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{{Infobox software
| name = Smoldyn
| logo =
| screenshot =
| caption =
| collapsible =
| author = Steve Andrews
| developer =
| released = {{Start date and age|2003|07|01}}
| latest release version = 2.71
| latest release date = {{Start date and age|2023|02|06}}
| programming language = [[C (programming language)|C]], [[C++]], [[Python (programming language)|Python]]
| operating system = [[Linux]], [[macOS]] and [[Microsoft Windows]]
| platform =
| size =
| language =
| status =
| genre =
| license = [[LGPL]]
| website = {{URL|http://www.smoldyn.org|smoldyn.org}}
}}

'''Smoldyn''' is an open-source software application for cell-scale biochemical simulations<ref name=Andrews_Arkin_2010>{{cite journal |last1=Andrews |first1=Steven S. |last2=Addy |first2= Nathan J. |last3= Brent |first3=Roger |last4=Arkin |first4=Adam P. |title=Detailed simulations of cell biology with Smoldyn 2.1 |journal=PLOS Comput. Biol. |date=2010 |volume=6 |issue=3 |pages=e1000705|doi=10.1371/journal.pcbi.1000705 |pmid=20300644 |pmc=2837389 |bibcode=2010PLSCB...6E0705A }}</ref><ref name=Andrews_2017>{{cite journal |last1=Andrews |first1=Steven S. |title=Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction, and a library interface |journal=Bioinformatics |date=2017 |volume=33 |issue=5 |pages=710–717|doi=10.1093/bioinformatics/btw700 |pmid=28365760 }}</ref>. 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<ref name=Andrews_Bray_2004>{{cite journal |last1=Andrews |first1=Steven S. |last2=Bray |first2=Dennis |title=Stochastic simulation of chemical reactions with spatial resolution and single molecule detail |journal=Physical Biology |date=2004 |volume=1 |issue=3–4 |pages=137–151|doi=10.1088/1478-3967/1/3/001 |pmid=16204833 |bibcode=2004PhBio...1..137A |s2cid=16394428 }}</ref>. Further development added support for surfaces<ref name=Andrews_Arkin_2010 />, multiscale simulation<ref name=Robinson_Erban_2015>{{cite journal |last1=Robinson |first1=Martin |last2=Andrews |first2=Steven S. |last3=Erban |first3=Radek |title=Multiscale reaction-diffusion simulations with Smoldyn |journal=Bioinformatics |date=2015 |volume=31 |issue=14 |pages=2406-2408 |doi=10.1093/bioinformatics/btv149}}</ref> molecules with excluded volume<ref name=Andrews_2017 />, rule-based modeling<ref name=Andrews_2019>{{cite journal |last1=Andrews |first1=Steven S. |title=Rule-based modeling using wildcards in the Smoldyn simulator |journal=Methods in Molecular Biology |date=2019 |volume=1945 |pages=179-202 |doi=10.1007/978-1-4939-9102-0_8}}</ref> and C/C++ and Python APIs <ref name=Singh_Andrews_2022>{{cite journal |last1=Singh |first1 =Dilawar |last2=Andrews |first2=Steven S. |title=Python interfaces for the Smoldyn simulator |journal=Bioinformatics |date=2022 |volume=38 |issue =1 |pages=291–293|doi =10.1093/bioinformatics/btab530 |pmid =34293100 }}</ref>. 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<ref name=Andrews_Arkin_2010 />, Martin Robinson<ref name=Robinson_Erban_2015 />, and Diliwar Singh<ref name=Singh_Andrews_2022 />.

== 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<ref>{{URL|https://www.smoldyn.org/SmoldynManual.pdf}}</ref>.

* '''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<ref name=Andrews_Arkin_2010 />, chemical reactions <ref name=Andrews_Bray_2004 /><ref name=Andrews_Arkin_2010 />, surface interactions <ref name=Andrews_2009>{{cite journal |last1=Andrews |first1=Steven S. |title=Accurate particle-based simulation of adsorption, desorption and partial transmission |journal=Physical Biology |volume=6 |issue=4 |pages=046015 |doi=10.1088/1478-3975/6/4/046015}}</ref>, excluded volume interactions <ref name=Andrews_2017 />, and on-surface diffusion <ref name=Andrews_2017 /> simulate with high quantitative accuracy, typically with substantially less than 1% error.
* '''[[Rule-based modeling]]''': Smoldyn supports two types of rule-based modeling. It reads the BNGL language<ref name=Andrews_2017 />, which it parses with the BioNetGen software. It also supports a method that is based on wildcard characters<ref name=Andrews_2019 />.
* '''Multi-scale simulation''': Because particle-based simulation is computationally intensive, Smoldyn also supports simulation using a spatial version of the [[Gillespie algorithm]]. These algorithms are linked together to enable both to be used in a single simulation<ref name=Robinson_Erban_2015 />.
* '''C/C++ and Python APIs''': All of Smoldyn's functions can be accessed through either a C/C++<ref name=Andrews_2017 /> or a Python<ref name=Singh_Andrews_2022 /> API.

== GPU acceleration ==
Smoldyn has been refactored twice to run on GPUs, each time offering approximately 200-fold speed improvements<ref>{{cite journal |last1=Dematte |first1=Lorenzo |title=Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations |journal=IEEE/ACM Transactions on Computational Biology and Bioinformatics |date=2012 |volume=9 |issue=3 |pages=655-667 |doi=10.1109/TCBB.2011.106}}</ref><ref>{{cite journal |last1=Gladkov |first1=Denis V. |last2=Alberts |first2=Samuel |last3= D'Souza |first3=Roshan M. |last4=Andrews |first4=Steven S. |title=Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator Using GPUs |journal=Proceedings of the 19th High Performance Computing Symposia |date=2011}}</ref>. 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]]

== References ==

{{Reflist}}

== External links ==
* [http://www.smoldyn.org Smoldyn home page]


[[Category:Systems biology]]

Smoldyn - Revision history

Ajay Kumar: Creating a new article