Simulation tools for particle-based reaction-diffusion dynamics in continuous space

BMC Biophysics

Table 1 Particle-based reaction-diffusion simulation tools in continuous space

Tool	Cell++	ChemCell	MCell	Smoldyn	CDS	eGFRD	Klann	Rigdway	SRSim	ReaDDy
Detail Level	1/2	2	2	2	3	3	3	3	4	4
Dynamics	MC BD	MC BD	MC BD	MC BD	MC BD	GFRD	MC BD	MC BD	odL BD	odL BD
Time treatment	fixed steps	fixed steps	fixed steps	fixed steps	event-based	event-based	fixed steps	fixed steps	fixed steps	fixed steps
BD dimensions	3	2, 3	2, 3	1, 2, 3	1, 2, 3	2, 3	1, 2, 3	3	3	1, 2, 3
Particles	points	points	points	points	arb. volumetric	points	spheres, cylinders	spheres	sets ofspheres	sets ofspheres
Interaction p-p	-	-	-	-	-	-	-	-	potentials	potentials
Excluded volume	-	-	-	-	overlap rej.	overlap rej.	overlap rej.	overlap rej.	p-p repulsion	p-p repulsion
Geometry	constraints	constraints	constraints	constraints	constraints	constraints	constraints	constraints	constraints	potentials
Geo building blocks	cubes	cubes, planes	triangles	arb.	triangles	cubes, planes	arb.	cubes	cubes	arb.
Reaction dim.	3	3	2, 3	1, 2, 3	2, 3	2, 3	3	3	3	1, 2, 3
Reactions p-p	cubic subvol.	sph. subvol.	ray tracing subvol.	sph. subvol.	p-p collision	p-p collision	p-p collision	p-p collision	sph. subvol.	p-p collision
Reactions p-geo	-	-	ray tracing subvol.	sph. subvol.	p-geocollision	-	p-geocollision	p-geocollision	-	p-geocollision
First published	2006	2003	1996	2004	2010	2010	2011	2006	2010	2013
Availability	GNU GPLv2	GNU GPL	GNU GPLv2	GNU LGPL	Open Source	GNU GPL	-	-	GNU GPL	BSD 3 cl.
Reference	[5]	[6]	[12],[13]	[16],[17]	[4]	[1]	[10]	[15]	[18]	[14]

The level of modeling detail offered by the different tools is shown in the second row (1: free diffusion, 2: confined diffusion, 3: volume exclusion, 4: particle-particle potentials, see text), as well as their algorithmic details and availability. Web links: Cell++: www.compsysbio.org/lab/cellpp_details, ChemCell: chemcell.sandia.gov, M-Cell: www.mcell.org Smoldyn: www.smoldyn.org, CDS: nba.uth.tmc.edu/cds, eGFRD: www.gfrd.org, Klann:-, Rigdway: -, SRsim: www.biosys.uni-jena.de/,Members/Gerd+Gruenert/SRSim.html ReaDDy: www.readdy-project.org. Abbreviations: MC BD Monte Carlo Brownian dynamics, GFRD Greens Function Reaction Diffusion, odL BD overdamped Langevin Brownian dynamics.

ISSN: 2046-1682