Papers that used or discuss Smoldyn:
Key
- research paper that used Smoldyn
- Smoldyn referenced,but not used.
2004
- 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 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]
2005
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 4th
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]
2006
- 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.
2007
- 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]
2008
- 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]
