It is now well established that cell interiors are significantly crowded by macromolecules, which impede diffusion and enhance binding rates. However, it is not fully appreciated that levels of crowding are heterogeneous, and can vary substantially between subcellular regions. In this article, starting from a microscopic model, we derive coupled nonlinear partial differential equations for the ...

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are bette...

Nonlinear electro-osmotic behaviour of dilute non-adsorbing polymer solutions with low salinity is investigated using Brownian dynamics simulations and a kinetic theory. In the Brownian simulations, the hydrodynamic interaction between the polymers and a no-slip wall is considered using the Rotne-Prager approximation of the Blake tensor. In a plug flow under a sufficiently strong applied electr...

A theory for (1+3) -dimensional relativistic Brownian motion under the influence of external force fields is put forward. Starting out from a set of relativistically covariant, but multiplicative Langevin equations we describe the relativistic stochastic dynamics of a forced Brownian particle. The corresponding Fokker-Planck equations are studied in the laboratory frame coordinates. In particul...

The influence of hydrodynamic interactions on lane formation of oppositely charged driven colloidal suspensions is investigated using Brownian dynamics computer simulations performed on the Rotne-Prager level of the mobility tensor. Two cases are considered, namely sedimentation and electrophoresis. In the latter case the Oseen contribution to the mobility tensor is screened due to the opposite...

The first algorithm for Emulsion Stability Simulations (ESS) was presented at the V Conferencia Iberoamericana sobre Equilibrio de Fases y Diseño de Procesos [Luis, J.; García-Sucre, M.; Urbina-Villalba, G. Brownian Dynamics Simulation of Emulsion Stability In: Equifase 99. Libro de Actas, 1(st) Ed., Tojo J., Arce, A., Eds.; Solucion's: Vigo, Spain, 1999; Volume 2, pp. 364-369]. The former vers...

Concentrated hard-sphere suspensions and glasses are investigated with rheometry, confocal microscopy, and Brownian dynamics simulations during start-up shear, providing a link between microstructure, dynamics, and rheology. The microstructural anisotropy is manifested in the extension axis where the maximum of the pair-distribution function exhibits a minimum at the stress overshoot. The inter...

We studied the stability and dynamics of a model of a nucleosome, the fundamental unit for the packing of long DNA in eukaryotes, using a Brownian dynamics simulation. For the proper folding of a stiff polymer on a core particle, moderate attractive interaction is shown to be essentially important, which explains the empirical experimental protocol for the reconstitution of nucleosomes. The eff...

This article presents a comparative analysis of two sets of data from recent experiments on kinetics of (i) protein unfolding by mechanical force and (ii) channel gating with membrane electric potential. Both situations necessitate a continuous Brownian-dynamic view of protein conformational kinetics. We show that the discrete approach traditional to biochemical kinetics is insufficient for und...

We have investigated effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules. For that, we have performed rigid-body Brownian dynamics simulations of aqueous solutions of hen egg-white lysozyme (HEWL), at concentrations ranging from 1.25 mg/mL to 250 mg/mL and evaluated the lysozyme's self-diffusion. In the long time limit (above 1 μs), t...