(807d) Coarse-Grained Model of Polymer Electrophoresis Including Conformation-Dependent Mobility

Many applications of charged polymers involve applying external electric fields or field gradients to separate, stretch, and manipulate molecules. It is well-known that in free solution the mobility of DNA is approximately independent of length, which has led to other separation methods such as gel electrophoresis. It was believed that the independence on length was due to partial screening of the hydrodynamic interactions between polymer segments. Recently, it has been shown that the mechanism for this length independence is due to a cancelation of interactions that only occurs near equilibrium. If the molecule’s conformation is deformed from equilibrium, the cancelation does not occur which leads to interesting and important behaviors. Simulations and experiments using fluid flow to deform the molecule have shown that the molecule can migrate across field lines due to variations in electrophoretic mobility. Experiments and theory have also shown that electric field gradients can stretch molecules and that mobility depends on the conformation.

We have developed a coarse-grained Brownian dynamics simulation model that incorporates the change in mobility with conformation. In this way, we are able to capture the effects seen experiments and in more detailed simulations with a computationally efficient way. We will describe the development and advantages of the new model. We will also show that the new model can both capture the cross-stream migration and the stretch dependent mobility seen experimentally.