Off-campus UMass Amherst users: To download dissertations, please use the following link to log into our proxy server with your UMass Amherst user name and password.

Non-UMass Amherst users, please click the view more button below to purchase a copy of this dissertation from Proquest.

(Some titles may also be available free of charge in our Open Access Dissertation Collection, so please check there first.)

Molecular modeling and Langevin dynamics simulations of viral genome packaging and DS-DNA translocation

Christopher Forrey, University of Massachusetts Amherst


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.

Subject Area

Polymer chemistry

Recommended Citation

Forrey, Christopher, "Molecular modeling and Langevin dynamics simulations of viral genome packaging and DS-DNA translocation" (2008). Doctoral Dissertations Available from Proquest. AAI3336954.