<> "The repository administrator has not yet configured an RDF license."^^ . <> . . "Developing a Reactive Molecular Simulation Method\r\nfor Protein Mechanochemistry"^^ . "Collagen has recently been found to form radicals when subjected to mechanical stress, followed by detoxification of DOPA radicals via hydrogen peroxide.\r\nHowever, it remains unclear how mechanoradicals reach DOPA. Within the\r\ncomplex environment of the collagen fibril, numerous different reactions are\r\npossible, including hydrogen atom transfer (HAT).\r\nIn this work a combined molecular dynamics (MD) and kinetic Monte Carlo\r\n(KMC) method is implemented within an adaptive KMC framework. The developed software, KIMMDY, is capable of simulating long timescale trajectories of reactive condensed phase systems. More than 600 HAT reactions are\r\nsimulated in a collagen fibril model with up to 20 consecutive reactions.\r\nTo make MD simulations of amino acid radicals possible, a highly accurate\r\nclassical force field is trained on QM energies and forces using the Grappa\r\nmethod. Furthermore, a graph neural network is adapted to predict HAT\r\nrates for ensembles generated from MD simulations in a novel approach to\r\ntransition path sampling.\r\nThese three methodological advances facilitate the application of reactive\r\nsimulations in the collagen fibril to observe HAT pathways from the homolysis\r\nsite to the post-translational oxidation product of phenylalanine and tyrosine,\r\nDOPA. The DOPA radical can be observed in simulations and kinetic properties confirm the radical scavenger role. Another radical scavenger, pyridinoline (PYD) is proposed and its mechanochemical properties characterised.\r\nKIMMDY provides a new perspective on radical reactions in collagen and is\r\ndesigned to be applied to novel molecules and reactions"^^ . "2025" . . . . . . . "Eric Hans"^^ . "Hartmann"^^ . "Eric Hans Hartmann"^^ . . . . . . "Developing a Reactive Molecular Simulation Method\r\nfor Protein Mechanochemistry (PDF)"^^ . . . "Hartmann_Eric_komplett.pdf"^^ . . . "Developing a Reactive Molecular Simulation Method\r\nfor Protein Mechanochemistry (Other)"^^ . . . . . . "indexcodes.txt"^^ . . . "Developing a Reactive Molecular Simulation Method\r\nfor Protein Mechanochemistry (Other)"^^ . . . . . . "lightbox.jpg"^^ . . . "Developing a Reactive Molecular Simulation Method\r\nfor Protein Mechanochemistry (Other)"^^ . . . . . . "preview.jpg"^^ . . . "Developing a Reactive Molecular Simulation Method\r\nfor Protein Mechanochemistry (Other)"^^ . . . . . . "medium.jpg"^^ . . . "Developing a Reactive Molecular Simulation Method\r\nfor Protein Mechanochemistry (Other)"^^ . . . . . . "small.jpg"^^ . . "HTML Summary of #37132 \n\nDeveloping a Reactive Molecular Simulation Method \nfor Protein Mechanochemistry\n\n" . "text/html" . . . "540 Chemie"@de . "540 Chemistry and allied sciences"@en . .