Related papers: Computing Surface Reaction Rates by Adaptive Multi…

Configuration transitions of individual molecules and atoms on surfaces are traditionally described with energy barriers and attempt rates using an Arrhenius law. This approach yields consistent energy barrier values, but also attempt rates…

Calculating transition probabilities between different states of multistable climate tipping systems is computationally challenging in high-dimensional models. Targeted algorithms, such as the Trajectory-Adaptive Multilevel Splitting (TAMS)…

We use approximate Bayesian computation (ABC) to estimate unknown parameter values, as well as their uncertainties, in Reynolds-averaged Navier-Stokes (RANS) simulations of turbulent flows. The ABC method approximates posterior…

This paper presents a heterogeneous adaptive mesh refinement (AMR) framework for efficient simulation of moderately stiff reactive problems. This framework features an elaborate subcycling-in-time algorithm along with a specialized…

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…

The high computational cost of evaluating atomic interactions recently motivated the development of computationally inexpensive kinetic models, which can be parametrized from MD simulations of complex chemistry of thousands of species or…

We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…

Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in…

We revisit the problem of determining the real-frequency density response in quantum fluids via analytical continuation of imaginary-time quantum Monte Carlo data. We demonstrate that the average spectrum method (ASM) is capable of…

Markov Chain Monte Carlo (MCMC) methods, such as the Metropolis-Hastings (MH) algorithm, are widely used for Bayesian inference. One of the most important issues for any MCMC method is the convergence of the Markov chain, which depends…

Implementation details and test cases of a newly developed hydrodynamic code, AMRA, are presented. The numerical scheme exploits the adaptive mesh refinement technique coupled to modern high-resolution schemes which are suitable for…

We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…

A combination of first principle molecular dynamics (MD) simulations with a rate equation model (MD-RE approach) is presented to study the trapping and the scattering of rare gas atoms from metal surfaces. The temporal evolution of the atom…

Knowledge of surface forces is the key to understanding a large number of processes in fields ranging from physics to material science and biology. The most common method to study surfaces is dynamic atomic force microscopy (AFM). Dynamic…

Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…

Understanding the fundamental mechanisms of single-atom catalysis (SAC) is important to design systems with improved performance and stability. This is problematic, however, because single-atom active sites are extremely difficult to…

Adaptive mesh refinement (AMR) is a classical technique about local refinement in space where needed, thus effectively reducing computational costs for HPC-based physics simulations. Although AMR has been used for many years, little…

High-resolution simulations often rely on the Adaptive Mesh Resolution (AMR) technique to optimize memory consumption versus attainable precision. While this technique allows for dramatic improvements in terms of computing performance, the…

We propose a methodology for fully automated calculation of thermal rate coefficients of gas phase chemical reactions, which is based on combining the ring polymer molecular dynamics (RPMD) with the machine-learning interatomic potentials…

We propose an efficient method to compute reaction rate constants of thermally activated processes occurring in many-body systems at finite temperature. The method consists in two steps: first, paths are sampled using a transition path…