A high dimensional and accurate atomistic neural network potential energy surface (ANN-PES) that describes the interaction between one O molecule and a highly oriented pyrolytic graphite (HOPG) surface has been constructed using the open-source package (aenet). The validation of the PES is performed by paying attention to static characteristics as well as by testing its performance in reproducing previous ab initio molecular dynamics simulation results. Subsequently, the ANN-PES is used to perform quasi-classical molecular dynamics calculations of the alignment-dependent scattering of O from HOPG. The results are obtained for 200 meV O molecules with different initial alignments impinging with a polar incidence angle with respect to the surface normal of 22.5° on a thermalized (110 and 300 K) graphite surface. The choice of these initial conditions in our simulations is made to perform comparisons to recent experimental results on this system. Our results show that the scattering of O from the HOPG surface is a rather direct process, that the angular distributions are alignment dependent, and that the final translational energy of end-on molecules is around 20% lower than that of side-on molecules. Upon collision with the surface, the molecules that are initially aligned perpendicular to the surface become highly rotationally excited, whereas a very small change in the rotational state of the scattered molecules is observed for the initial parallel alignments. The latter confirms the energy transfer dependence on the stereodynamics for the present system. The results of our simulations are in overall agreement with the experimental observations regarding the shape of the angular distributions and the alignment dependence of the in-plane reflected molecules.
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Curr Opin Struct Biol
January 2025
Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA. Electronic address:
Machine-learning methods have gained significant attention in the computational chemistry community as a viable approach to molecular modeling and analysis. Recent successes in utilizing neural networks to learn atomistic force-fields which 'coarse-grain' electronic structure have inspired similar applications to the thermodynamic coarse-graining of chemical and biological systems. In this review, we discuss the current viability and challenges in using machine-learning methods to represent coarse-grained force-fields, as well as the utility of machine-learning in various aspects of coarse-grained modeling.
View Article and Find Full Text PDFMater Horiz
January 2025
School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of HBNI, Bhubaneswar, 752050, Odisha, India.
Neuromorphic and fully analog in-memory computations are promising for handling vast amounts of data with minimal energy consumption. We have synthesized and studied a series of homo-bimetallic silver purine MOFs (1D and 2D) having direct metal-metal bonding. The N7-derivatized purine ligands are designed to form bi-metallic complexes under ambient conditions, extending to a 1D or 2D metal-organic framework.
View Article and Find Full Text PDFACS Appl Mater Interfaces
December 2024
TCS Research, Sahyadri Park 2, Rajiv Gandhi Infotech Park, Hinjewadi Phase 3, Pune 411057, India.
Realization of a sustainable hydrogen economy in the future requires the development of efficient and cost-effective catalysts for its production at scale. MXenes (MX) are a class of 2D materials with 'n' layers of carbon or nitrogen (X) interleaved by 'n+1' layers of transition metal (M) and have emerged as promising materials for various applications including catalysts for hydrogen evolution reaction (HER). Their properties are intimately related to both their composition and their atomic structure.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA.
Molecular dynamics calculations have been used to explore the influence of knots on the strength of a polymer strand. In particular, the mechanism of breaking 31, 41, 51, and 52 prime knots has been studied using two very different models to represent the polymer: (1) the generic coarse-grained (CG) bead model of polymer physics and (2) a state-of-the-art machine learned atomistic neural network (NN) potential for polyethylene derived from electronic structure calculations. While there is a broad overall agreement between the results on the influence of the pulling rate on chain rupture based on the CG and atomistic NN models, for the simple 31 and 41 knots, significant differences are found for the more complex 51 and 52 knots.
View Article and Find Full Text PDFInt J Biol Macromol
December 2024
Department of Civil Engineering, National Taiwan University, Taipei 106, Taiwan; Department of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan. Electronic address:
Collagen plays a crucial role in human bodies and has a significant presence in connective tissues. As such, the impact of collagen mutations can be devastating. Osteogenesis imperfecta (OI), a rare genetic disease affecting 1 in every 15,000 to 20,000 people, is one such example characterized by brittle bones.
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