Molecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code. This charge-implicit ReaxFF potential is five times faster than the conventional ReaxFF potential for a simulation of keV particle bombardment with a sample size of over 800 000 atoms.
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http://dx.doi.org/10.1021/acs.jpclett.7b03155 | DOI Listing |
Int J Mol Sci
November 2024
School of Engineering and Design, Atlantic Technological University, Ash Lane, F91 YW50 Sligo, Ireland.
Water shortages and pharmaceutical pollution are two interconnected crises that pose severe threats to global health, environmental sustainability, and economic stability. Pharmaceutical pollution is widespread and has reached potentially toxic levels in over 258 rivers in 104 countries. So far, more interest has been paid towards efficient water treatment processes in recent years.
View Article and Find Full Text PDFCarbohydr Polym
January 2025
School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
J Phys Chem B
November 2024
Department of Materials, Loughborough University, Loughborough LE11 3TU, U.K.
Due to the importance of the understanding of dissolution behavior of phosphate-based bioglasses (PBGs) in different biomedical applications, binary sodium and calcium phosphate glasses have been simulated for the first time using a newly developed ReaxFF force field and a standard melt-quench method with the LAMMPS classical molecular dynamics software. The partial radial distribution function of P-O within the first coordination shell indicated two distinct peaks corresponding to phosphorus bonding to NBO and BO, respectively, at distances consistent with those observed experimentally and a P-O coordination number of 4.0.
View Article and Find Full Text PDFMolecules
October 2024
Joint BioEnergy Institute, Emeryville, CA 94608, USA.
The valorization and dissolution of lignin using ionic liquids (ILs) is critical for developing sustainable biorefineries and a circular bioeconomy. This review aims to critically assess the current state of computational and machine learning methods for understanding and optimizing IL-based lignin dissolution and valorization processes reported since 2022. The paper examines various computational approaches, from quantum chemistry to machine learning, highlighting their strengths, limitations, and recent advances in predicting and optimizing lignin-IL interactions.
View Article and Find Full Text PDFJ Chem Theory Comput
November 2024
Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
The computational complexity of quantum chemistry methods has prompted the development of reactive force fields, facilitating practical applications of molecular dynamics simulations for large-scale reactive systems. Current reactive force fields typically employ intricate corrections based on prior chemical knowledge, which severely impedes their further advancement. This study presents a new atomic multipole-based reactive model with bond free (OPERATOR).
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