- Mathematical biology: Mathematical methods for molecular biology; Implicit solvent models; Biomolecular solvation analysis; Ensemble averaged electrostatics; Regularization for singular charges; PDE modeling of molecular surface; Variational multiscale models; Fast molecular surface triangulation.
- Scientific computing: Material interface problems; Electrostatic analysis; Biomolecular simulations; Computational electromagnetics and optics; Short wave problems; Heat transfer.
- Numerical Methods for PDEs: O(N logN) fast algorithms for PDEs; High order finite difference methods; Discontinuous Galerkin method; Weak Galerkin method; Wavelet collocation method; Discrete singular convolution (DSC) method; Matched interface and boundary (MIB) method; Alternating direction implicit (ADI) methods; Locally one-dimensional (LOD) methods; Operator splitting methods.
Preprints and publications
- Y. Shao, M. McGowan, S. Wang, E. Alexov, and S. Zhao, Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: a unified regularization formulation, preprint, (2021).
- Y. Ren, H. Feng, and S. Zhao, A FFT accelerated high order finite difference method for elliptic boundary value problems over irregular domains, preprint, (2021).
- T. Hazra and S. Zhao, Physics-guided multiple regression analysis for calculating electrostatic free energies of proteins in different reference states, preprint, (2021).
- S. Wang, Y. Shao, E. Alexov, and S. Zhao, A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions, preprint, (2021).
- Full list of journal publications
Research profile and citations
- Regularized Matched Interface and Boundary Poisson-Boltzmann Solver
This package contains a regularized Matched Interface and Boundary (rMIB) Poisson-Boltzmann (PB) solver and Python-based wrappers for biological applications. This package is maintained by Dr. Weihua Geng at Southern Methodist University.
- Current group members:
Mark McGowan, PhD student.
Yimin Ren, PhD student.
Sylvia Amihere, PhD student.
- Recent group alumni:
Hongsong Feng, (PhD 2021). First position after: Postdoctoral fellow, Michigan State University.
Siwen Wang, (PhD 2021). First position after: Instructor, University of Alabama.
Benjamin Jones, (MSc 2021). First position after: PhD student in Mathematics, Michigan State University.
Sheik Ahmed-Ullah, (PhD 2019). First position after: Assistant Professor, Stillman College.
Arum Lee, (MSc 2019). First position after: PhD student in Mathematics, Penn State University.
Zhihan Wei, (PhD 2018). First position after: Algorithm Engineer, Motionloft.
Tania Hazra, (PhD 2018). First position after: Assistant Professor, Misericordia University.
Lunji Song, (Visitor 2015, Postdoc 2016). Permanent position: Associate Professor, School of Mathematics and Statistics, Lanzhou University, China.
Chuan Li, (Postdoc 2015). First position after: Assistant Professor, Department of Mathematics, West Chester University.
Duc Nguyen, (PhD 2015). Assistant Professor, Department of Mathematics, University of Kentucky.
Leighton Wilson, (BSc and MSc 2015). Received Randall Research Award. First position after: PhD student in Mathematics, University of Michigan.
Wufeng Tian, (PhD 2014). Assistant Professor, University of Wisconsin Eau Claire.
Guangqing Long, (Visitor 2013). Permanent position: Professor, School of Mathematics Sciences, Nanning Normal University, China.
Pengfei Yao, (PhD 2011). First position after: Assistant Professor, Southwest Tennessee College
Guoqiao Wang, (MSc 2010). First position after: PhD candidate in Biostatistics, University of Alabama at Birmingham.
- Positions available:
Graduate research and teaching assistantship positions are available in our group. Qualified students should have a background in applied mathematics, computational mathematics, scientific computing, or a closely related area. Preference is given to self-motivated students who have research experience in the aforementioned areas and effective oral communication skills in English. Please contact me if you are qualified and interested.