ArticlePLoS computational biology2010
Detailed simulations of cell biology with Smoldyn 2.1.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers.
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Who cites it
147 citing papers in PubMed.
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- MobsPy: A programming language for biochemical reaction networks.PLoS computational biology · 2025Article
- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
- Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling.Bulletin of mathematical biology · 2024Article
- AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis.PLoS computational biology · 2024Article
- Modeling Diffusion Between Regions with Different Diffusion Coefficients.IEEE transactions on molecular, biological, and multi-scale communications · 2024Article
- Particle-based simulations reveal two positive feedback loops allow relocation and stabilization of the polarity site during yeast mating.PLoS computational biology · 2023Article
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- Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.Briefings in bioinformatics · 2023Article
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- A generative model to simulate spatiotemporal dynamics of biomolecules in cells.Biological imaging · 2023Article
- Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation.PLoS computational biology · 2022Article
- On the formation of ordered protein assemblies in cell-cell interfaces.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Stochastic model of ERK-mediated progesterone receptor translocation, clustering and transcriptional activity.Scientific reports · 2022Article
87 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells.
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Registered trials
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