Related papers: A simple and accurate algorithm for path integral …
Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…
Mean-field molecular dynamics based on path integrals is used to approximate canonical quantum observables for particle systems consisting of nuclei and electrons. A computational bottleneck is the sampling from the Gibbs density of the…
Performing thermodynamic tasks within finite time while minimizing thermodynamic costs is a central challenge in stochastic thermodynamics. Here, we develop a unified framework for optimizing the thermodynamic cost of performing various…
This study demonstrates the efficacy of ML-based trend inference using data from the Large Plasma Device (LAPD). The LAPD is a flexible basic plasma science device with a high discharge repetition rate (0.25-1 Hz) and reproducible plasmas…
This article proposes a novel thermostat applicable to any particle-based dynamic simulation. Each pair of particles is thermostated either (with probability P) with a pairwise Lowe-Andersen thermostat, or (with probability 1-P) with a…
We present new results of full QCD at nonzero chemical potential. In PRD 92, 094516 (2015) the complex Langevin method was shown to break down when the inverse coupling decreases and enters the transition region from the deconfined to the…
We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nos'e-Poincar'e thermostat, recently developed by Bond, Leimkuhler and Laird…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
Sampling the parameter space of artificial neural networks according to a Boltzmann distribution provides insight into the geometry of low-loss solutions and offers an alternative to conventional loss minimization for training. However,…
A novel adaptive technique for electromagnetic Particle In Cell (PIC) plasma simulations is presented here. Two main issues are identified in designing adaptive techniques for PIC simulation: first, the choice of the size of the particle…
The uniform electron gas (UEG) at finite temperature is of high current interest due to its key relevance for many applications including dense plasmas and laser excited solids. In particular, density functional theory heavily relies on…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
We demonstrate that the multicanonical approach is not restricted to Monte Carlo simulations, but can also be applied to simulation techniques such as molecular dynamics, Langevin, and hybrid Monte Carlo algorithms. The effectiveness of the…
We report a novel multi-scale simulation methodology to quantitatively predict the thermodynamic behaviour of polymer mixtures, that exhibit phases with broken orientational symmetry. Our system consists of a binary mixture of oligomers and…
This work introduces novel unconditionally stable operator splitting methods for solving the time dependent nonlinear Poisson-Boltzmann (NPB) equation for the electrostatic analysis of solvated biomolecules. In a pseudo-transient…
We study the temperature control problem for Langevin diffusions in the context of non-convex optimization. The classical optimal control of such a problem is of the bang-bang type, which is overly sensitive to errors. A remedy is to allow…
In the case of quantum systems interacting with multiple environments, the time-evolution of the reduced density matrix is described by the Liouvillian. For a variety of physical observables, the long-time limit or steady state solution is…
In our recent work [H. Zhang, F.X. Trias, A. Oliva, D. Yang, Y. Tan, Y. Sheng. PIBM: Particulate immersed boundary method for fluid-particle interaction problems. Powder Technology. 272(2015), 1-13.], a particulate immersed boundary method…