Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs

Multiscale reaction-diffusion simulations with Smoldyn

UNLABELLED Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using ...

Particle Tracking and the Diffusion - Reaction

Particle tracking and the diffusion-reaction equation

[1] Particle tracking algorithms are very useful methods to model conservative transport in surface and subsurface hydrological systems. Recently, a novel ad hoc particle-based method was proposed to account for multicomponent reactive transport by Benson and Meerschaert (2008). This one-dimensional particle method has been shown to match theoretical predictions, but, to date, there has been no...

Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems

There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort charact...

Coarse-Grained Stochastic Particle-based Reaction-Diffusion Simulation Algorithm

In recent years, several particle-based stochastic simulation algorithms (PSSA) have been developed to study the spatially resolved dynamics of biochemical networks at a molecular scale. A challenge all these approaches have to address is to allow for simulations at cell-biologically relevant timescales without neither neglecting important spatial and biochemical properties of the simulated sys...