اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدFast simulation of Brownian dynamics in a crowded environment
70
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics simulations, however these methods are extremely slow owing to the sheer number of possible collisions between particles. Here we propose a rigorous crowder-free method to dramatically increase simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the case where the reactive particles are point particles, and where they themselves occupy a volume. We use simulations of simple chemical reaction networks to confirm that our simplification is just as accurate as the original algorithm, and that it corresponds to a large speed increase.
قيم البحث
اقرأ أيضاً
Diffusion of a two component fluid is studied in the framework of differential equations, but where these equations are systematically derived from a well-defined microscopic model. The model has a finite carrying capacity imposed upon it at the meso
scopic level and this is shown to lead to non-linear cross diffusion terms that modify the conventional Fickean picture. After reviewing the derivation of the model, the experiments carried out to test the model are described. It is found that it can adequately explain the dynamics of two dense ink drops simultaneously evolving in a container filled with water. The experiment shows that molecular crowding results in the formation of a dynamical barrier that prevents the mixing of the drops. This phenomenon is successfully captured by the model. This suggests that the proposed model can be justifiably viewed as a generalization of standard diffusion to a multispecies setting, where crowding and steric interferences are taken into account.
The transport of suspended Brownian particles dc-driven along corrugated narrow channels is numerically investigated in the regime of finite damping. We show that inertial corrections cannot be neglected as long as the width of the channel bottleneck
s is smaller than an appropriate particle diffusion length, which depends on the the channel corrugation and the drive intensity. Being such a diffusion length inversely proportional to the damping constant, transport through sufficiently narrow obstructions turns out to be always sensitive to the viscosity of the suspension fluid. The inertia corrections to the transport quantifiers, mobility and diffusivity, markedly differ for smoothly and sharply corrugated channels.
We numerically investigate the transport of a suspended overdamped Brownian particle which is driven through a two-dimensional rectangular array of circular obstacles with finite radius. Two limiting cases are considered in detail, namely, when the c
onstant drive is parallel to the principal or the diagonal array axes. This corresponds to studying the Brownian transport in periodic channels with reflecting walls of different topologies. The mobility and diffusivity of the transported particles in such channels are determined as functions of the drive and the array geometric parameters. Prominent transport features, like negative differential mobilities, excess diffusion peaks, and unconventional asymptotic behaviors, are explained in terms of two distinct lengths, the size of single obstacles (trapping length) and the lattice constant of the array (local correlation length). Local correlation effects are further analyzed by continuously rotating the drive between the two limiting orientations.
The temperature dependence of the solid-liquid interfacial free energy, {gamma}, is investigated for Al and Ni at the undercooled temperature regime based on a recently developed persistent-embryo method. The atomistic description of the nucleus shap
e is obtained from molecular dynamics simulations. The computed {gamma} shows a linear dependence on the temperature. The values of {gamma} extrapolated to the melting temperature agree well with previous data obtained by the capillary fluctuation method. Using the temperature dependence of {gamma}, we estimate the nucleation free energy barrier in a wide temperature range from the classical nucleation theory. The obtained data agree very well with the results from the brute-force molecular dynamics simulations.
The Klein-Kramers equation, governing the Brownian motion of a classical particle in quantum environment under the action of an arbitrary external potential, is derived. Quantum temperature and friction operators are introduced and at large friction
the corresponding Smoluchowski equation is obtained. Introducing the Bohm quantum potential, this Smoluchowski equation is extended to describe the Brownian motion of a quantum particle in quantum environment.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
