Force field-based models are a Newtonian mechanics approximation of reality and are inherently noisy. Coupling models from different molecular scale domains (including single, gas-phase molecules up to multimolecule, condensed phase ensembles) is difficult, which is also the case for finding solutions that transfer well between the scales. In this contribution, we introduce a surrogate-assisted algorithm to optimize Lennard-Jones parameters for target data from different scale domains to overcome the difficulties named above. Specifically, our approach combines a surrogate-assisted global evolutionary optimization method with a presampling phase that takes advantage of one scale domain being less computationally expensive to evaluate. The algorithm's components were evaluated individually, elucidating their individual merits. Our findings show that the process of parametrizing force fields can significantly benefit from both the presampling method, which alleviates the need to have a good initial guess for the parameters, and the surrogate model, which improves efficiency.
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http://dx.doi.org/10.1021/acs.jcim.2c01231 | DOI Listing |
J Mol Model
January 2025
School of Semiconductors and Physics, North University of China, Xueyuan Road #3, 030051, Taiyuan, China.
Context: Based on the transition state theory, a molecular diffusion model in the narrow channels of Brewsterite zeolite was established. In this model, the molecular interaction at the potential barrier was simplified to only consider the repulsive potential, so that the analytical relationship between the diffusion coefficient and the temperature and the Lennard-Jones interaction parameter was derived. We used the molecular dynamics method to simulate the diffusion of four molecules, CF, CH, Ar, and Ne, in Brewsterite zeolite and evaluated the rationality of the model.
View Article and Find Full Text PDFJ Phys Chem A
December 2024
Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States.
Radical-radical reaction channels are important in the pyrolysis and oxidation chemistry of perfluoroalkyl substances (PFAS). In particular, unimolecular dissociation reactions within unbranched -perfluoroalkyl chains, and their corresponding reverse barrierless association reactions, are expected to be significant contributors to the gas-phase thermal decomposition of families of species such as perfluorinated carboxylic acids and perfluorinated sulfonic acids. Unfortunately, experimental data for these reactions are scarce and uncertain.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.
In simulations, particles are traditionally treated as rigid platforms with variable sizes, shapes, and interaction parameters. While this representation is applicable for rigid core platforms, particles consisting of soft platforms (e.g.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Dpto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
The Madrid-2019 force field was recently developed to perform simulations of electrolytes in water. The model was specifically parameterized for TIP4P/2005 water and uses scaled charges for the ions. In this work, we test the compatibility of the Madrid-2019 force field with another water model: TIP4P/Ice.
View Article and Find Full Text PDFSoft Matter
December 2024
Institute for Multiscale Simulation, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.
Quasicrystals are unique materials characterized by long-range order without periodicity. They are observed in systems such as metallic alloys, soft matter, and particle simulations. Unlike periodic crystals, which are invariant under real-space symmetry operations, quasicrystals possess symmetry that requires description by a space group in reciprocal space.
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