3 papers
math.NA2025
A Nonlocal size modified Poisson-Boltzmann Model and Its Finite Element Solver for Protein in Multi-Species Ionic Solution
Dexuan Xie, Liam Jemison, Yi Jiang
The Poisson-Boltzmann (PB) model is a widely used implicit solvent model in protein simulations. Although variants, such as the size modified PB and nonlocal modified PB models, ha…
q-bio.BM2024
VDAC Solvation Free Energy Calculation by a Nonuniform Size Modified Poisson-Boltzmann Ion Channel Model
Liam Jemison, Matthew Stahl, Ranjan K. Dash +1
The Voltage-Dependent Anion Channel (VDAC) protein is the primary conduit for the regulated passage of ions and metabolites into and out of mitochondria. Calculating its solvation…
math.NA2024
An Efficient Finite Element Solver for a Nonuniform size-modified Poisson-Nernst-Planck Ion Channel Model
Dexuan Xie
This paper presents an efficient finite element iterative method for solving a nonuniform size-modified Poisson-Nernst-Planck ion channel (SMPNPIC) model, along with a SMPNPIC prog…