Simulating nonlinear dynamical transitions of single molecule DNA (INVITED)

Abstract eng:
The dynamics of DNA molecules play essential roles in the life cycle of cells. Large dynamical transitions in the conformations of single DNA molecules are required for many cellular functions including, for example, DNA transcription, replication and repair. This paper summarizes how dynamical transitions of DNA can be simulated using a nonlinear rod theory that captures the nonlinear bending and twisting of the molecule on long length/time scales. The resulting numerical solutions describe conformational changes of DNA in the context of two examples; namely 1) the dynamic relaxation of DNA supercoils induced by enzymes, and 2) the dynamic ejection of DNA from viruses during host infection.

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