed in a bath of particles evolving under ballistic annihilation dynamics is investigated. The Fokker-Planck equation for this system is derived and the peculiarities of the corresponding diffusive behavior are worked out. In the long time limit, the intruder velocity distribution function approaches a Gaussian form, but with a different temperature ...

Abstract. In this paper a direct correspondence is made between the effective stochastic dynamics of elastic structures of an Immersed Boundary Method incorporating thermal fluctuations and Stokesian-Brownian Dynamics. The correspondence is made in the limit of small Reynolds number, in which the fluid relaxes rapidly on the time scale of the motion of the immersed structures, by performing an ...