Papers that used or discussed Smoldyn:

Key

2010

Andrews, Steven S., Nathan J. Addy, Roger Brent, and Adam P. Arkin "Detailed simulations of cell biology with Smoldyn 2.1" PLoS Comp. Biol. 6:e1000705, 2010. (Description of Smoldyn program, with yeast signaling example.)
Khan, Shahid, Yixiao Zou, Asma Amjad, Ailia Gardezi, Carolyn L. Smith, Christine Winters, and Thomas S. Reese "Sequestration of CaMKII in dendritic spines by live cell imaging and in silico" Biophys. J. submitted, 2010. (Used Smoldyn.)
Arjunan, Satya Nanda Vel and Masaru Tomita "A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation" Syst. Synth. Biology 4:35-53, 2010.

Andrews, Steven S. "Accurate particle-based simulation of adsorption, desorption, and partial transmission" Phys. Biol. 6:046015 (15 pp), 2009. (Description of Smoldyn molecule-surface interaction algorithms.)
DePristo, Mark A., Lynne Chang, Ronald D. Vale, Shahid M. Khan, and Karen Lipkow "Introducing simulated cellular architecture to the quantitative analysis of fluorescent microscopy" Prog. Biophys. Mol. Biol. 100:25-32, 2009. (Uses for Smoldyn-like programs.)
Andrews, Steven S., Tuan Dinh, and Adam P. Arkin "Stochastic models of biological processes" Encyclopedia of Complexity and Systems Science Meyers, Robert (Ed.) Volume 9:8730-8749, 2009. (Review.)
Erban, Radek and S. Jonathan Chapman "Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions" Phys. Biol. 6:046001, 2009. (Derivation of reaction algorithms.)

Ray, Subhasis, Raamesh Deshpande, Niraj Dudani, and Upinder S. Bhalla "A general biological simulator: the multiscale object oriented simulation environment, MOOSE" BMC Neuroscience 9(Suppl I):P93, 2008. (Reports the integration of the Smoldyn code into the MOOSE simulation framework.) [PubMed]
Lipkow, Karen and David J. Odde "Model for protein concentration gradients in the cytoplasm" Cell and Mol. Bioeng. 1:84-92, 2008. (Used Smoldyn.)
Ridgway, Douglas, Gordon Broderick, Ana Lopez-Campistrous, Melania Ru'aini, Philip Winter, Matthew Hamilton, Pierre Bouanger, Andriy Kovalenko, and Michael J. Ellison "Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm" Biophys. J. 94:3748-3759, 2008. (Developed a different spatial simulator.) [PubMed]
Boulianne, Laurier, Sevin Al Assaad, Michel Dumontier, and Warren J. Gross "GridCell: A stochastic particle-based biological system simulator" BMC Systems Biol. 2:66, 2008. (Developed a different spatial simulation algorithm.) [PubMed]
Tindall, M.J., S.L. Porter, P.K. Maini, G. Gaglia, and J.P. Armitage "Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell" Bulletin of Mathematical Biology 70:1525-1569, 2008. (Review.) [PubMed]
Grima, Ramon and Santiago Schnell "Modelling reaction kinetics inside cells" Essay. Biochem. 45:41-56, 2008. (Review.) [PubMed]

Grima, Ramon and Santiago Schnell "A mesoscopic simulation approach for modeling intracellular reactions" J. Stat. Phys. 128:139-164, 2007. (Developed an alternative algorithm.)
Bray, Dennis, Matthew D. Levin, and Karen Lipkow "The chemotactic behavior of computer-based surrogate bacteria" Curr. Biol. 17:12-19, 2007. (Used a non-spatial simulation method.) [PubMed]
Dobrzynski, Maciej, Jordi Vidal Rodríguez, Jaap A. Kaandorp, and Joke G. Blom "Computational methods for diffusion-influenced biochemical reactions" Bioinformatics 23:1969-1977, 2007. (Comparison of the GMP, MesoRD, Smoldyn simulators, along with GFRD methods.) [PubMed]
Bhalla, Upinder "Can spatial models test spatial mechanisms of cell signaling?" Science STKE, 2007.

Lipkow, Karen "Changing cellular location of CheZ predicted by molecular simulations" PLoS Comp. Biol. 2:0301-0310, 2006. (Used Smoldyn).
Andrews, Steven S. and Adam P. Arkin. "Simulating cell biology" Curr. Biol. 16:R523-R527, 2006. (Used Smoldyn.)
Tolle, Dominic P. and Nicolas Le Novère "Particle-based stochastic simulation in systems biology" Curr. Bioinf. 1:315-320, 2006. (Review.)
Ridgway, Douglas, Gordon Broderick, and Michael J. Ellison "Accomodating space, time and randomness in network simulation" Curr. Opinion Biotechnol. 17:493-498, 2006. (Review.)
Tournier, Alexander L., Paul W. Fitzjohn, and Paul A. Bates "Probability-based model of protein-protein interactions on biological timescales" Algorithms Molec. Biol. 1:25, 2006. (Investigated an alternative reaction algorithm to the one that Smoldyn uses.)
Fange, David and Johan Elf "Noise-induced Min phenotypes in E. coli" PLoS Comput. Biol. 2:637-648, 2006. (Used Meso-RD simulation program.)
Grati, M'hamed, Mark E. Schneider, Karen Lipkow, Emanuel E. Strehler, Robert J. Wenthold, and Bechara Kachar "Rapid turnover of stereocilia membrane proteins: evidence from the trafficking and mobility of plasma membrane Ca2+-ATPase 2" The J. Neurosci. 26:6386-6395, 2006.

Andrews, Steven S. "Serial rebinding of ligands to clustered receptors as exemplified by bacterial chemotaxis" Phys. Biol. 2:111-122, 2005. (Different code, but identical algorithm.) [PubMed]
Lipkow, Karen, Steven S. Andrews, and Dennis Bray "Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli" J. Bact., 187:45-53, 2005. (Used Smoldyn.)[PubMed]
Hazelbauer, Gerald L. "Myriad molecules in motion: Simulated diffusion as a new tool to study molecular movement and interaction in a living cell" J. Bact., 187:23-25, 2005. (Commentary.)[PubMed]
Takahashi, Kouichi, Satya Nanda Vel Arjunan, Masaru Tomita "Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico" FEBS Lett., 579:1783-1788, 2005. (Review.)[PubMed]
Plimpton, Steven J. and Alex Slepoy "Microbial cell modeling via reacting diffusive particles" J. Phys.: Conf. Ser., 16:305-309, 2005. (About ChemCell.)[PubMed]
Le Novère, Nicolas and Dominic Tolle "Particle-based stochastic simulations" Proceedings of the 4^th Workshop on Computation of Biochemical Pathways and Genetic Networks. Logos, Berlin, pp. 41-45. (Review.)
Lemerle, Caroline, Barbara Di Ventura, and Luis Serrano "Space as the final frontier in stochastic simulations of biological systems" FEBS Lett. 579:1789-1794, 2005. (Review.) [PubMed]

Andrews, Steven S. and Dennis Bray "Stochastic simulation of chemical reactions with spatial resolution and single molecule detail" Phys. Biol. 1:137-151, 2004. (Description and analysis of Smoldyn reaction and diffusion algorithms). [PubMed]
Ander, M., P. Beltrao, B. Di Ventura, J. Ferkinghoff-Borg, M. Foglierini, A. Kaplan, C. Lemerle, I. Tomás-Oliveira, and L. Serrano "SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks" Syst. Biol., 1:129-138, 2004. (Alternate software for spatial stochastic simulation.) [PubMed]
Rivas, Germán, Frank Ferrone, and Judith Herzfeld "Life in a crowded world" EMBO Reports 5:23-27, 2004. (Meeting report.) [PubMed]