Related papers: Piece-wise Multipole-expansion Implicit Solvation …
The Many-Body Expansion (MBE) is a useful tool to simulate condensed phase chemical systems, often avoiding the steep computational cost of usual electronic structure methods. However, it often requires higher than 2-body terms to achieve…
Fragmentation methods such as the many-body expansion (MBE) are a common strategy to model large systems by partitioning energies into a hierarchy of decreasingly significant contributions. The number of fragments required for chemical…
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…
In this manuscript, we extend the variational multiscale enrichment (VME) method to model the dynamic response of hyperelastic materials undergoing large deformations. This approach enables the simulation of wave propagation under…
A non-empirical minimal atomic multipole expansion (MAME) defines atomic charges or higher multipoles that reproduce electrostatic potential outside molecules. MAME eliminates problems associated with redundancy and with statistical…
In this study, we utilize the many-body expansion (MBE) framework to decompose electronic structures into fragments by incrementing the virtual orbitals. Our work aims to accurately solve the ground and excited state energies of each…
A general polarizable embedded (PE) quantum mechanics/molecular mechanics scheme for periodic systems is presented, describing mutual polarization of the two subsystems. The QM system, described with density functional theory (DFT), is…
We consider adaptive finite element methods for solving a multiscale system consisting of a macroscale model comprising a system of reaction-diffusion partial differential equations coupled to a microscale model comprising a system of…
In this paper, we propose a multiscale empirical interpolation method for solving nonlinear multiscale partial differential equations. The proposed method combines empirical interpolation techniques and local multiscale methods, such as the…
We propose an efficient algorithm for the evaluation of the potential and its gradient of gravitational/electrostatic $N$-body systems, which we call particle mesh multipole method (PMMM or PM$^3$). PMMM can be understood both as an…
Highly oscillatory differential equations present significant challenges in numerical treatments. The Modulated Fourier Expansion (MFE), used as an ansatz, is a commonly employed tool as a numerical approximation method. In this article,…
The many-body expansion (MBE) is an efficient tool which has a long history of use for calculating interaction energies, binding energies, lattice energies, and so on. In the past, applications of MBE to correlation energy have been…
Energy-based fragmentation methods approximate the potential energy of a molecular system as a sum of contribution terms built from the energies of particular subsystems. Some such methods reduce to truncations of the many-body expansion…
The polarizable embedding (PE) model is a fragment-based quantum-classical approach aimed at accurate inclusion of environment effects in quantum-mechanical response property calculations. The aim of this tutorial is to give insight into…
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…
The mean field limits of systems of interacting diffusions (also called stochastic interacting particle systems (SIPS)) have been intensively studied since McKean \cite{mckean1966class}. The interacting diffusions pave a way to…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
Solving partial differential equations (PDEs) on shapes underpins many shape analysis and engineering tasks; yet, prevailing PDE solvers operate on polygonal/triangle meshes while modern 3D assets increasingly live as neural…
Partial Differential Equations (PDEs) are fundamental for modeling physical systems, yet solving them in a generic and efficient manner using machine learning-based approaches remains challenging due to limited multi-input and multi-scale…
The Modified Quasichemcial Model in the Distinguishable-Pair Approximation (MQMDPA) for manifold short-range orders in liquids has been successfully extended to multicomponent solutions. The extension is conducted by means of the…