相关论文: Parallel Tempering Algorithm for Conformational St…

This paper presents parallel-in-time state estimation methods for systems with Slow-Rate inTegrated Measurements (SRTM). Integrated measurements are common in various applications, and they appear in analysis of data resulting from…

A numerical method for the direct numerical simulation of incompressible wall turbulence in rectangular and cylindrical geometries is presented. The distinctive feature resides in its design being targeted towards an efficient…

Population annealing is a promising recent approach for Monte Carlo simulations in statistical physics, in particular for the simulation of systems with complex free-energy landscapes. It is a hybrid method, combining importance sampling…

Skin modeling is an ongoing research area that highly benefits from modern parallel algorithms. This article aims at applying shape optimization to compute cell size and arrangement for elastic energy minimization of a cellular composite…

The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…

Serial and parallel algorithms for simulation of tandem queueing systems with infinite buffers are presented, and their performance is examined. It is shown that the algorithms which are based on a simple computational procedure involve low…

We review and compare numerical methods that simultaneously control temperature while preserving the momentum, a family of particle simulation methods commonly used for the modelling of complex fluids and polymers. The class of methods…

We introduce an optimisation method for variational quantum algorithms and experimentally demonstrate a 100-fold improvement in efficiency compared to naive implementations. The effectiveness of our approach is shown by obtaining…

Simulated tempering is a widely used strategy for sampling from multimodal distributions. In this paper, we consider simulated tempering combined with an arbitrary local Markov chain Monte Carlo sampler and present a new decomposition…

An efficient numerical algorithm is presented for massively parallel simulations of dispersion-managed wavelength-division-multiplexed optical fiber systems. The algorithm is based on a weak nonlinearity approximation and independent…

Metastability is one of the major encountered obstacle when performing long molecular dynamics simulations, and many methods were developed to address this challenge. The "Parallel Replica" (ParRep) dynamics is known for allowing to…

A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular…

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…

We present new algorithms for the parallelization of Eulerian-Lagrangian interaction operations in the immersed boundary method. Our algorithms rely on two well-studied parallel primitives: key-value sort and segmented reduce. The use of…

The goal of entanglement distillation is to turn a large number of weakly entangled states into a smaller number of highly entangled ones. Practical entanglement distillation schemes offer a tradeoff between the fidelity to the target…

The heat capacity and isomer distributions of the 38 atom Lennard-Jones cluster have been calculated in the canonical ensemble using parallel tempering Monte Carlo methods. A distinct region of temperature is identified that corresponds to…

We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…

Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of…

Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond…

Approximate Bayes Computations (ABC) are used for parameter inference when the likelihood function of the model is expensive to evaluate but relatively cheap to sample from. In particle ABC, an ensemble of particles in the product space of…