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We present an inference scheme of long timescale, non-exponential kinetics from Molecular Dynamics simulations accelerated by stochastic resetting. Standard simulations provide valuable insight into chemical processes but are limited to timescales sh
Externí odkaz:
http://arxiv.org/abs/2410.09805
Stochastic resetting, the procedure of stopping and re-initializing random processes, has recently emerged as a powerful tool for accelerating processes ranging from queuing systems to molecular simulations. However, its usefulness is severely limite
Externí odkaz:
http://arxiv.org/abs/2409.14419
Autor:
Church, Jonathan R., Blumer, Ofir, Keidar, Tommer D., Ploutno, Leo, Reuveni, Shlomi, Hirshberg, Barak
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible using standard simulati
Externí odkaz:
http://arxiv.org/abs/2409.10115
Controlling the size distribution in the nucleation of copper particles is crucial for achieving nanocrystals with desired physical and chemical properties. However, their synthesis involves a complex system of solvents, ligands, and copper precursor
Externí odkaz:
http://arxiv.org/abs/2402.02568
Infrequent Metadynamics is a popular method to obtain the rate of long timescale processes from accelerated simulations. The inference procedure is based on rescaling the first-passage times of Metadynamics trajectories using a bias-dependent acceler
Externí odkaz:
http://arxiv.org/abs/2401.14237
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective variables are us
Externí odkaz:
http://arxiv.org/abs/2307.06037
Publikováno v:
J. Phys. Chem. Lett. 2022, 13, 11230
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. This is o
Externí odkaz:
http://arxiv.org/abs/2210.00558
Akademický článek
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Autor:
Blumer O; School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel., Reuveni S; School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.; The Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel.; The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel., Hirshberg B; School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.; The Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel.; The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel.
Publikováno v:
Journal of chemical theory and computation [J Chem Theory Comput] 2024 May 14; Vol. 20 (9), pp. 3484-3491. Date of Electronic Publication: 2024 Apr 26.
Autor:
Elishav O; Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA.; School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel., Blumer O; School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel., Vanderlick TK; Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA., Hirshberg B; School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.; The Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel.; The Ratner Center for Single Molecule Science, Tel Aviv University, Tel Aviv 6997801, Israel.; The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel.
Publikováno v:
The Journal of chemical physics [J Chem Phys] 2024 Apr 28; Vol. 160 (16).