Related papers: The ENUF Method -- Ewald Summation based on Non-Un…
Mixed quantum-classical mechanics descriptions are critical to modeling coupled electron-nuclear dynamics, i.e. non-adiabatic molecular dynamics, relevant to photochemical and photophysical processes. We argue that, for polyatomic…
By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semi-local density functional theory (DFT), and thereby furnish a more accurate and reliable description of the electronic structure in…
Simulating charged many-body systems has been a computational demanding task due to the long-range nature of electrostatic interaction. For the multi-scale model of electrolytes which combines the strengths of atomistic/continuum…
We introduce an Eulerian approach for problems involving one or more soft solids immersed in a fluid, which permits mechanical interactions between all phases. The reference map variable is exploited to simulate finite-deformation…
We evaluate the practical performance of the zero-multiple summation method (ZMM), a method for approximately calculating electrostatic interactions in molecular dynamics simulations. The performance of the ZMM is compared with that of the…
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that…
A computational fluid dynamics methodology for the simulation of electromagnetic interactions in compressible reacting flows has been formulated. The developed code, named EMI, is based on the SENGA Direct Numerical Simulation (DNS)…
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious…
Large-scale applications of energy density functional (EDF) methods depend on fast and reliable algorithms to solve the associated non-linear self-consistency problem. When dealing with large single-particle variational spaces, existing…
Current state-of-the-art generative models map noise to data distributions by matching flows or scores. A key limitation of these models is their inability to readily integrate available partial observations and additional priors. In…
We present an efficient method to perform overdamped Brownian dynamics simulations in external force fields and for particle interactions that include a hardcore part. The method applies to particle motion in one dimension, where it is…
Machine learning techniques are powerful tools for construction of emulators for complex systems. We explore different machine learning methods and conceptual methodologies, ranging from functional approximations to dynamical…
We present a simulation method that allows us to calculate the titration curves for systems undergoing protonation/deprotonation reactions -- such as charged colloidal suspensions with acidic/basic surface groups, polyelectrolytes,…
The proposed numerical method, "FLAME-slab," solves electromagnetic wave scattering problems for aperiodic slab structures by exploiting short-range regularities in these structures. The computational procedure involves special difference…
In this paper, we consider numerical approximation of an electrically conductive ferrofluid model, which consists of Navier-Stokes equations, magnetization equation, and magnetic induction equation. To solve this highly coupled, nonlinear,…
The computational bottleneck of molecular dynamics is the pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, but…
Elastic contact in hydrodynamic environments is a complex multiphysics phenomenon and can be found in applications ranging from engineering to biological systems. Understanding the intricacies of this coupled problem requires the…
Bubbly flows, as present in bubble column reactors, can be simulated using a variety of simulation techniques. In order to gain high resolution CFD methods are used to simulate a pseudo 2D bubble column using EL and EE techniques. The…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…
In molecular dynamics, penalized overdamped Langevin dynamics are used to model the motion of a set of particles that follow constraints up to a parameter $\varepsilon$. The most used schemes for simulating these dynamics are the Euler…