Molecular modeling and Langevin dynamics simulations of viral genome packaging and DS-DNA translocation
Over recent decades, molecular biology has been transformed by the progression towards a more physical understanding of biological macromolecules, such that familiar biochemical behavior can be understood in terms of individual macromolecular structure. Such physical insight now guides modern approaches to biotechnology and fundamental biology. Langevin dynamics simulations offer the opportunity to build upon static structural models by treating macromolecules as dynamic entities. Results will be presented of the application of Langevin dynamics simulations to viral genome packaging and voltage-induced polyelectrolyte translocation. An overview will be given demonstrating how Langevin dynamics, taken together with remarkable experimental efforts, has revealed the central importance of DNA/RNA dynamics in each of these phenomena. Based on the success of these studies, it is suggested that Langevin dynamics, in coordination with experimental efforts, represents a powerful tool for improving the fundamental understanding of various phenomena of biological and biotechnological import.