相关论文: Resolution exchange simulation with incremental co…
In statistical physics, the efficiency of tempering approaches strongly depends on ingredients such as the number of replicas $R$, reliable determination of weight factors and the set of used temperatures, ${\mathcal T}_R = \{T_1, T_2,…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
Met-enkephalin, one of the smallest opiate peptides and an important neurotransmitter, is a widely used benchmarking problem in the field of molecular simulation. Through its range of possible low-temperature conformations separated by…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
The trapped-ion quantum charge-coupled device (QCCD) architecture is a leading candidate for advanced quantum information processing. In current QCCD implementations, imperfect ion transport and anomalous heating can excite ion motion…
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…
Cosimulation methods allow combination of simulation tools of physical systems running in parallel to act as a single simulation environment for a big system. As data is passed across subsystem boundaries instead of solving the system as…
Algorithms for simulating complex physical systems or solving difficult optimization problems often resort to an annealing process. Rather than simulating the system at the temperature of interest, an annealing algorithm starts at a…
Parallel tempering, also known as replica exchange sampling, is an important method for simulating complex systems. In this algorithm simulations are conducted in parallel at a series of temperatures, and the key feature of the algorithm is…
Thermal analysis provides deeper insights into electronic chips behavior under different temperature scenarios and enables faster design exploration. However, obtaining detailed and accurate thermal profile on chip is very time-consuming…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh,…
We introduce an algorithm to systematically improve the efficiency of parallel tempering Monte Carlo simulations by optimizing the simulated temperature set. Our approach is closely related to a recently introduced adaptive algorithm that…
Because of growing interest in temperature-based sampling methods like replica exchange, this note aims to make some observations and raise some potentially important questions which we have not seen addressed sufficiently in the…
Recently, sparsity-based algorithms are proposed for super-resolution spectrum estimation. However, to achieve adequately high resolution in real-world signal analysis, the dictionary atoms have to be close to each other in frequency,…
This paper compares two approaches for investigating the near-surface composition profile that results from surface segregation in the so-called Cantor alloy, an equi-molar alloy of CoCrFeMnNi. One approach consists of atomistic computer…
We consider in this contribution a simplified idealized one-dimensional model in a nuclear core reactor coupling the diffusion equation on the neutron flux withthe enthalpy equation for the water which collects the heat produced by this…
In this study, we explore the potential of machine learning for modeling molecular electronic spectral intensities as a continuous function in a given wavelength range. Since presently available chemical space datasets provide excitation…
We propose an efficient Monte Carlo algorithm for simulating a ``hardly-relaxing" system, in which many replicas with different temperatures are simultaneously simulated and a virtual process exchanging configurations of these replica is…