Related papers: Nudged Elastic Membranes for Constructing Reduced …
The rise of machine learning has greatly influenced the field of computational chemistry, and that of atomistic molecular dynamics simulations in particular. One of its most exciting prospects is the development of accurate,…
The goal of the present work is to obtain accurate potential energy surfaces (PES) for high-dimensional molecular systems with a small number of ${\it ab}$ ${\it initio}$ calculations in a system-agnostic way. We use probabilistic modeling…
Recent developments in vortex particle methods for simulating three-dimensional incompressible flows are presented. A lightweight, dynamic Large-Eddy Simulation model is tested, featuring a dynamic procedure that relies solely on Lagrangian…
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of…
This article is the second of a three-part series that derives a self-consistent theoretical framework of the electromechanics of arbitrarily curved lipid membranes. Existing continuum theories commonly treat lipid membranes as strictly…
An arbitrary Lagrangian--Eulerian finite element method and numerical implementation for curved and deforming lipid membranes is presented here. The membrane surface is endowed with a mesh whose in-plane motion need not depend on the…
Machine-learning-based interatomic potential energy surface (PES) models are revolutionizing the field of molecular modeling. However, although much faster than electronic structure schemes, these models suffer from costly computations via…
Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying…
Theoretical design of global optimization algorithms can profitably utilize recent statistical mechanical treatments of potential energy surfaces (PES's). Here we analyze a particular method to explain its success in locating global minima…
We propose a method that exploits sparse representation of potential energy surfaces (PES) on a polynomial basis set selected by compressed sensing. The method is useful for studies involving large numbers of PES evaluations, such as the…
In order to predict the potential energy surface (PES) from measured structure in equilibrium state, one should typically perform trial-and-error statistical thermodynamic simulation with assumed multibody interactions. Very recently, we…
There has been a veritable explosion of methods and software to perform machine-learned regression on datasets of electronic energies and forces to develop high-dimensional machine learned potential energy surfaces (ML-PESs). A major, but…
Stochastic electronic structure theories, e.g., Quantum Monte Carlo methods, enable highly accurate total energy calculations which in principle can be used to construct highly accurate potential energy surfaces. However, their stochastic…
Interfacial energy plays an important role in equilibrium morphologies of nanosized microstructures of solid materials due to the high interface-to-volume ratio, and can no longer be neglected as it does in conventional mechanics analysis.…
We present 2-D, 3-D, and spherical mesh generators for the Finite Element Method (FEM) using triangular and tetrahedral elements. The mesh nodes are treated as if they were linked by virtual springs that obey Hooke's law. Given the desired…
The modeling of solid-state transformations, such as polymorphic transitions and chemical reactions in molecular crystals, is vital for many applications including drug design or the development of new synthesis methods. However, a…
We present an isotropic ab initio (para-H$_2$)$_4$ four-body interaction potential energy surface (PES). The electronic structure calculations are performed at the correlated coupled-cluster theory level, with single, double, and…
The potential energy surface (PES) is crucial for interpreting a variety of chemical reaction processes. However, predicting accurate PESs with high-level electronic structure methods is a challenging task due to the high computational…
The immersed isogeometric Boundary Element Method is presented and applied to the simulation of underground excavations. Nonuniform rational B-splines (NURBS) are used for the accurate definition of complex geometries with few parameters.…
Non-adiabatic effects play an important role in many chemical processes. In order to study the underlying non-adiabatic potential-energy surfaces (PESs), we present a locally-constrained density-functional theory approach, which enables us…