Detailed simulations of cell biology with Smoldyn 2.1

• Published in: PLoS computational biology Vol. 6; no. 3; p. e1000705
• Main Authors: Andrews, Steven S, Addy, Nathan J, Brent, Roger, Arkin, Adam P
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.03.2010; Public Library of Science (PLoS)
• Subjects: Algorithms; BASIC BIOLOGICAL SCIENCES; Behavior; Biochemistry & Molecular Biology; Biochemistry/Theory and Simulation; Biology; Biophysics/Theory and Simulation; Cell Biology/Cell Signaling; Cell division; Cellular proteins; Chemical reactions; Computational Biology/Computational Neuroscience; Computational Biology/Synthetic Biology; Computational Biology/Systems Biology; Computer Simulation; Cytology; Experiments; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Mathematical & Computational Biology; MATHEMATICS AND COMPUTING; Methods; Models, Biological; Operating systems; Pheromones; Physiological aspects; Programming languages; Properties; Proteases; Proteins; Proteome - metabolism; Signal Transduction - physiology; Simulation; Software; Yeast; United States; Proteome; Software; Algorithms; Signal Transduction; Models, Biological; Computer Simulation
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1000705

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.