Interface Methods for Implicitly Solvated Biomolecular Simulation
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Title: Interface Methods for Implicitly Solvated Biomolecular Simulation
Speaker: Prof. Geng Weihua (Department ofMathematics , Southern Methodist University )
Time: 4:30-6:30pm, Dec.19
Location: Room 200-9, Sir Shaw Run RunBusiness Administration building, School of Mathematical Sciences, YuquanCampus
Abstract: The Poisson-Boltzmann (PB) modelis an effective implicit solvent approach for simulating solvated biomolecularsystems. By treating the solvent with a mean field approximation and capturingthe mobile ions with the Boltzmann distribution, the PB model largely reducesthe degree of freedom and computational cost. However, solving the PB equationsuffers from many numerical difficulties arising from interface jumpconditions, complex geometry, charge singularities, and boundary conditions atinfinity. In order to resolve these difficulties, we investigated interfacemethods under the frameworks of finite difference and boundary element. In thistalk, we summarize our recent contributions in developing interface methods andprovide insights for the pros and cons of these methods. Inaddition, we provide several biological applications such as the calculationsof free energies and pKa values using interface methods as well as a newlydeveloped machine learning scheme for accuracy and efficiency improvements.
Contact Person: Qinghai Zhang (qinghai@zju.edu.cn)