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.)

Computer simulations of polyelectrolyte stretching and translocation

Yanbo Wang, University of Massachusetts Amherst


Over recent decades, the structure and movement of a linear, flexible polyelectrolyte is a phenomenon of fundamental interest, both in experiment and theory. The investigation of the phenomenon guides approaches to fundamental biological sciences and polymer sciences. Computer simulations offer us the opportunity to treat macromolecules as entity and build structural models. This dissertation effectively modeled the polyelectrolyte with a coarse-grained model. We applied Langevin dynamics to the modeled system with a flexible polyelectrolyte chain and counterions. The globule-coil transition of the polyelectrolyte chain was induced by changing the solvent quality or by tensions on the ends of the polyelectrolyte. With Langevin dynamics simulations, we demonstrated that the counterion condensation was changed corresponding to changes of solvent quality or stretching forces. In accordance with the theory of polymer translocation, simulations in this dissertation uncovered the nonuniversal features of polymer translocation through a short solid state nanopore. Based on these studies, we presented the dependence of the polymer translocation events and the polymer translocation time on the applied voltage and the sequence of the polymer chain. We also modeled a system of template DNA, MspA pore and phi29 DNA polymerase with coarse-grained models and applied Langevin dynamics to the simulation. This simulation investigated and uncovered how the phi29 DNA polymerase controlled the DNA sequencing under the applied external voltage. Polymer dynamics of the template DNA during the replicative activity of phi29 DNA polymerase were also investigated.^

Subject Area


Recommended Citation

Wang, Yanbo, "Computer simulations of polyelectrolyte stretching and translocation" (2013). Doctoral Dissertations Available from Proquest. AAI3603175.