Related papers: Resolution exchange simulation
In engineering, it is a common desire to couple existing simulation tools together into one big system by passing information from subsystems as parameters into the subsystems under influence. As executed at fixed time points, this data…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
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…
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…
A simple reweighting scheme is proposed for Monte Carlo simulations of interacting particle systems, permitting one to study various parameter values in a single study, and improving efficiency by an order of magnitude. Unlike earlier…
Stochastic simulators are ubiquitous in many fields of applied sciences and engineering. In the context of uncertainty quantification and optimization, a large number of simulations is usually necessary, which becomes intractable for…
Regular resolution is a refinement of the resolution proof system requiring that no variable be resolved on more than once along any path in the proof. It is known that there exist sequences of formulas that require exponential-size proofs…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper we explore the…
The computational treatment of many-electron systems capable of exchanging {electrons and nuclei} with the environment represents one of the outermost frontiers in simulation methodology. The exchanging process occurs in a large variety of…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
Simulation is used extensively in autonomous systems, particularly in robotic manipulation. By far, the most common approach is to train a controller in simulation, and then use it as an initial starting point for the real system. We…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
We present a parallel implementation of cellular automata to simulate chemical reactions on surfaces. The scaling of the computer time with the number of processors for this parallel implementation is quite close to the ideal T/P, where T…
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To address this, we have developed a novel method termed…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
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…