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Cellular automaton simulation of pulsed field gel electrophoresis
Author(s) -
Smith Mark A.,
BarYam Yaneer
Publication year - 1993
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.1150140157
Subject(s) - radius of gyration , polymer , massively parallel , scaling , monte carlo method , cellular automaton , relaxation (psychology) , molecular dynamics , field (mathematics) , gyration , biological system , nanopore , radius , materials science , computer science , statistical physics , physics , nanotechnology , algorithm , parallel computing , geometry , psychology , social psychology , statistics , mathematics , computer security , quantum mechanics , pure mathematics , composite material , biology
We describe simulation techniques well suited to detailed investigation of the microscopic behavior of DNA during electrophoretic separation in the diffusive regime. Long polymers moving diffusively in a medium are simulated using microscopic Monte‐Carlo steps. Simulations rely upon a recently introduced two‐space abstract polymer that enables fine‐grained massively parallel simulation. Tests of the two‐space polymer dynamics are reviewed. The scaling with polymer length of the size and relaxation time of isolated polymers are shown to agree with universal scaling relations. The relaxation time is found to be significantly faster than the alternative bond‐fluctuation method. Simplicity of implementation enables simulation on cellular automaton machines (CAM) including CAM‐6, and a prototype of the new CAM‐8, as well as other massively parallel architectures. Preliminary simulations of polymers migrating under an external field through a random medium of obstacles in two dimensions are described. Two sequences of simulations are performed, with different obstacle densities corresponding to pore sizes larger and smaller than the polymer radius of gyration. In the dilute medium polymers are characteristically draped on single obstacles. In the denser medium draping across multiple obstacles results in reduced orientation in the field direction. A demonstration of rapid 90° field direction switching results in polymer motion toward the expected intermediate direction.