The advent of machine learning potentials (MLPs) provides a unique opportunity to access simulation time scales and to directly compute physicochemical properties that are typically intractable using density functional theory (DFT). In this study, we use an active learning curriculum to train a generalizable MLP using the DeepMD-kit architecture. By using sufficiently long MLP-based molecular dynamics (MD) simulations, which provide DFT-level accuracy, we investigate the diffusion of key surface-bound adsorbates on a Ag(111) facet. Detailed analysis of the MLP/MD-calculated diffusivities sheds light on the potential shortcomings of using DFT-based nudged elastic band to estimate surface diffusion barriers. More generally, while this study is focused on a specific system, we anticipate that the underlying workflows and the resulting models can be extended to other adsorbates and other materials in the future.
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http://dx.doi.org/10.1021/acs.jpcc.4c02250 | DOI Listing |
J Phys Chem Lett
January 2025
Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), 08028 Barcelona, Spain.
Incorporation of environment and vibronic effects in simulations of optical spectra and excited state dynamics is commonly done by combining molecular dynamics with excited state calculations, which allows to estimate the spectral density describing the frequency-dependent system-bath coupling strength. The need for efficient sampling, however, usually leads to the adoption of classical force fields despite well-known inaccuracies due to the mismatch with the excited state method. Here, we present a multiscale strategy that overcomes this limitation by combining EMLE simulations based on electrostatically embedded ML potentials with the QM/MMPol polarizable embedding model to compute the excited states and spectral density of 3-methyl-indole, the chromophoric moiety of tryptophan that mediates a variety of important biological functions, in the gas phase, in water solution, and in the human serum albumin protein.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Scuola Superiore Meridionale, Napoli, Italy.
Light-driven molecular rotary motors are nanometric machines able to convert light into unidirectional motions. Several types of molecular motors have been developed to better respond to light stimuli, opening new avenues for developing smart materials ranging from nanomedicine to robotics. They have great importance in the scientific research across various disciplines, but a detailed comprehension of the underlying ultrafast photophysics immediately after photo-excitation, that is, Franck-Condon region characterization, is not fully achieved yet.
View Article and Find Full Text PDFSci Data
January 2025
IBM Research, Hursley, SO21 2JN, UK.
A significant challenge in computational chemistry is developing approximations that accelerate ab initio methods while preserving accuracy. Machine learning interatomic potentials (MLIPs) have emerged as a promising solution for constructing atomistic potentials that can be transferred across different molecular and crystalline systems. Most MLIPs are trained only on energies and forces in vacuum, while an improved description of the potential energy surface could be achieved by including the curvature of the potential energy surface.
View Article and Find Full Text PDFNat Commun
January 2025
State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, China.
Recent advances in direct electron detectors and low-dose imaging techniques have opened up captivating possibilities for real-space visualization of radiation-induced structural dynamics. This has significantly contributed to our understanding of electron-beam radiation damage in materials, serving as the foundation for modern electron microscopy. In light of these developments, the exploration of more precise and specific beam damage mechanisms, along with the development of associated descriptive models, has expanded the theoretical framework of radiation damage beyond classical mechanisms.
View Article and Find Full Text PDFSci Rep
December 2024
Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, 34132, Kassel, Germany.
The ultrafast ionic dynamics in solids induced by intense femtosecond laser excitation are controlled by two fundamentally different yet interrelated phenomena. First, the substantial generation of hot electron-hole pairs by the laser pulse modifies the interatomic bonding strength and characteristics, inducing nonthermal ionic motion. Second, incoherent electron-ion collisions facilitate thermal equilibration between electrons and ions, achieving a uniform temperature on a picosecond timescale.
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