Diffusion in alloys is an important class of atomic processes. However, atomistic simulations of diffusion in chemically complex solids are confronted with the timescale problem: the accessible simulation time is usually far shorter than that of experimental interest. In this work, long-timescale simulation methods are developed using reinforcement learning (RL) that extends simulation capability to match the duration of experimental interest. Two special limits, RL transition kinetics simulator (TKS) and RL low-energy states sampler (LSS), are implemented and explained in detail, while the meaning of general RL are also discussed. As a testbed, hydrogen diffusivity is computed using RL TKS in pure metals and a medium entropy alloy, CrCoNi, and compared with experiments. The algorithm can produce counter-intuitive hydrogen-vacancy cooperative motion. We also demonstrate that RL LSS can accelerate the sampling of low-energy configurations compared to the Metropolis-Hastings algorithm, using hydrogen migration to copper (111) surface as an example.
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http://dx.doi.org/10.1002/advs.202304122 | DOI Listing |
Colloids Surf B Biointerfaces
January 2025
School of Physical Science and Technology, Ningbo University, Ningbo 315211, China; Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States. Electronic address:
The formation of functional bacterial amyloids by phenol-soluble modulins (PSMs) in Staphylococcus aureus is a critical component of biofilm-associated infections, providing robust protective barriers against antimicrobial agents and immune defenses. Clarifying the molecular mechanisms of PSM self-assembly within the biofilm matrix is essential for developing strategies to disrupt biofilm integrity and combat biofilm-related infections. In this study, we analyzed the self-assembly dynamics of PSM-β1 and PSM-β2 by examining their folding and dimerization through long-timescale atomistic discrete molecular dynamics simulations.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
Aix Marseille University, CNRS, ICR, Marseille 13397, France.
Nonadiabatic dynamics simulations complement time-resolved experiments by revealing ultrafast excited-state mechanistic information in photochemical reactions. Understanding the relaxation mechanisms of photoexcited molecules finds application in energy, material, and medicinal research. However, with substantial computational costs, the nonadiabatic dynamics simulations have been restricted to ultrafast timescales, typically less than a few picoseconds, thus neglecting a wide range of photoactivated processes occurring in much longer timescales.
View Article and Find Full Text PDFJ Chem Phys
December 2024
School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.
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 shorter than ∼1μs. Slower processes require the use of enhanced sampling methods to expedite them and inference schemes to obtain the unbiased kinetics.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA.
Studying the kinetics of long-timescale rare events is a fundamental challenge in molecular simulation. To address this problem, we propose an integration of two different rare-event sampling philosophies: biased enhanced sampling and unbiased path sampling. Enhanced sampling methods, e.
View Article and Find Full Text PDFAdv Mater
November 2024
National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8565, Japan.
Recent advances in neural network-based computing have enabled human-like information processing in areas such as image classification and voice recognition. However, many neural networks run on conventional computers that operate at GHz clock frequency and consume considerable power compared to biological neural networks, such as human brains, which work with a much slower spiking rate. Although many electronic devices aiming to emulate the energy efficiency of biological neural networks have been explored, achieving long timescales while maintaining scalability remains an important challenge.
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