Related papers: Reaction rates for mesoscopic reaction-diffusion k…
Cataloging the complex behaviors of dynamical systems can be challenging, even when they are well-described by a simple mechanistic model. If such a system is of limited analytical tractability, brute force simulation is often the only…
We study a large deviation principle for a system of stochastic reaction--diffusion equations (SRDEs) with a separation of fast and slow components and small noise in the slow component. The derivation of the large deviation principle is…
We consider a system of reaction-diffusion equations in a bounded interval of the real line, with emphasis on the metastable dynamics, whereby the time-dependent solution approaches the steady state in an asymptotically exponentially long…
The dynamics of pulse solutions in a bistable reaction-diffusion system are studied analytically by reducing partial differential equations (PDEs) to finite-dimensional ordinary differential equations (ODEs). For the reduction, we apply the…
In this work, we consider the problem of estimating summary statistics to characterise biochemical reaction networks of interest. Such networks are often described using the framework of the Chemical Master Equation (CME). For…
A Multi-scale Boltzmann Equation (MBE) is found from the gas-kinetic theory and the direct modeling philosophy as a master equation for complex physical systems of neutral gases across all flow regimes, which locates between the continuum…
The ring-polymer molecular dynamics (RPMD) was used to calculate the thermal rate coefficients of the two-channel roaming reaction H + MgH. Both reaction channels, tight and roaming, are explicitly considered. This is a pioneering attempt…
We consider the estimation of a non-linear reaction term in the stochastic heat or more generally in a semi-linear stochastic partial differential equation (SPDE). Consistent inference is achieved by studying a small diffusivity level,…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
The existing literature on stochastic simulation of chemical reaction networks has a tendency to move as quickly as possible to the abstract formulation of the stochastic dynamics in terms of probabilities based on the concept of the…
Population dynamics are often affected by sudden environmental perturbations. Parameters of stochastic models are often imprecise due to various uncertainties. In this paper, we formulate a stochastic multimolecular biochemical reaction…
We study the numerical approximation of the stochastic heat equation with a distributional reaction term. Under a condition on the Besov regularity of the reaction term, it was proven recently that a strong solution exists and is unique in…
In synaptic molecular communication (MC), the activation of postsynaptic receptors by neurotransmitters (NTs) is governed by a stochastic reaction-diffusion process. This randomness of synaptic MC contributes to the randomness of the…
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to…
The dynamics of low-dimensional Brownian particles coupled to time-dependent driven anisotropic heavy particles (mesogens) in a uniform bath (solvent) have been described through the use of a variant of the stochastic Langevin equation. The…
Many important applications are available for nonlinear reaction-diffusion equation especially in the area of biology and engineering. Therefore a mathematical model for Lie symmetry reduction of system of nonlinear reaction-diffusion…
The reversible reactions like A+B <-> C in the many-component diffusive system affect the diffusive properties of the constituents. The effective conjugation of irreversible processes of different dimensionality takes place due to the…
Ring polymer molecular dynamics (RPMD) is an accurate method for calculating thermal chemical reaction rates. It has recently been discovered that low-temperature calculations are strongly affected by the simulation parameters. Here, for…
We expand on a previous study of fronts in finite particle number reaction-diffusion systems in the presence of a reaction rate gradient in the direction of the front motion. We study the system via reaction-diffusion equations, using the…
Trimolecular reaction models are investigated in the compartment-based (lattice-based) framework for stochastic reaction-diffusion modelling. The formulae for the first collision time and the mean reaction time are derived for the case…