PULSED FIELD GEL ELECTROPHORESIS SIMULATIONS IN THE DIFFUSIVE REGIME

In order to improve our ability to simulate the complex behavior of polymers, we have introduced a new “two-space” algorithm that is well suited to parallel processing. This algorithm can simulate the dynamics of abstract polymers and is suitable for modeling a variety of polymeric systems including dilute, dense, confined and grafted polymers. A medium such as a model of a gel may be implemented through the initial conditions without change in the algorithm. Using the two-space algorithm, the microscopic behavior of DNA during electrophoretic separation may be simulated in the diffusive regime. The diffusive motion of long polymers in a medium is simulated using microscopic Monte-Carlo steps. We describe preliminary simulations of polymers migrating under an external field through a random medium of obstacles in 2-dimensions. 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. Simulations of 90° field direction switching at different rates demonstrate the reorientation time and the influence of field pulse duration. The preliminary simulations were performed on a Cellular Automaton Machine, CAM-6, and further investigations are to be performed on the newly completed CAM-8, as well as other massively parallel computers.