Journal
PHYSICAL REVIEW E
Volume 78, Issue 3, Pages -Publisher
AMER PHYSICAL SOC
DOI: 10.1103/PhysRevE.78.031910
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Funding
- NCRR NIH HHS [P20 RR018754-030006, RR18754, P20 RR018754] Funding Source: Medline
- NIGMS NIH HHS [R01 GM076570-01A2, R01 GM076570, GM076570] Funding Source: Medline
- NATIONAL CENTER FOR RESEARCH RESOURCES [P20RR018754] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM076570] Funding Source: NIH RePORTER
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We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the molecular components involved in a transformation, how these components change, conditions that affect whether a transformation occurs, and a rate law. The computational cost of the method, unlike conventional simulation approaches, is independent of the number of possible reactions, which need not be specified in advance or explicitly generated in a simulation. To demonstrate the method, we apply it to study the kinetics of multivalent ligand-receptor interactions. We expect the method will be useful for studying cellular signaling systems and other physical systems involving aggregation phenomena.
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