Related papers: The AGBNP2 Implicit Solvation Model
Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified…
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving…
Computational high-throughput studies, especially in research on high-entropy materials and catalysts, are hampered by high-dimensional composition spaces and myriad structural microstates. They present bottlenecks to the conventional use…
In this work we present a deduction of the Saint-Venant-Exner model through an asymptotic analysis of the Navier-Stokes equations. A multi-scale analysis is performed in order to take into account that the velocity of the sediment layer is…
In this study, we propose a graph neural network (GNN) model for efficiently predicting the flow behavior of non-Newtonian fluids with free surface dynamics. The numerical analysis of non-Newtonian fluids presents significant challenges, as…
This work is concerned with a simple model for a polar fluid, a Gaussian field model based on the excess density and on the polarization. It is a convenient framework to implement the dielectric properties of correlated liquids that stem…
A new approach to modelling free surface flows is developed that enables, for the first time, 3D consistent non-hydrostatic baroclinic physics that wets and dries in the large aspect ratio spatial domains that characterise geophysical…
Three different polarizable ion models for molten AgBr have been studied by molecular dynamics simulations. The three models are based on a rigid ion model (RIM) with a pair potential of the type proposed by Vashishta and Rahman for…
Volume parameterizations abound in recent literature, from the classic voxel grid to the implicit neural representation and everything in between. While implicit representations have shown impressive capacity and better memory efficiency…
The standard continuum model of a lithium-ion battery, the Doyle-Fuller-Newman (DFN) model, is computationally expensive to solve. Typically simpler models, such as the single particle model (SPM), are used to provide insight for control…
The response of polar solvents to ions and polar molecules dictates many fundamental molecular processes. To understand such electrostatically-driven solvation processes, one ideally would probe the dielectric response of a solvent to an…
Experiment Directed Simulations (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce certain experimental observables. In a previous application of…
Accurate real-time buoyancy modeling is essential for high-fidelity Autonomous Underwater Vehicle (AUV) simulations, yet NVIDIA Isaac Sim lacks a native buoyancy system, requiring external solutions for precise underwater physics. This…
Comparison of horizon-scale observations of Sgr A* and M87* with numerical simulations has provided considerable insight in their interpretation. Most of these simulations are variations of the same physical scenario consisting of a…
Ultrasound-guided drug and gene delivery (usdg) enables controlled and spatially precise delivery of drugs and macromolecules, encapsulated in microbubbles (embs) and submicron gas vesicles (gvs), to target areas such as cancer tumors. It…
In the present paper we consider a 2-D shallow-water equations (SWE) model on a $\beta$-plane solved using an alternating direction fully implicit (ADI) finite-difference scheme on a rectangular domain. The scheme was shown to be…
One essential goal of constructing coarse-grained molecular dynamics (CGMD) models is to accurately predict non-equilibrium processes beyond the atomistic scale. While a CG model can be constructed by projecting the full dynamics onto a set…
We use the general framework of summation-by-parts operators to construct conservative, energy-stable, and well-balanced semidiscretizations of two different nonlinear systems of dispersive shallow water equations with varying bathymetry:…
The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the…
We propose a new model for estimating the free energy of forming a molecular cavity in a solvent, by assuming this energy is dominated by the electrostatic energy associated with creating the static (interface) potential inside the cavity.…