Professor Udayan Mohanty is supported by the Theoretical and Computational Chemistry Program and the Molecular Biophysics program to perform statistical mechanical studies on complex systems. Using the theoretical and computational machinery of statistical mechanics, Mohanty will simulate the dynamics of circularly permuted DNA molecules, study how asymmetric charge neutralization induces bending in DNA molecules, and generalize the current understanding on the degree to which electrostatic polarization of DNA is governed by charge redistribution at the ends of the molecules. The goals of these studies are to describe the behavior of curved DNA sequences in gels and to determine which forces govern DNA bending in the nucleosome. A combination of theoretical techniques is used which include density functional theory, continuum models, integral equations and computer simulations.
Sequencing and separating DNA fragments is often accomplished by electrophoretic induced migration of such fragments through gels. At the simplest level migration rates would be governed by friction coefficients and molecular weight. However fragments of certain sizes exhibit anomalous migration rates, which necessitate a more complete understanding of how size-dependent shape transitions, fragment polarization, and charge dependencies affect fragment migration. The ability to predict and understand these dependencies will aid in determining likely protein binding sites and help in unraveling DNA replication and recombination. Such studies rely on development of theoretical tools that probe the oligoelectrolyte properties of DNA. Parallel to the development of these tools is a strong educational outreach effort to high-school and undergraduate students in addition to undergraduate and graduate education.
