Statistical Mechanical Studies of Complex Systems

Udayan Mohanty教授由理论和计算化学计划和分子生物物理计划支持，对复杂系统进行统计力学研究。 使用统计力学的理论和计算机器，Mohanty将模拟循环排列的DNA分子的动力学，研究不对称电荷中和如何诱导DNA分子的弯曲，并概括目前对DNA静电极化程度的理解由分子末端的电荷再分布决定。 这些研究的目的是描述凝胶中弯曲DNA序列的行为，并确定哪些力支配核小体中的DNA弯曲。DNA分子的测序和分离通常是通过电泳诱导DNA片段在凝胶中的迁移来完成的。 在最简单的水平上，迁移率将由摩擦系数和分子量决定。 然而，某些大小的片段表现出异常的迁移率，这需要一个更完整的了解如何大小依赖的形状转变，片段极化，和电荷依赖性影响片段迁移。 预测和理解这些依赖性的能力将有助于确定可能的蛋白质结合位点，并有助于解开DNA复制和重组。 这些研究依赖于探测DNA的寡电解质性质的理论工具的发展。 在开发这些工具的同时，除了本科生和研究生教育外，还大力向高中生和本科生开展教育推广工作。

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.