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

• Figure 1: cluster.py
• Figure 2: DimesionalityEffect.py
• Callback function: integrate_with_moose.py

Rule-based modeling using wildcards in the Smoldyn simulator

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

• Note 1: lrm.txt
• Note 2: transposase.txt
• Note 3: abba.txt
• Note 4: MinDdimer.txt
• Note 5: polymer_end1.txt polymer_end2.txt polymer_mid.txt
• Note 6: expression.txt

Particle-based stochastic simulators

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

• Table 1: SmoldynBenchmark.txt SmoldynBireact.txt

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

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

• excluded volume: bounce.txt crowding.txt crowding2.txt crowding3.txt crowding4.txt
• particle tracking: tracking.txt
• species groups: speciesgroups.txt
• surface diffusion: trisphere.txt trispheretriangles.txt ribbon.txt branch.txt
• wildcards: abba.txt lrm.txt polymer_end.txt polymer_mid.txt

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

• simulation file: smoldyn_script_Fig3.txt

Spatial and stochastic cellular modeling with the Smoldyn simulator

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

• published paper: Andrews_2012.pdf
• Figure 1: Bar30.txt ellipse_12_12.txt
• Figure 2: carboxy.txt
• Box 1: box1.txt

Ultrasensitivity in Multisite Phosphorylation of Membrane-Anchored Proteins

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

• simulation file: Dushek_Shahrezaei_2011_Smoldyn.txt

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

• published paper: Andrews_Arkin_2010.pdf
• Figure 1: ecoli.txt, hopdiffpos.txt, MoroneData.txt, spine.txt
• Table 2: SuppA.pdf, bireactAB.txt, benchmark.txt
• Figure 3: SuppB.pdf, diffi.txt, unireact1.txt, bireactABB.txt, stickrate.txt
• Computational efficiency: SuppC.pdf, systemsize.txt
• Bar1 model: SuppD.pdf, Bar29.txt, ellipse_12_12.txt

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

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

• published paper: Andrews_2009.pdf
• Figure 1: Fig1A.txt Fig1B.txt
• Figure 6: Fig6.txt Fig6eq1.txt
• Figure 7: Fig7.txt CubeSurface.txt

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

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

• published paper: Andrews_Bray_2004.pdf
• Figure 8: lotvolt.txt