Related papers: Accurate stochastic simulation of nonlinear reacti…
Based on the theory of stochastic chemical kinetics, the inherent randomness and stochasticity of biochemical reaction networks can be accurately described by discrete-state continuous-time Markov chains. The analysis of such processes is,…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
We present a spatially-extended system of chemical reactions exhibiting adaptation to time-dependent influxes of reactants. Here adaptation is defined as improved reproductive success, namely the ability of one of the many locally stable…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
Particle approximations for certain nonlinear and nonlocal reaction-diffusion equations are studied using a system of Brownian motions with killing. The system is described by a collection of i.i.d. Brownian particles where each particle is…
A stochastic model is proposed for the acceleration of non-relativistic particles yielding to energy spectra with a shape of a Weibull\textquoteright s function. Such particle distribution is found as the stationary solution of a…
A self-consistent equation to derive a discreteness-induced stochastic steady state is presented for reaction-diffusion systems. For this formalism, we use the so-called Kuramoto length, a typical distance over which a molecule diffuses in…
Reaction diffusion systems describe the behaviour of dynamic, interacting, particulate systems. Quantum stochastic processes generalise Brownian motion and Poisson processes, having operator valued It\^{o} calculus machinery. Here it is…
In many natural and industrial applications, turbulent flows encompass some form of dispersed particles. Although this type of multiphase turbulent flow is omnipresent, its numerical modeling has proven to be a remarkably challenging…
Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the…
The dynamical reaction of the particles accelerated at a shock front by the first order Fermi process can be determined within kinetic models that account for both the hydrodynamics of the shocked fluid and the transport of the accelerated…
Q-conditional symmetries (nonclassical symmetries) for the general class of two-component reaction-diffusion systems with non-constant diffusivities are studied. Using the recently introduced notion of Q-conditional symmetries of the first…
We consider diffusion-controlled release of particles from $d$-dimensional radially-symmetric geometries. A quantity commonly used to characterise such diffusive processes is the proportion of particles remaining within the geometry over…
We present a collision model for particle-particle and particle-wall interactions in interface-resolved simulations of particle-laden flows. Three types of inter-particle interactions are taken into account: (1) long- and (2) short-range…
The reaction process $A+B->C$ is modelled for ballistic reactants on an infinite line with particle velocities $v_A=c$ and $v_B=-c$ and initially segregated conditions, i.e. all A particles to the left and all B particles to the right of…
Single-particle traces of the diffusive motion of molecules, cells, or animals are by-now routinely measured, similar to stochastic records of stock prices or weather data. Deciphering the stochastic mechanism behind the recorded dynamics…
Time course measurement of single molecules on a cell surface provides detailed information on the dynamics of the molecules, which is otherwise inaccessible. To extract the quantitative information, single particle tracking (SPT) is…
The multi-level method for discrete state systems, first introduced by Anderson and Higham [Multiscale Model. Simul. 10:146--179, 2012], is a highly efficient simulation technique that can be used to elucidate statistical characteristics of…
An efficient technique to simulate turbulent particle-laden flow at high mass loadings within the four-way coupled simulation regime is presented. The technique implements large eddy simulation, discrete phase simulation, a deterministic…