314 Publications (Page 1 of 13)
2024
A Combined Computational and Experimental Approach to Studying Tropomyosin Kinase Receptor B Binders for Potential Treatment of Neurodegenerative Diseases. Molecules
. | Journal Article
 
Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential.
Zhao, Shan⋅Ijaodoro, Idowu⋅McGowan, Mark and Alexov, Emil
Journal of computational physics, vol. 497, January 15, 2024. | Journal Article
2023
A Fast Sine Transform Accelerated High-Order Finite Difference Method for Parabolic Problems over Irregular Domains. Journal of Scientific Computing
. | Journal Article
 
A FFT accelerated fourth order finite difference method for solving three-dimensional elliptic interface problems. Journal of Computational Physics
. | Journal Article
 
Bridging Eulerian and Lagrangian Poisson-Boltzmann solvers by ESES.
Ullah, Sheik Ahmed⋅Yang, Xin⋅Jones, Ben⋅Zhao, Shan⋅Geng, Weihua and Wei, Guo-Wei
Journal of computational chemistry, October 13, 2023. | Journal Article
 
Bridging Eulerian and Lagrangian Poisson–Boltzmann solvers by ESES. Journal of Computational Chemistry
. | Journal Article
 
Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential. Journal of Computational Physics
. | Journal Article
 
Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: A unified regularization formulation. Applied Mathematics and Computation
2022
A FFT accelerated high order finite difference method for elliptic boundary value problems over irregular domains
Ren, Yiming⋅Feng, Hongsong and Zhao, Shan
Journal of Computational Physics, vol. 448, Jan 1, 2022. | Journal Article
 
A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions
Wang, Siwen⋅Wang, Siwen⋅Wang, Siwen⋅Shao, Yuanzhen⋅Shao, Yuanzhen⋅Shao, Yuanzhen⋅Alexov, Emil⋅Alexov, Emil⋅Alexov, Emil⋅Zhao, Shan⋅Zhao, Shan and Zhao, Shan
Journal of Computational Physics, pp. 111340. | Journal Article
2021
A FFT accelerated high order finite difference method for elliptic boundary value problems over irregular domains
Journal of Computational Physics. | Journal Article
 
Alternating Direction Implicit (ADI) Methods for Solving Two-Dimensional Parabolic Interface Problems with Variable Coefficients
Li, Chuan⋅Long, Guangqing⋅Li, Yiquan and Zhao, Shan
Computation. | Journal Article
 
FFT-Based High Order Central Difference Schemes for Poisson’s Equation with Staggered Boundaries
Journal of Scientific Computing. | Journal Article
 
On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary.
Wang, Siwen⋅Wang, Siwen⋅Alexov, Emil⋅Alexov, Emil⋅Zhao, Shan and Zhao, Shan
Mathematical biosciences and engineering : MBE, vol. 18, (no. 2), pp. 1370-1405, January 21, 2021. | Journal Article
 
Regularization methods for the Poisson-Boltzmann equation: Comparison and accuracy recovery
Lee, Arum⋅Geng, Weihua and Zhao, Shan
Journal of Computational Physics, vol. 426, Feb 1, 2021. | Journal Article
2020
A fourth order finite difference method for solving elliptic interface problems with the FFT acceleration
Feng, Hongsong and Zhao, Shan
Journal of Computational Physics, vol. 419, pp. 109677. | Journal Article
 
Alternating direction ghost-fluid methods for solving the heat equation with interfaces
Li, Chuan⋅Wei, Zhihan⋅Long, Guangqing⋅Campbell, Cameron⋅Ashlyn, Stacy and Zhao, Shan
Computers & Mathematics with Applications. | Journal Article
 
A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation.
Li, Chuan⋅Li, Chuan⋅McGowan, Mark⋅McGowan, Mark⋅Alexov, Emil⋅Alexov, Emil⋅Zhao, Shan and Zhao, Shan
Mathematical biosciences and engineering : MBE, vol. 17, (no. 6), pp. 6259-6277, September 21, 2020. | Journal Article
 
Capturing the effects of explicit waters in implicit electrostatics modeling: Qualitative justification of Gaussian-based dielectric models in DelPhi.
Chakravorty, Arghya⋅Pandey, Shailesh⋅Pahari, Swagata⋅Zhao, Shan and Alexov, Emil
Journal of chemical information and modeling, March 10, 2020. | Journal Article
 
FFT-based high order central difference schemes for three-dimensional Poisson s equation with various types of boundary conditions
Journal of Computational Physics. | Journal Article
 
Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
Journal of Computational Physics. | Journal Article
2019
An augmented matched interface and boundary (MIB) method for solving elliptic interface problem
Feng, Hongsong⋅Long, Guangqing and Zhao, Shan
Journal of Computational and Applied Mathematics. | Journal Article
 
A regularization approach for solving Poisson’s equation with singular charge sources and diffuse interfaces
Applied Mathematics Letters. | Journal Article
 
A super-Gaussian Poisson–Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
Journal of Mathematical Biology. | Journal Article
2018
Accurate pKa Computation Using Matched Interface and Boundary (MIB) Method Based Poisson-Boltzmann Solver
Hu, Jingzhen⋅Zhao, Shan and Geng, Weihua
Communications in Computational Physics, vol. 23, pp. 520-539. | Journal Article