Related papers: Replica-Permutation Method with the Suwa-Todo Algo…
Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This…
The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we have devised a new algorithmic procedure based on the transition interface sampling technique. In the same…
Path sampling allows the study of rare events like chemical reactions, nucleation and protein folding via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short molecular dynamics (MD)…
We present the Monte Carlo with Absorbing Markov Chains (MCAMC) method for extremely long kinetic Monte Carlo simulations. The MCAMC algorithm does not modify the system dynamics. It is extremely useful for models with discrete state spaces…
We present a new method, the analytical rebridging scheme, for Monte Carlo simulation of proline-containing, cyclic peptides. The cis/trans isomerization is accommodated by allowing for two states of the amide bond. We apply our method to…
Generative models have the potential to transform the way we emulate Earth's changing climate. Previous generative approaches rely on weather-scale autoregression for climate emulation, but this is inherently slow for long climate horizons…
The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in…
In this work, Transition Probability Matrix (TPM) is proposed as a new method for extracting the features of nodes in the graph. The proposed method uses random walks to capture the connectivity structure of a node's close neighborhood. The…
Monte Carlo simulations are an essential tool in particle physics data analysis. Events are typically generated alongside weights that redistribute the cross section of the simulated process across the phase space. These weights can be…
In conventional molecular simulation, metastable structures often survive over considerable computational time, resulting in difficulties in simulating equilibrium states. In order to overcome this difficulty, here we propose a newly…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
High-performance computing, together with a neural network model trained from data generated with first-principles methods, has greatly boosted applications of \textit{ab initio} molecular dynamics in terms of spatial and temporal scales on…
We present a new implementation of radiation hydrodynamics (RHD) in the adaptive mesh refinement (AMR) code RAMSES. The multi-group radiative transfer (RT) is performed on the AMR grid with a first-order Godunov method using the M1 closure…
We present a numerical code for radiation hydrodynamics designed as a module for the freely available PLUTO code. We adopt a gray approximation and include radiative transfer following a two-moment approach by imposing the M1 closure to the…
Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual…
We briefly review the principles, mathematical bases, numerical shortcuts and applications of fast random walk (FRW) algorithms. This Monte Carlo technique allows one to simulate individual trajectories of diffusing particles in order to…
We present the spatial regime conversion method (SRCM), a novel hybrid modelling framework for simulating reaction-diffusion systems that adaptively combines stochastic discrete and deterministic continuum representations. Extending the…
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…
We present a real-space method for computing the random phase approximation (RPA) correlation energy within Kohn-Sham density functional theory, leveraging the low-rank nature of the frequency-dependent density response operator. In…
We describe a new Hybrid Monte Carlo (HMC) algorithm for dynamical overlap fermions, which improves the rate of topological index changes by adding an additional (intensive) term to the action for the molecular dynamics part of the…