Related papers: Adaptive pseudo-time methods for the Poisson-Boltz…
We present a compatible finite element discretisation for the vertical slice compressible Euler equations, at next-to-lowest order (i.e., the pressure space is bilinear discontinuous functions). The equations are numerically integrated in…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
Recently, diffusion models have achieved great success in generative tasks. Sampling from diffusion models is equivalent to solving the reverse diffusion stochastic differential equations (SDEs) or the corresponding probability flow…
In this article we study adaptive finite element methods (AFEM) with inexact solvers for a class of semilinear elliptic interface problems. We are particularly interested in nonlinear problems with discontinuous diffusion coefficients, such…
A novel Gaussian mixture model (GMM) aided sparse Bayesian learning (SBL) framework is proposed for channel state information (CSI) estimation in orthogonal time-frequency space (OTFS) modulated systems. The key attribute of the proposed…
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, $\Delta…
The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to…
Eulerian smoothed particle hydrodynamics (Eulerian SPH) is considered as a potential meshless alternative to a traditional Eulerian mesh-based method, i.e. finite volume method (FVM), in computational fluid dynamics (CFD). While researchers…
Uncertainty Quantification for nonlinear hyperbolic problems becomes a challenging task in the vicinity of shocks. Standard intrusive methods lead to oscillatory solutions and can result in non-hyperbolic moment systems. The intrusive…
Simulations of physical phenomena are essential to the expedient design of precision components in aerospace and other high-tech industries. These phenomena are often described by mathematical models involving partial differential equations…
Recently, the general synthetic iterative scheme (GSIS) has been proposed to find the steady-state solution of the Boltzmann equation in the whole range of gas rarefaction, where its fast-converging and asymptotic-preserving properties lead…
The aim of this paper is to investigate the unstable nature of pressure computation focusing on incompressible flow modeling through the projection-based particle methods. A new approach from the original viewpoint of the momentum…
We present an efficient nodal discontinuous Galerkin method for approximating nearly incompressible flows using the Boltzmann equations. The equations are discretized with Hermite polynomials in velocity space yielding a first order…
Computational studies of electrochemical interfaces based on density-functional theory (DFT) play an increasingly important role in present research on electrochemical processes for energy conversion and storage. The homogeneous background…
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the dielectric interface between the biomolecule and solvent is…
We develop a new numerical technique for approximating solutions of the Navier-Stokes equations on moving domains. The method aims at simulating an incompressible fluid past an object whose motion is assigned a priori using a level-set…
Discharge of hazardous substances into the marine environment poses a substantial risk to both public health and the ecosystem. In such incidents, it is imperative to accurately estimate the release strength of the source and reconstruct…
Enhanced sampling and free energy calculation algorithms of the Thermodynamic Integration family (such as the Adaptive Biasing Force method, ABF) are not based on the direct computation of a free energy surface, but rather of its gradient.…
In this paper we analyze a space-time unfitted finite element method for the discretization of scalar surface partial differential equations on evolving surfaces. For higher order approximations of the evolving surface we use the technique…
In this paper we present an error analysis of an Eulerian finite element method for solving parabolic partial differential equations posed on evolving hypersurfaces in $\mathbb{R}^d$, $d=2,3$. The method employs discontinuous piecewise…