Related papers: Resolution exchange simulation
In order to mitigate the sample complexity of real-world reinforcement learning, common practice is to first train a policy in a simulator where samples are cheap, and then deploy this policy in the real world, with the hope that it…
We introduce polynomial couplings, a generalization of probabilistic couplings, to develop an algorithm for the computation of equivalence relations which can be interpreted as a lifting of probabilistic bisimulation to polynomial…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
A new algorithm for Monte Carlo calculation of the double exchange model is studied. The algorithm is commonly applicable to wide classes of strongly correlated electron systems which involve itinerant electrons coupled with…
This paper is about partitioning in parallel and distributed simulation. That means decomposing the simulation model into a numberof components and to properly allocate them on the execution units. An adaptive solution based on…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
This paper focuses on the derivation and simulation of mathematical models describing new plasma fraction in blood for patients undergoing simultaneous extracorporeal membrane oxygenation and therapeutic plasma exchange. Models for plasma…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
We introduce a new update scheme to systematically improve the efficiency of parallel tempering simulations. We show that by adapting the number of sweeps between replica exchanges to the canonical autocorrelation time, the average…
Continuum solvation models are becoming increasingly relevant in condensed matter simulations, allowing to characterize materials interfaces in the presence of wet electrified environments at a reduced computational cost with respect to all…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
In particle-in-cell simulations, excessive or even unfeasible computational demands can be caused by the growth of the number of particles in the course of prolific ionization or cascaded pair production due to the effects of quantum…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
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…
Computer simulators are nowadays widely used to understand complex physical systems in many areas such as aerospace, renewable energy, climate modeling, and manufacturing. One fundamental issue in the study of computer simulators is known…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…