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

From: Simulation tools for particle-based reaction-diffusion dynamics 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]
  1. 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.