Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

DOI10.1137/070692017zbMath1178.65004OpenAlexW2082221311WikidataQ33641314 ScholiaQ33641314MaRDI QIDQ3648613

Terrence J. Sejnowski, Markus Dittrich, Rex A. Kerr, Boris Kaminsky, Thomas M. Bartol, Joel R. Stiles, Jen-Chien Jack Chang, Scott B. Baden

Publication date: 27 November 2009

Published in: SIAM Journal on Scientific Computing (Search for Journal in Brave)

Full work available at URL: http://europepmc.org/articles/pmc2819163

zbMATH Keywords

algorithmschemical reactionMonte Carlo simulation methodsmicroscopic reversibilitycell simulationbiological reaction-diffusion systemsconcentration clampMCell simulation program

Mathematics Subject Classification ID

Related Items (17)

Convergence analysis and error estimate of second-order implicit–explicit scheme for Gray-Scott model ⋮ Simulation of stochastic diffusion via first exit times ⋮ Analysis and Design of Jump Coefficients in Discrete Stochastic Diffusion Models ⋮ Multiscale Simulation of Stochastic Reaction-Diffusion Networks ⋮ A Review of Stochastic and Delay Simulation Approaches in Both Time and Space in Computational Cell Biology ⋮ Connecting the dots: semi-analytical and random walk numerical solutions of the diffusion-reaction equation with stochastic initial conditions ⋮ Comparative study of metaheuristics for the curve-fitting problem: modeling neurotransmitter diffusion and synaptic receptor activation ⋮ Multiscale models and stochastic simulation methods for computing rare but key binding events in cell biology ⋮ Multiscale modeling of diffusion in a crowded environment ⋮ Efficient Green's function reaction dynamics (GFRD) simulations for diffusion-limited, reversible reactions ⋮ Accurate Particle-Based Reaction Algorithms for Fixed Timestep Simulators ⋮ Stochastic reaction-diffusion processes with embedded lower-dimensional structures ⋮ A comparison of bimolecular reaction models for stochastic reaction-diffusion systems ⋮ Fractional Gray-Scott model: well-posedness, discretization, and simulations ⋮ Galerkin finite element method for time-fractional stochastic diffusion equations ⋮ Diffusion-controlled reactions modeling in Geant4-DNA ⋮ An unstructured mesh convergent reaction-diffusion master equation for reversible reactions

Uses Software

• PPM
• DReAMM
• MCELL
• Ziggurat

This page was built for publication: Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces