Related papers: Function-Space Based Solution Scheme for the Size-…
We present an embedding scheme for periodic systems that facilitates the treatment of the physically important part (here the unit cell) with advanced electronic-structure methods, that are computationally too expensive for periodic…
This paper presents a novel framework for enclosing solutions of Poisson's equation based on generalized sub- and super-solutions constructed using fundamental solutions. The conventional definition of sub- and super-solutions based on…
In this article, we develop goal-oriented error indicators to drive adaptive refinement algorithms for the Poisson-Boltzmann equation. Empirical results for the solvation free energy linear functional demonstrate that goal-oriented…
We have developed efficient numerical algorithms for solving 3D steady-state Poisson-Nernst-Planck (PNP) equations with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are…
We present an algorithm for solving the self-consistency equations of the dynamical mean-field theory (DMFT) with high precision and efficiency at low temperatures. In each DMFT iteration, the impurity problem is mapped to an auxiliary…
Wereportonanewmultiscalemethodapproachforthestudyofsystemswith wide separation of short-range forces acting on short time scales and long-range forces acting on much slower scales. We consider the case of the Poisson-Boltzmann equation that…
The Poisson-Boltzmann equation (PBE) is a nonlinear elliptic PDE that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges…
The dynamical mean field theory (DMFT), which is successful in the study of strongly correlated fermions, was recently extended to boson systems [Phys. Rev. B {\textbf 77}, 235106 (2008)]. In this paper, we employ the bosonic DMFT to study…
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…
Static electric response properties of atoms and molecules are reported within the real-space Cartesian grid implementation of pseudopotential Kohn-Sham (KS) density functional theory (DFT). A detailed systematic investigation is made for a…
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…
The Poisson-Boltzmann equation (PBE) is an implicit solvent continuum model for calculating the electrostatic potential and energies of ionic solvated biomolecules. However, its numerical solution remains a significant challenge due strong…
In this paper, we propose multi-scale deep neural networks (MscaleDNNs) using the idea of radial scaling in frequency domain and activation functions with compact support. The radial scaling converts the problem of approximation of high…
Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is…
In computational biochemistry and biophysics, understanding the role of electrostatic interactions is crucial for elucidating the structure, dynamics, and function of biomolecules. The Poisson-Boltzmann (PB) equation is a foundational tool…
The Poisson-Boltzmann mean-field description of ionic solutions has been successfully used in predicting charge distributions and interactions between charged macromolecules. While the electrostatic model of charged fluids, on which the…
We present a general computational protocol for the evaluation of extensive molecular response properties in complex environments within a polarizable quantum embedding framework. The approach extends multilevel density functional theory…
In this paper, a domain decomposition method for the Poisson-Boltzmann (PB) solvation model that is widely used in computational chemistry is proposed. This method, called ddLPB for short, solves the linear Poisson-Boltzmann (LPB) equation…
We present a spectrally accurate, efficient FFT-based method for the three-dimensional free-space Poisson equation with smooth, compactly supported sources. The method adopts a super-potential formulation: we first compute the convolution…
We present a novel implementation of the complete active space self-consistent field (CASSCF) method that makes use of the many-body expanded full configuration interaction (MBE-FCI) method to incrementally approximate electronic structures…