Accurate method for the Brownian dynamics simulation of spherical particles with hard-body interactions

Space-time histories approach to fast stochastic simulation of bimolecular reactions

Computational models of reaction-diffusion systems involving low copy numbers or strongly heterogeneous molecular spatial distributions, such as those frequently found in cellular signaling pathways, require approaches that account for the stochastic dynamics of individual particles, as opposed to approaches representing them through their average concentrations. Efforts to remedy the high computational cost associated with particle-based stochastic approaches by taking advantage of Green's functions are hampered by the need to draw random numbers from complicated, and therefore costly, non-standard probability distributions to update particle positions. Here, we introduce an approach that permits the reconstruction of entire molecular trajectories, including bimolecular encounters, in retrospect, after a simulated time step, while avoiding inefficient draws from non-standard distributions. This means that highly accurate stochastic simulations can be performed for system sizes that would be prohibitively costly to simulate with conventional Green's function based methods. The algorithm applies equally well to one, two, and three dimensional systems and can be readily extended to include deterministic forces specified by an interaction potential, such as the Coulomb potential.

Kubo formulas for dispersion in heterogeneous periodic nonequilibrium systems

We consider the dispersion properties of tracer particles moving in nonequilibrium heterogeneous periodic media. The tracer motion is described by a Fokker-Planck equation with arbitrary spatially periodic (but constant in time) local diffusion tensors and drifts, eventually with the presence of obstacles. We derive a Kubo-like formula for the time-dependent effective diffusion tensor valid in any dimension. From this general formula, we derive expressions for the late time effective diffusion tensor and drift in these systems. In addition, we find an explicit formula for the late finite-time corrections to these transport coefficients. In one dimension, we give a closed analytical formula for the transport coefficients. The formulas derived here are very general and provide a straightforward method to compute the dispersion properties in arbitrary nonequilibrium periodic advection-diffusion systems.

Diffusion-limited encounter rate in a three-dimensional lattice of connected compartments studied by Brownian-dynamics simulations

We considered the rate at which a diffusing particle encounters a target in a three-dimensional lattice of compartments with semipermeable walls. This work expands a previous theory [Li et al., Phys. Rev. Lett. 113, 028303 (2014)] for the encounter rate in the dilute limit of targets to the general case of any density of targets. We also used Brownian dynamics simulations to evaluate the approximations in the analytical theory. We find that the largest errors in the analytical theory are on the order of 10%. This work therefore demonstrates an analytical theory capable of describing the encounter rates in compartmentalized environments for any level of confinement and any target density.

Kinetics of loop formation in worm-like chain polymers

A common theoretical approach to calculating reaction kinetics is to approximate a high-dimensional conformational search with a one-dimensional diffusion along an effective reaction coordinate. We employed Brownian dynamics simulations to test the validity of this approximation for loop formation kinetics in the worm-like chain polymer model. This model is often used to describe polymers that exhibit backbone stiffness beyond the monomer length scale. We find that one-dimensional diffusion models overestimate the looping time and do not predict the quantitatively correct dependence of looping time on chain length or capture radius. Our findings highlight the difficulty of describing high-dimensional polymers with simple kinetic theories.

Brownian dynamics simulations with hard-body interactions: spherical particles

A novel approach to account for hard-body interactions in (overdamped) Brownian dynamics simulations is proposed for systems with non-vanishing force fields. The scheme exploits the analytically known transition probability for a Brownian particle on a one-dimensional half-line. The motion of a Brownian particle is decomposed into a component that is affected by hard-body interactions and into components that are unaffected. The hard-body interactions are incorporated by replacing the "affected" component of motion by the evolution on a half-line. It is discussed under which circumstances this approach is justified. In particular, the algorithm is developed and formulated for systems with space-fixed obstacles and for systems comprising spherical particles. The validity and justification of the algorithm is investigated numerically by looking at exemplary model systems of soft matter, namely at colloids in flow fields and at protein interactions. Furthermore, a thorough discussion of properties of other heuristic algorithms is carried out.

A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling

Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling.

Event-driven Langevin simulations of hard spheres

The blossoming of interest in colloids and nanoparticles has given renewed impulse to the study of hard-body systems. In particular, hard spheres have become a real test system for theories and experiments. It is therefore necessary to study the complex dynamics of such systems in presence of a solvent; disregarding hydrodynamic interactions, the simplest model is the Langevin equation. Unfortunately, standard algorithms for the numerical integration of the Langevin equation require that interactions are slowly varying during an integration time step. This is not the case for hard-body systems, where there is no clear-cut distinction between the correlation time of the noise and the time scale of the interactions. Starting first from a splitting of the Fokker-Plank operator associated with the Langevin dynamics, and then from an approximation of the two-body Green's function, we introduce and test two algorithms for the simulation of the Langevin dynamics of hard spheres.

Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations

The isotropic-nematic spinodals of solutions of rigid spherocylindrical colloids with various shape anisotropies L/D in a wide range from 10 to 60 are investigated by means of Brownian dynamics simulations. To make these simulations feasible, we developed a new event-driven algorithm that takes the excluded volume interactions between particles into account as instantaneous collisions, but neglects the hydrodynamic interactions. This algorithm is applied to dense systems of highly elongated rods and proves to be efficient. The calculated isotropic-nematic spinodals lie between the previously established binodals in the phase diagram and extrapolate for infinitely long rods to Onsager's [Ann. N. Y. Acad. Sci. 51, 627 (1949)] theoretical predictions. Moreover, we investigate the shear induced shifts of the spinodals, qualitatively confirming the theoretical prediction of the critical shear rate at which the two spinodals merge and the isotropic-nematic phase transition ceases to exist.