Current machine learning (ML) models aimed at learning force fields are plagued by their high computational cost at every integration time step. We describe a number of practical and computationally efficient strategies to parametrize traditional force fields for molecular liquids from ML: the particle decomposition ansatz to two- and three-body force fields, the use of kernel-based ML models that incorporate physical symmetries, the incorporation of switching functions close to the cutoff, and the use of covariant meshing to boost the training set size. Results are presented for model molecular liquids: pairwise Lennard-Jones, three-body Stillinger-Weber, and bottom-up coarse-graining of water. Here, covariant meshing proves to be an efficient strategy to learn canonically averaged instantaneous forces. We show that molecular dynamics simulations with tabulated two- and three-body ML potentials are computationally efficient and recover two- and three-body distribution functions. Many-body representations, decomposition, and kernel regression schemes are all implemented in the open-source software package VOTCA.
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http://dx.doi.org/10.1021/acs.jctc.9b01256 | DOI Listing |
Commun Chem
January 2025
Department of Materials Science and Metallurgical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, India.
Liquid cell transmission electron microscopy (LCTEM) is a powerful technique for investigating crystallisation dynamics with nanometre spatial resolution. However, probing phenomena occurring in liquids while mixing two precursor solutions has proven extremely challenging, requiring sophisticated liquid cell designs. Here, we demonstrate that introducing and withdrawing solvents in sequence makes it possible to maintain optimal imaging conditions while mixing liquids in a commercial liquid cell.
View Article and Find Full Text PDFNat Protoc
January 2025
Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ, USA.
Sensitive, rapid and label-free biochemical sensors are needed for many applications. In this protocol, we describe biochemical detection using FLOWER (frequency locked optical whispering evanescent resonator)-a technique that we have used to detect single protein molecules in aqueous solution as well as exosomes, ribosomes and low part-per-trillion concentrations of volatile organic compounds. Whispering gallery mode microtoroid resonators confine light for extended time periods (hundreds of nanoseconds).
View Article and Find Full Text PDFNat Commun
January 2025
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
The advancement of an effective hydrogen liberation technology from liquid organic hydrogen carriers, particularly cycloalkanes such as cyclohexane and methylcyclohexane, holds significance in realizing a hydrogen-centric society. However, the attainment of homogeneous catalytic acceptorless dehydrogenation characterized by elevated selectivity for thorough aromatization under mild conditions remains unrealized. In this study, a catalyst system, facilitated by a double hydrogen atom transfer processes, has been devised for the catalytic acceptorless dehydrogenation of inert cycloalkanes at ambient temperature under visible light irradiation.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Department of Chemical Engineering, IIT Gandhinagar, Gandhinagar, Gujarat 382055, India.
We compare the structures of polymer globules, composed of flexible polymer chains, with liquid droplets made of nonbonded monomers of the same polymer in poor solvents. This comparison is performed in three different poor solvents, with and without the addition of cosolvents. Molecular dynamics simulations are used to analyze the properties of the polymer globules, while semigrand canonical Monte Carlo simulations are used to form metastable liquid droplets of nonbonded monomers through homogeneous nucleation in the same solvents.
View Article and Find Full Text PDFAnal Chim Acta
January 2025
College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea. Electronic address:
Background: The simplicity of synthesis methods has facilitated the illegal manufacture of various fentanyl analogs, leading to numerous fatal overdoses worldwide, particularly in North America. Fentanyl analogs with similar structures are difficult to distinguish due to their fragmentation patterns, making separation using chromatography essential. Additionally, because fentanyl analogs are lethal even in trace amounts, they are easily smuggled, and commonly used fentanyl test strips often fail to detect them due to their low sensitivity.
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