Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers

Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations

(2016) I. Hepburn et al.   JOURNAL OF CHEMICAL PHYSICS

3D-printer visualization of neuron models

(2015) Robert A. McDougal et al.   Frontiers in Neuroinformatics

Dendritic diameters affect the spatial variability of intracellular calcium dynamics in computer models

(2014) Haroon Anwar et al.   Frontiers in Cellular Neuroscience

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

(2014) Daniele D’Agostino et al.   Biomed Research International

Stochastic Calcium Mechanisms Cause Dendritic Calcium Spike Variability

(2013) H. Anwar et al.   JOURNAL OF NEUROSCIENCE

Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS

(2013) Iain Hepbur et al.   Frontiers in Computational Neuroscience

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

(2012) Brian Drawert et al.   BMC Systems Biology

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

(2012) Iain Hepburn et al.   BMC Systems Biology

Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

(2012) Elijah Roberts et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Human Brain Project

(2012) Henry Markram   SCIENTIFIC AMERICAN

Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations

(2011) L. Dematte   IEEE-ACM Transactions on Computational Biology and Bioinformatics

An accelerated algorithm for discrete stochastic simulation of reaction–diffusion systems using gradient-based diffusion and tau-leaping

(2011) Wonryull Koh et al.   JOURNAL OF CHEMICAL PHYSICS

Accelerating reaction–diffusion simulations with general-purpose graphics processing units

(2010) Matthias Vigelius et al.   BIOINFORMATICS

The Role of Type 4 Phosphodiesterases in Generating Microdomains of cAMP: Large Scale Stochastic Simulations

(2010) Rodrigo F. Oliveira et al.   PLoS One

A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks

(2008) Alexander Slepoy et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING