# Smoldyn

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Smoldyn Original author Steve Andrews Release July 1, 2003; 22 years ago (2003-07-01) Stable release 2.71 / February 6, 2023; 3 years ago (2023-02-06) Written in C, C++, Python Operating system Linux, macOS and Windows Type Simulation software License LGPL Website www.smoldyn.org Repository github.com/ssandrews/Smoldyn

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**Smoldyn** is an open-source software application for cell-scale biochemical simulations.[1][2] It uses particle-based simulation, meaning that it simulates each molecule of interest individually, in order to capture natural stochasticity and yield nanometer-scale spatial resolution. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes in similar manners as in real biochemical systems.

## History

Smoldyn was initially released in 2003 as a simulator that represented chemical reactions between diffusing particles in rectilinear volumes.[3] Further development added support for surfaces,[1] multiscale simulation[4] molecules with excluded volume,[2] rule-based modeling[5] and C/C++ and Python APIs.[6] Smoldyn development has been funded by a postdoctoral NSF grant awarded to Steve Andrews, a US DOE contract awarded to Adam Arkin, a grant from the Computational Research Laboratories (Pune, India) awarded to Upinder Bhalla, a MITRE contract and several NIH grants awarded to Roger Brent, and a Simons Foundation grant awarded to Steve Andrews.

## Development team

Smoldyn has been developed primarily by Steve Andrews, over the course of multiple research and teaching positions. Other contributors have included Nathan Addy,[1] Martin Robinson,[4] and Diliwar Singh.[6]

## Features

Smoldyn is primarily a tool for biophysics and systems biology research. It focuses on spatial scales that are between nanometers and microns. The following features descriptions are drawn from the Smoldyn documentation.[7]

- **Model definition**: Models are entered as text files that describe the system. This includes: lists of molecule species, their diffusion coefficients, and their chemical reactions; lists of surfaces and their interactions with molecules; initial molecule and surface locations; and actions that a "virtual experimenter" carries out during the simulation.

- **Real-time graphics**: Smoldyn displays the simulated system to a graphics window as the simulation runs.

- **Simulated behaviors**: Smoldyn's simulated behaviors focus on molecular diffusion, interaction with surfaces, and interactions with each other. This enables simulation of: molecular diffusion and drift, chemical reactions, excluded volume interactions, macromolecular crowding, allosteric interactions, surface adsorption and desorption, partial transmission through surfaces, on-surface diffusion, and long-range intermolecular forces.

- **Accuracy**: Smoldyn development has focused strongly on quantitative accuracy. Tests have been run and published to show that diffusion,[1] chemical reactions,[3][1] surface interactions,[8] excluded volume interactions,[2] and on-surface diffusion [2] simulate with high quantitative accuracy, typically with substantially less than 1% error.

- **[Rule-based modeling](/source/Rule-based_modeling)**: Smoldyn supports two types of rule-based modeling. It reads the BNGL language,[2] which it parses with the BioNetGen software. It also supports a method that is based on wildcard characters.[5]

- **Multi-scale simulation**: Because particle-based simulation is computationally intensive, Smoldyn also supports simulation using a spatial version of the [Gillespie algorithm](/source/Gillespie_algorithm). These algorithms are linked together to enable both to be used in a single simulation.[4]

- **C/C++ and Python APIs**: All of Smoldyn's functions can be accessed through either a C/C++[2] or a Python[6] API.

## GPU acceleration

Smoldyn has been refactored twice to run on GPUs, each time offering approximately 200-fold speed improvements.[9][10] However, neither version supports the full range of features that is available in the CPU version. They are not being supported currently.

## See also

- [List of systems biology modeling software](/source/List_of_systems_biology_modeling_software)

## References

1. ^ [***a***](#cite_ref-Andrews_Arkin_2010_1-0) [***b***](#cite_ref-Andrews_Arkin_2010_1-1) [***c***](#cite_ref-Andrews_Arkin_2010_1-2) [***d***](#cite_ref-Andrews_Arkin_2010_1-3) [***e***](#cite_ref-Andrews_Arkin_2010_1-4) Andrews, Steven S.; Addy, Nathan J.; Brent, Roger; Arkin, Adam P. (2010). ["Detailed simulations of cell biology with Smoldyn 2.1"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837389). *PLOS Comput. Biol*. **6** (3) e1000705. [Bibcode](/source/Bibcode_(identifier)):[2010PLSCB...6E0705A](https://ui.adsabs.harvard.edu/abs/2010PLSCB...6E0705A). [doi](/source/Doi_(identifier)):[10.1371/journal.pcbi.1000705](https://doi.org/10.1371%2Fjournal.pcbi.1000705). [PMC](/source/PMC_(identifier)) [2837389](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837389). [PMID](/source/PMID_(identifier)) [20300644](https://pubmed.ncbi.nlm.nih.gov/20300644).

1. ^ [***a***](#cite_ref-Andrews_2017_2-0) [***b***](#cite_ref-Andrews_2017_2-1) [***c***](#cite_ref-Andrews_2017_2-2) [***d***](#cite_ref-Andrews_2017_2-3) [***e***](#cite_ref-Andrews_2017_2-4) [***f***](#cite_ref-Andrews_2017_2-5) Andrews, Steven S. (2017). ["Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction, and a library interface"](https://doi.org/10.1093%2Fbioinformatics%2Fbtw700). *Bioinformatics*. **33** (5): 710–717. [doi](/source/Doi_(identifier)):[10.1093/bioinformatics/btw700](https://doi.org/10.1093%2Fbioinformatics%2Fbtw700). [PMID](/source/PMID_(identifier)) [28365760](https://pubmed.ncbi.nlm.nih.gov/28365760).

1. ^ [***a***](#cite_ref-Andrews_Bray_2004_3-0) [***b***](#cite_ref-Andrews_Bray_2004_3-1) Andrews, Steven S.; Bray, Dennis (2004). "Stochastic simulation of chemical reactions with spatial resolution and single molecule detail". *Physical Biology*. **1** (3–4): 137–151. [Bibcode](/source/Bibcode_(identifier)):[2004PhBio...1..137A](https://ui.adsabs.harvard.edu/abs/2004PhBio...1..137A). [doi](/source/Doi_(identifier)):[10.1088/1478-3967/1/3/001](https://doi.org/10.1088%2F1478-3967%2F1%2F3%2F001). [PMID](/source/PMID_(identifier)) [16204833](https://pubmed.ncbi.nlm.nih.gov/16204833). [S2CID](/source/S2CID_(identifier)) [16394428](https://api.semanticscholar.org/CorpusID:16394428).

1. ^ [***a***](#cite_ref-Robinson_Erban_2015_4-0) [***b***](#cite_ref-Robinson_Erban_2015_4-1) [***c***](#cite_ref-Robinson_Erban_2015_4-2) Robinson, Martin; Andrews, Steven S.; Erban, Radek (2015). ["Multiscale reaction-diffusion simulations with Smoldyn"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495299). *Bioinformatics*. **31** (14): 2406–2408. [doi](/source/Doi_(identifier)):[10.1093/bioinformatics/btv149](https://doi.org/10.1093%2Fbioinformatics%2Fbtv149). [PMC](/source/PMC_(identifier)) [4495299](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495299). [PMID](/source/PMID_(identifier)) [25788627](https://pubmed.ncbi.nlm.nih.gov/25788627).

1. ^ [***a***](#cite_ref-Andrews_2019_5-0) [***b***](#cite_ref-Andrews_2019_5-1) Andrews, Steven S. (2019). "Rule-Based Modeling Using Wildcards in the Smoldyn Simulator". *Modeling Biomolecular Site Dynamics*. Methods in Molecular Biology. Vol. 1945. pp. 179–202. [doi](/source/Doi_(identifier)):[10.1007/978-1-4939-9102-0_8](https://doi.org/10.1007%2F978-1-4939-9102-0_8). [ISBN](/source/ISBN_(identifier)) [978-1-4939-9100-6](https://en.wikipedia.org/wiki/Special:BookSources/978-1-4939-9100-6). [PMID](/source/PMID_(identifier)) [30945247](https://pubmed.ncbi.nlm.nih.gov/30945247). [S2CID](/source/S2CID_(identifier)) [92998562](https://api.semanticscholar.org/CorpusID:92998562).

1. ^ [***a***](#cite_ref-Singh_Andrews_2022_6-0) [***b***](#cite_ref-Singh_Andrews_2022_6-1) [***c***](#cite_ref-Singh_Andrews_2022_6-2) Singh, Dilawar; Andrews, Steven S. (2022). "Python interfaces for the Smoldyn simulator". *Bioinformatics*. **38** (1): 291–293. [doi](/source/Doi_(identifier)):[10.1093/bioinformatics/btab530](https://doi.org/10.1093%2Fbioinformatics%2Fbtab530). [PMID](/source/PMID_(identifier)) [34293100](https://pubmed.ncbi.nlm.nih.gov/34293100).

1. **[^](#cite_ref-7)** [www.smoldyn.org/SmoldynManual.pdf](https://www.smoldyn.org/SmoldynManual.pdf)

1. **[^](#cite_ref-Andrews_2009_8-0)** Andrews, Steven S. (2009). ["Accurate particle-based simulation of adsorption, desorption and partial transmission"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847898). *Physical Biology*. **6** (4) 046015. [Bibcode](/source/Bibcode_(identifier)):[2009PhBio...6d6015A](https://ui.adsabs.harvard.edu/abs/2009PhBio...6d6015A). [doi](/source/Doi_(identifier)):[10.1088/1478-3975/6/4/046015](https://doi.org/10.1088%2F1478-3975%2F6%2F4%2F046015). [PMC](/source/PMC_(identifier)) [2847898](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847898). [PMID](/source/PMID_(identifier)) [19910670](https://pubmed.ncbi.nlm.nih.gov/19910670).

1. **[^](#cite_ref-9)** Dematte, Lorenzo (2012). "Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations". *IEEE/ACM Transactions on Computational Biology and Bioinformatics*. **9** (3): 655–667. [doi](/source/Doi_(identifier)):[10.1109/TCBB.2011.106](https://doi.org/10.1109%2FTCBB.2011.106). [PMID](/source/PMID_(identifier)) [21788675](https://pubmed.ncbi.nlm.nih.gov/21788675). [S2CID](/source/S2CID_(identifier)) [14763924](https://api.semanticscholar.org/CorpusID:14763924).

1. **[^](#cite_ref-10)** Gladkov, Denis V.; Alberts, Samuel; D'Souza, Roshan M.; Andrews, Steven S. (2011). "Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator Using GPUs". *Proceedings of the 19th High Performance Computing Symposia*.

## External links

- [Official website](https://www.smoldyn.org/)

- [Smoldyn](https://github.com/ssandrews/Smoldyn) on [GitHub](/source/GitHub)

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Adapted from the Wikipedia article [Smoldyn](https://en.wikipedia.org/wiki/Smoldyn) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Smoldyn?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.