Related papers: Mesoscopic modeling of stochastic reaction-diffusi…
Several different methods exist for efficient approximation of paths in multiscale stochastic chemical systems. Another approach is to use bursts of stochastic simulation to estimate the parameters of a stochastic differential equation…
Mesoscale phenomena -- involving a level of description between the finest atomistic scale and the macroscopic continuum -- can be studied by a variation on the usual atomistic-level molecular dynamics (MD) simulation technique. In…
We propose a model to study symmetric binary fluids, based in the mesoscopic molecular simulation technique known as multiparticle collision, where space and state variables are continuous while time is discrete. We include a repulsion rule…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
This paper is concerned with analysis of coupled fractional reaction-diffusion equations. It provides analytical comparison for the fractional and regular reaction-diffusion systems. As an example, the reaction-diffusion model with cubic…
We consider the modeling of the dynamics of the chemostat at its very source. The chemostat is classically represented as a system of ordinary differential equations. Our goal is to establish a stochastic model that is valid at the scale…
Reaction dynamics involving subdiffusive species is an interesting topic with only few known results, especially when the motion of different species is characterized by different anomalous diffusion exponents. Here we study the reaction…
Complex physical dynamics can often be modeled as a Markov jump process between mesoscopic configurations. When jumps between mesoscopic states are mediated by thermodynamic reservoirs, the time-irreversibility of the jump process is a…
We revisit the mesoscopic hydrodynamic description of the dynamics of sessile partially wetting compound drops, i.e., of drops that consist of two immiscible nonvolatile partially wetting liquids and are situated on a smooth rigid solid…
At the macroscopic scale, many important models of collective motion fall into the class of kinematic flows for which both velocity and diffusion terms depend only on particle density. When total particle numbers are fixed and finite,…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
We present a modelling approach for diffusion in a complex medium characterized by a random length scale. The resulting stochastic process shows subdiffusion with a behavior in qualitative agreement with single particle tracking experiments…
We present a non-isothermal mesoscopic model for investigation of the phase transition dynamics of thermoresponsive polymers. Since this model conserves energy in the simulations, it is able to correctly capture not only the transient…
We consider the reaction zone that grows between separated regions of diffusing species $A$ and $B$ that react according to $mA+nB\to 0$, within the framework of the mean-fieldlike reaction-diffusion equations. For distances from the centre…
Biochemical reactions can happen on different time scales and also the abundance of species in these reactions can be very different from each other. Classical approaches, such as deterministic or stochastic approach, fail to account for or…
The modelling of linear and nonlinear reaction-subdiffusion processes is more subtle than normal diffusion and causes different phenomena. The resulting equations feature a spatial Laplacian with a temporal memory term through a time…
Stochastic dynamical systems arise naturally across nearly all areas of science and engineering. Typically, a dynamical system model is based on some prior knowledge about the underlying dynamics of interest in which probabilistic features…
Cell-cell adhesion plays a vital role in the development and maintenance of multicellular organisms. One of its functions is regulation of cell migration, such as occurs, e.g. during embryogenesis or in cancer. In this work, we develop a…