- Referenced in 31 articles
- Stochastic reaction-diffusion simulation with MesoRD. Summary: MesoRD is a tool for stochastic simulation ... chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method ... simulate the Markov process corresponding to the reaction-diffusion master equation. Availability: MesoRD is free...
- Referenced in 7 articles
- certain class of stochastic reaction-diffusion processes. Straightforward simulations of such process do not scale...
- Referenced in 25 articles
- framework for stochastic simulation of reaction-transport processes in complex geometries. We have developed URDME ... flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular ... relies on the Reaction-Diffusion Master Equation formalism to model the processes under study...
- Referenced in 2 articles
- modeling and simulation of stochastic reaction-diffusion processes on unstructured, tetrahedral (3D) and triangular ... algorithm is based on the mesoscopic reaction-diffusion master equation (RDME) model. PyURDME was originally...
- Referenced in 18 articles
- modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions ... Setting up such models is a complicated process that consists of many phases. Initial versions...
- Referenced in 4 articles
- ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments. We introduce ... mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution...
- Referenced in 6 articles
- TαS process, we simulate the moment statistics of stochastic reaction-diffusion equations with additive TαS ... density by approximating the TαS processes as CP processes; second, we directly solve the tempered...
- Referenced in 1 article
- models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale ... simulation to visualization, archiving and batch processing. Availability and implementation: Binary packages are available...
- Referenced in 0 articles
- particle reaction-diffusion systems. The program called pSpatiocyte was created bearing in mind reaction networks ... subdomain and tri-stage lockstep communication for process-level, and voxel-locking techniques for thread...
- Referenced in 37 articles
- FIDAP (A Fluid Dynamics Analysis Program). This paper...
- Referenced in 170 articles
- BoomerAMG: A parallel algebraic multigrid solver and preconditioner...
- Referenced in 370 articles
- The goal of the CGAL Open Source Project...
- Referenced in 184 articles
- Expokit provides a set of routines aimed at...
- Referenced in 56 articles
- COMSOL Multiphysics, vormals FEMLAB, ist eine Software zur...
- Referenced in 635 articles
- Gmsh is a 3D finite element grid generator...
- Referenced in 274 articles
- HSL (formerly the Harwell Subroutine Library) is a...
- Referenced in 1649 articles
- LAPACK is written in Fortran 90 and provides...
- Referenced in 5199 articles
- The result of over 30 years of cutting...
- Referenced in 396 articles
- MATCONT: Matlab software for bifurcation study of dynamical...
- Referenced in 6090 articles
- Almost any workflow involves computing results, and that...