SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.

ABSTRACT:

Summary

Rule-based modeling is a powerful approach for studying biomolecular site dynamics. Here, we present SPATKIN, a general-purpose simulator for rule-based modeling in two spatial dimensions. The simulation algorithm is a lattice-based method that tracks Brownian motion of individual molecules and the stochastic firing of rule-defined reaction events. Because rules are used as event generators, the algorithm is network-free, meaning that it does not require to generate the complete reaction network implied by rules prior to simulation. In a simulation, each molecule (or complex of molecules) is taken to occupy a single lattice site that cannot be shared with another molecule (or complex). SPATKIN is capable of simulating a wide array of membrane-associated processes, including

SUBMITTER: Kochanczyk M 

PROVIDER: S-EPMC5860254 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature