Interface Methods for Implicitly Solvated Biomolecular Simulation

Title: Interface Methods for Implicitly Solvated Biomolecular Simulation

Speaker: Prof. Geng Weihua (Department of Mathematics , Southern Methodist University )

Time: 4:30-6:30pm, Dec.19

Location: Room 200-9, Sir Shaw Run Run Business Administration building, School of Mathematical Sciences, Yuquan Campus

Abstract: The Poisson-Boltzmann (PB) model is an effective implicit solvent approach for simulating solvated biomolecular systems. By treating the solvent with a mean field approximation and capturing the mobile ions with the Boltzmann distribution, the PB model largely reduces the degree of freedom and computational cost. However, solving the PB equation suffers from many numerical difficulties arising from interface jump conditions, complex geometry, charge singularities, and boundary conditions at infinity. In order to resolve these difficulties, we investigated interface methods under the frameworks of finite difference and boundary element. In this talk, we summarize our recent contributions in developing interface methods and provide insights for the pros and cons of these methods.  In addition, we provide several biological applications such as the calculations of free energies and pKa values using interface methods as well as a newly developed machine learning scheme for accuracy and efficiency improvements.

Contact Person: Qinghai Zhang (qinghai@zju.edu.cn)