ddX: Polarizable continuum solvation from small molecules to proteins
Polarizable continuum solvation models are popular in both, quantum chemistry and in
biophysics, though typically with different requirements for the numerical methods. However …
biophysics, though typically with different requirements for the numerical methods. However …
Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson–Boltzmann Framework: An Analytical Treatment
This work considers the interaction of two dielectric particles of arbitrary shape immersed
into a solvent containing a dissociated salt and assuming that the linearized Poisson …
into a solvent containing a dissociated salt and assuming that the linearized Poisson …
Accurate Boundary Integral Formulations for the Calculation of Electrostatic Forces with an Implicit-Solvent Model
I Addison-Smith, HV Guzman… - Journal of Chemical …, 2023 - ACS Publications
An accurate force calculation with the Poisson–Boltzmann equation is challenging, as it
requires the electric field on the molecular surface. Here we present a calculation of the …
requires the electric field on the molecular surface. Here we present a calculation of the …
Linear scaling computation of forces for the domain-decomposition linear Poisson–Boltzmann method
The Linearized Poisson–Boltzmann (LPB) equation is a popular and widely accepted model
for accounting solvent effects in computational (bio-) chemistry. In the present article, we …
for accounting solvent effects in computational (bio-) chemistry. In the present article, we …
The boundary element method for acoustic transmission with nonconforming grids
E van't Wout - Journal of Computational and Applied Mathematics, 2024 - Elsevier
Acoustic wave propagation through a homogeneous material embedded in an unbounded
medium can be formulated as a boundary integral equation and accurately solved with the …
medium can be formulated as a boundary integral equation and accurately solved with the …
Coupling finite and boundary element methods to solve the Poisson–Boltzmann equation for electrostatics in molecular solvation
Abstract The Poisson–Boltzmann equation is widely used to model electrostatics in
molecular systems. Available software packages solve it using finite difference, finite …
molecular systems. Available software packages solve it using finite difference, finite …
CUDA-accelerated protein electrostatics in linear space
Protein interactions are a key for understanding biological function and processes. Among
interaction terms, molecular electrostatics is the dominant influencing factor on the long …
interaction terms, molecular electrostatics is the dominant influencing factor on the long …