Related papers: Efficient mixed-force first-principles molecular d…
We present a method for calculating ab initio interatomic forces which scales quadratically with the size of the system and provides a physically transparent representation of the force in terms of the spatial variation of the electronic…
Multiple importance sampling (MIS) methods use a set of proposal distributions from which samples are drawn. Each sample is then assigned an importance weight that can be obtained according to different strategies. This work is motivated by…
A composite likelihood is a combination of low-dimensional likelihood objects useful in applications where the data have complex structure. Although composite likelihood construction is a crucial aspect influencing both computing and…
This paper presents a novel mass-conservative mixed multiscale method for solving flow equations in heterogeneous porous media. The media properties (the permeability) contain multiple scales and high contrast. The proposed method solves…
The density-functional theory proves that an ion-electron mixture can be treated as a one-component liquid interacting only via a {\it pairwise} interaction in the evaluation of the ion-ion radial distribution function (RDF), and provides a…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
A key ingredient for single particle diffractive imaging experiments is the successful and efficient delivery of sample. Current sample-delivery methods are based on aerosol injectors in which the samples are driven by fluid-dynamic forces.…
It is shown how mixed finite element methods for symmetric positive definite eigenvalue problems related to partial differential operators can provide guaranteed lower eigenvalue bounds. The method is based on a classical compatibility…
To leverage the redundancy between the electronic structure computed at each step of first-principles molecular dynamics, we present a data-driven modeling framework for Kohn-Sham Density Functional Theory that bypasses the explicit…
The matrix element method utilizes ab initio calculations of probability densities as powerful discriminants for processes of interest in experimental particle physics. The method has already been used successfully at previous and current…
Simulations involving the Lennard-Jones potential usually employ a cut-off at $r=2.5\sigma$. This paper investigates the possibility of reducing the cut-off. Two different cut-off implementations are compared, the standard shifted potential…
In finite mixture models, apart from underlying mixing measure, true kernel density function of each subpopulation in the data is, in many scenarios, unknown. Perhaps the most popular approach is to choose some kernel functions that we…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
High-fidelity physics simulations are powerful tools in the design and optimization of charged particle accelerators. However, the computational burden of these simulations often limits their use in practice for design optimization and…
In recent several years, the tensor force, one of the most important components of the nucleon-nucleon force, has been implemented in time-dependent density functional theories and it has been found to influence many aspects of low-energy…
Estimating force constants for crystal structures is crucial for calculating various phonon-related properties. However, this task becomes particularly challenging when dealing with a large number of atoms or when third- and higher-order…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
The efficient calculation of rare-event kinetics in complex dynamical systems, such as the rate and pathways of ligand dissociation from a protein, is a generally unsolved problem. Markov state models can systematically integrate ensembles…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
We introduce the FCHL19 representation for atomic environments in molecules or condensed-phase systems. Machine learning models based on FCHL19 are able to yield predictions of atomic forces and energies of query compounds with chemical…