Related papers: Multidimensional Replica Exchange simulations for …
We discuss multi-dimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function $E_0$ by adding any physical quantity $V$ of interest as a new…
Although the diffusion model has achieved remarkable performance in the field of image generation, its high inference delay hinders its wide application in edge devices with scarce computing resources. Therefore, many training-free sampling…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
The ability of widely distributed radar systems to capture diverse spatial scattering properties substantially improves radar imaging performance. Traditional imaging methods leverage regularized optimization techniques to reconstruct…
We investigate to what extend the replica-exchange Monte Carlo method is able to equilibrate a simple liquid in its supercooled state. We find that this method does indeed allow to generate accurately the canonical distribution function…
In replica exchange Monte Carlo (REM), tuning of the temperature set and the exchange scheduling are crucial in improving the accuracy and reducing calculation time. In multi-dimensional simulated tempering, the first order phase transition…
Numerical radiation-hydrodynamics (RHD) for non-relativistic flows is a challenging problem because it encompasses processes acting over a very broad range of timescales, and where the relative importance of these processes often varies by…
We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations[1]. Here, we demonstrate a generally…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
The control of acidity influences the structural assembly of biopolymers that are essential for a wide range of applications. Its miniaturization can increase the speed and the possibilities of combinatorial throughput for their…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
Relativistic magnetic reconnection is one of the most fundamental mechanisms considered responsible for the acceleration of relativistic particles in astrophysical jets and magnetospheres of compact objects. Understanding the properties of…
Replica exchange Monte Carlo (reMC), also known as parallel tempering, is an important technique for accelerating the convergence of the conventional Markov Chain Monte Carlo (MCMC) algorithms. However, such a method requires the evaluation…
The validation, verification, and uncertainty quantification of computationally expensive theoretical models of quantum many-body systems require the construction of fast and accurate emulators. In this work, we develop emulators for…
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…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
In this work we present a proof of concept of CUDA-capable, resistive, multi-fluid models of relativistic magnetohydrodynamics (RMHD). Resistive and multi-fluid codes for simulating models of RMHD suffer from stiff source terms, so it is…