Related papers: Reaction rates for reaction-diffusion kinetics on …
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…
In this paper we perform a formal asymptotic analysis on a kinetic model for reactive mixtures in order to derive a reaction-diffusion system of Maxwell-Stefan type. More specifically, we start from the kinetic model of simple reacting…
Reaction-diffusion equations with a nonlinear source have been widely used to model various systems, with particular application to biology. Here, we provide a solution technique for these types of equations in $N$-dimensions. The…
We propose a solution formula for chemical diffusion master equations of birth and death type. These equations, proposed and formalized in the recent paper [5], aim at incorporating the spatial diffusion of molecules into the description…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
With the chemical reaction rate database UMIST95 (Millar et al. 1997) we analyze how uncertainties in rate constants of gas-phase chemical reactions influence the modelling of molecular abundances in the interstellar medium. Random…
The ring polymer molecular dynamics (RPMD) rate theory is an efficient and accurate method for estimating rate coefficients of chemical reactions affected by nuclear quantum effects. The commonly used RPMD treatment of gas-phase bimolecular…
In this paper, we study a parabolic reaction diffusion system with constraints that model biofilm growth. Within a unified framework encompassing multiple numerical schemes, we derive the first general convergence rates for approximating…
We consider a single-species diffusion-limited annihilation reaction with reactants confined to a two-dimensional surface with one arbitrarily large dimension and the other comparable in size to interparticle distances. This situation could…
One-dimensional reaction-diffusion systems are mapped through a similarity transformation onto integrable (and a priori non-stochastic) quantum chains. Time-dependent properties of these chemical models can then be found exactly. The…
Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
Text-book concepts of diffusion- versus kinetic-control are well-defined for reaction-kinetics involving macroscopic concentrations of diffusive reactants that are adequately described by rate-constants -- the inverse of the…
Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice…
We consider the reaction diffusion problem and present efficient ways to discretize and precondition in the singular perturbed case when the reaction term dominates the equation. Using the concepts of optimal test norm and saddle point…
The probability distribution describing the state of a Stochastic Reaction Network evolves according to the Chemical Master Equation (CME). It is common to estimated its solution using Monte Carlo methods such as the Stochastic Simulation…
We use a generic framework, namely the gradient discretisation method (GDM), to propose a unified numerical analysis for general time-dependent convection-diffusion-reaction models. We establish novel results for convergence rates of…
The interplay between stochastic chemical reactions and diffusion can generate rich spatiotemporal patterns. While the timescale for individual reaction or diffusion events may be very fast, the timescales for organization can be much…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…