Related papers: Mesoscopic Model for Diffusion-Influenced Reaction…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of…
The viscosity and self-diffusion constant of particle-based mesoscale hydrodynamic methods, multi-particle collision dynamics (MPC) and dissipative particle dynamics (DPD), are investigated, both with and without angular-momentum…
A new class of multiscale scheme is presented for micro-hydrodynamic problems based on a dual representation of the fluid observables. The hybrid model is first tested against the classical flow between two parallel plates and then applied…
Dissipative particle dynamics (DPD) and multi-particle collision (MPC) dynamics are powerful tools to study mesoscale hydrodynamic phenomena accompanied by thermal fluctuations. To understand the advantages of these types of mesoscale…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
An investigation of the mesoscopic dynamics of chemical systems whose mass action equation gives rise to a deterministic chaotic attractor is carried out. A reactive lattice-gas model for the three-variable autocatalator is used to provide…
Multi-particle collision dynamics is an appealing numerical technique aiming at simulating fluids at the mesoscopic scale. It considers molecular details in a coarse-grained fashion and reproduces hydrodynamic phenomena. Here, the…
Kinetics of model catalytic processes proceeding on inhomogeneous surfaces is studied. We employ an extended mean-field model that takes into account surface inhomogeneities. The influence of surface diffusion of adsorbent on the kinetics…
Molecular dynamics simulations are carried out to investigate the diffusion behavior of penetrable-sphere model fluids characterized by a finite energy barrier $\epsilon$. The self-diffusion coefficient is evaluated from the time-dependent…
A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…
We develop a mesoscopic modeling framework for diffusion in a crowded environment, particularly targeting applications in the modeling of living cells. Through homogenization techniques we effectively coarse-grain a detailed microscopic…
We present a mesoscopic approach to granular crystal dynamics, which comprises a three-dimensional finite-element model and a one-dimensional regularized contact model. The approach investigates the role of vibrational-energy trapping…
One-dimensional reaction-diffusion models A+A -> 0, A+A -> A, and $A+B -> 0, where in the latter case like particles coagulate on encounters and move as clusters, are solved exactly with anisotropic hopping rates and assuming synchronous…
Derivation of macroscopic models for advection-diffusion processes in the presence of dominant heterogeneous (e.g., surface) reactions using homogenisation theory or volume averaging is often deemed unfeasible due to the strong coupling…
In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD).…
We develop and present a unified multi-scale model (involving three scales of spatial organisation) to study the dynamics of rigid aggregating particles suspended in a viscous fluid medium and subject to a steady poiseuille flow. At…
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…
Multiparticle collision dynamics (MPCD) enables to simulate fluid dynamics including both hydrodynamics and thermal fluctuations. Its main use concerns complex fluids, where the solvent interacts with concentrated solutes, may they be…
The transition from a microscopic model for the movement of many particles to a macroscopic continuum model for a density flow is studied. The microscopic model for the free flow is completely deterministic, described by an interaction…