Related papers: Adaptive pseudo-time methods for the Poisson-Boltz…
The parallel solver of the general synthetic iterative scheme (GSIS), as recently developed by Zhang \textit{et. al.} in Comput. Fluids 281 (2024) 106374, is an efficient method to find the solution of the Boltzmann equation…
Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most efficient methods are currently based on particle-mesh Ewald…
We propose and analyze an extended Fourier pseudospectral (eFP) method for the spatial discretization of the Gross-Pitaevskii equation (GPE) with low regularity potential by treating the potential in an extended window for its discrete…
Time discretization along with space discretization is important in the numerical simulation of subsurface flow applications for long run. In this paper, we derive theoretical convergence error estimates in discrete-time setting for…
The ab-initio computational treatment of electrochemical systems requires an appropriate treatment of the solid/liquid interfaces. A fully quantum mechanical treatment of the interface is computationally demanding due to the large number of…
We extend the entropy-stable oscillation-eliminating discontinuous Galerkin spectral element method (ES-OEDG) on curvilinear meshes to adaptive mesh refinement (AMR) grids with nonconforming interfaces. The formulation targets…
The Poisson-Boltzmann equation (PBE) is a relevant partial differential equation commonly used in biophysical applications to estimate the electrostatic energy of biomolecular systems immersed in electrolytic solutions. A conventional mean…
An exponential time-integrator scheme of second-order accuracy based on the predictor-corrector methodology, denoted PCEXP, is developed to solve multi-dimensional nonlinear partial differential equations pertaining to fluid dynamics. The…
Efficient simulation of nonlinear and dispersive free-surface flows governed by the incompressible Navier-Stokes equations remains a central challenge in ocean and coastal engineering. The computational bottleneck arises from solving a…
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like…
Physics-informed neural networks (PINN) is a machine learning (ML)-based method to solve partial differential equations that has gained great popularity due to the fast development of ML libraries in the last few years. The…
The purpose of the research is to find the numerical solutions to the system of time dependent nonlinear parabolic partial differential equations (PDEs) utilizing the Modified Galerkin Weighted Residual Method (MGWRM) with the help of…
Recently, a nonlinear Poisson equation has been introduced to model nonlinear and nonlocal hyperpolarization effects in electrostatic solute-solvent interaction for biomolecular solvation analysis. Due to a strong nonlinearity associated…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
The Immersed Boundary Method (IBM) is one of the popular one-fluid mixed Eulerian-Lagrangian methods to simulate motion of droplets. While the treatment of a moving complex boundary is an extremely time consuming and formidable task in a…
Discrete particle simulation, a combined approach of computational fluid dynamics and discrete methods such as DEM (Discrete Element Method), DSMC (Direct Simulation Monte Carlo), SPH (Smoothed Particle Hydrodynamics), PIC…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
It is found that the wave functions of the Gross-Pitaevskii equation (GPE) often vary significantly in different spatial regions, with some components exhibiting sharp variations while others remain smooth. Solving the GPE on a single mesh,…
Oscillatory rarefied gas flows are frequently encountered in MEMS, and their efficient numerical simulation remains a major challenge due to the time dependent nature of the problem and the high dimensionality of the Boltzmann kinetic…