应兰州大学萃英学院和数学与统计学院邀请，Alabama大学数学系赵山教授于近期访问我校并作学术报告。

题目：A pseudo-time coupled nonlinear model for biomolecular solvation simulations.

时间：2015年6月12日（周五）下午14：30

地点：观云楼813

报告人：赵山

报告人简介：Dr. Shan Zhao received the B.S. degree in mathematics from Lanzhou University, China, in 1997, and the Ph.D. degree in scientific computing from National University of Singapore, in 2003. From 2003 to 2006, he was a postdoctoral fellow with the Michigan State University. In 2006, he joined the Faculty of the Mathematics Department, University of Alabama, as an Assistant Professor. He has been promoted to the Associate Professor and Full Professor, respectively, in 2011 and 2015. Dr. Zhao’s current research interests include high-order methods for solving PDEs, computational electromagnetics and optics, high-order interface and boundary treatments, mathematical modeling of molecular surfaces in the implicit solvent theory, and fast biomolecular simulation. Dr. Zhao’s research has been supported continuously by the National Science Foundation (NSF) since 2006. He has published more than 40 peer-reviewed journal articles, and received over 1000 citations on the Google Scholar. Dr. Zhao currently serves in the editorial board for the Journal of Applied Mathematics and Molecular Based Mathematical Biology, and he has reviewed articles for more than 40 international journals.

报告提要：

When an apolar molecule, such as protein, DNA or RNA, is immersed in a polar solvent, the surface free energy minimization naturally leads to the minimal molecular surface (MMS) as the dielectric boundary for implicit solvent biomolecular simulation. In this talk, I will introduce a pseudo-time coupled partial differential equation (PDE) model to balance the polar and nonpolar contributions in the free energy functional. The energy optimization naturally couples a time dependent nonlinear Poisson-Boltzmann (NPB) equation for electrostatic potential with the potential driven geometric flow PDE for MMS generation. Such a coupling also allows for a fast numerical solution of governing nonlinear PDEs. For biomolecular surface generation, we have developed unconditionally stable alternating direction implicit (ADI) schemes for solving unscaled divergence form of the geometric flow equations. For electrostatic analysis, we have developed operator splitting ADI and locally one-dimensional (LOD) schemes based on analytical nonlinear treatment for solving the NPB equation. These fast schemes reduce 3D linear systems into 1D tridiagonal systems, which can be solved efficiently by the Thomas algorithm. Being unconditionally stable in dealing with real proteins with source singularities and nonsmooth solutions, a large time increment can be used in our computations. The resulting PB solver scales linearly with respect to the number of atoms, and is promising for studying large macromolecules.

欢迎感兴趣的师生参加

萃英学院

2015年6月8日