Old Smoldyn versions

We have old versions of Smoldyn starting from 1.72; email support@smoldyn.org if you want one of them.

Example configuration files

S1_intro: bounce1.txt, bounce2.txt, bounce3.txt

S2_config: config.txt, configcolors.txt, configmolecs.txt, define.txt, definecolors.txt, definemolecs.txt, ifdefine.txt

S3_space: bounds1.txt, bounds2.txt

S4_molecules: diffa.txt, diffa.tif, drift.txt, diffi.tif, diffi.txt, molecule.txt, mollist.txt

S5_graphics: better.txt, graphics1.txt, graphics2.txt, graphics3.txt

S6_commands: addspecies.txt, cmdfile.txt, cmdmanipulate.txt, cmdmovesurfacemol.txt, cmdobserve.txt, cmdtime1.txt, cmdtime2.txt, meansqrdisp2.txt

S7_surfaces: absorb1.txt, absorb2.txt, absorb3.txt, cellmesh.txt, cellmeshfile.txt, diffuse2.txt, diffuse3.txt, jump1.txt, jump2.txt, jump3.txt, rafts.txt, reflect1.txt, reflect2.txt, reflect3.txt, stick2.txt, stickrate.txt, surf1.txt, surf2.txt, surf2react.txt, surf3.txt, surfrxn.txt, transmit1.txt, transmit2.txt, transmit3.txt, emitter1.txt, sphere.txt

S8_reactions: allostery.txt, allostery.tif, benchmark.txt, bireactAA.txt, bireactAB.txt, bireactABB.txt, bounce.tif, bounce.txt, crowding.tif, crowding.txt, confspread.tif, confspread.txt, equil.txt, lotvolt.tif, lotvolt.txt, lotvolt2.txt, lotvolt3.txt, unireact1.txt, unireactn.txt, wallreact.txt, zeroreact.txt

S9_compartments: compart.tif, compart.txt, compartlogic.tif, compartlogic.txt, compartrxn.txt

S10_boxes: box.txt, systemsize.txt

S11_ports: port.txt

S12_moleculizer: allostery.txt, allreceptor.txt, binding.txt, cmdtrial.txt, modifications.txt, oligo.txt, omniReceptor.txt, receptor-on-surface.txt, smallmol.txt, transformation-reactions.txt

S98_utilityprograms: out2D50.txt, sample-surface.wrl.txt, sample.txt, sphere.txt, spherebot.wrl.txt, spheretop.wrl.txt, tetrahedron.txt, tetrahedron.wrl.txt

S99_more: crowd.txt, crwd2D60.txt, neuron.txt

Published configuration files

To Smoldyn users: please help others build on your work by making any configuration files for research that you published available for others to use. Appropriate places for posting them are (1) in the supplementary information of your published paper, (2) on your webpage, and (3) here, on this webpage, by e-mailing them to us. We will happily archive any and all Smoldyn configuration files.

Python Interfaces for the Smoldyn Simulator

Singh, D. and Andrews, S.S., Bioinf. In revision, 2021

Rule-based modeling using wildcards in the Smoldyn simulator

Andrews, S.S., Methods in Mol. Biol. 1945:179-202, 2019

Particle-based stochastic simulators

Andrews, S.S., Encyclopedia of Computational Neuroscience, 2018

Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface

Andrews, S.S., Bioinformatics 33:710, 2017

Oscillations of Min-proteins in micropatterned environments: a three-dimensional particle-based stochastic simulation approach

Max Hoffmann and Ulrich S. Schwarz, Soft Matter 10:2388, 2014

Spatial and stochastic cellular modeling with the Smoldyn simulator

Andrews, S.S., In Bacterial Molecular Networks: Methods and Protocols

Ultrasensitivity in Multisite Phosphorylation of Membrane-Anchored Proteins

Dushek, O., P.A. van der Merwe, and V. Shahrezaei, Biophys. J. 100:1189-1197, 2011

Detailed Simulations of Cell Biology with Smoldyn 2.1

Andrews, S.S., N.J. Addy, R. Brent, and A.P. Arkin, PLoS Comp. Biol. 6:e1000705, 2010

Accurate particle-based simulation of adsorption, desorption and partial transmission

Andrews, S.S., Phys. Biol. 6:046015, 2009

Stochastic simulation of chemical reactions with spatial resolution and single molecule detail

Andrews, S.S. and D. Bray, Phys. Biol. 1:137, 2004