<> "The repository administrator has not yet configured an RDF license."^^ . <> . . "Predicting Hydrogen Atom Transfer in Collagen"^^ . "Molecular Dynamics (MD) simulation is an established method for studying bi-\r\nological systems and materials at the molecular level. For example, it can predict\r\nthe effects of mutations on the folding behavior of proteins, or elucidate the binding\r\nmechanisms of drugs to receptors. To achieve this, a molecular system is modeled as\r\nbeads connected via springs or sticks. Goal of this thesis is to develop a method to\r\ndeepen our understanding of mechanoradicals undergoing hydrogen atom transfer\r\n(HAT) reactions. Usually, no new chemical bonds can be formed during an MD\r\nsimulation, prohibiting the analysis of HAT and other reactions.\r\nIn this thesis, a method called KIMMDY is implemented, enabling reactive MD\r\nthrough the use of kinetic Monte Carlo steps. While it has previously been used\r\nfor homolysis reactions, here its scope is extended to also allow HAT during an MD\r\nsimulation. First, a data set of HAT reaction barriers is crafted using quantum\r\nmechanical (QM) calculations. Then, a graph neural network (GNN) is trained on\r\nthis data set to predict HAT reaction barriers. The inputs to the GNN are structures\r\nsampled from MD simulations, requiring no prior optimization. Thus, the model\r\noffers a significant speed-up compared to traditional methods, like reactive force\r\nfields, or direct QM calculations.\r\nFurthermore, the KIMMDY 2.0 software package is presented, which can perform\r\nkinetic Monte Carlo driven reactive MD simulations in a flexible and user-friendly\r\nmanner. It supports HAT and homolysis reactions, and can be easily extended to any\r\nreaction for which rates are available. For HAT, they are obtained using the afore-\r\nmentioned GNN. However, this approach is not limited to HAT. Through the use of\r\nmachine learning models, reaction rates for arbitrary reactions become accessible,\r\nonly requiring a limited amount of QM calculations during training. In KIMMDY,\r\nthese models enable combining the accuracy and flexibility of QM calculations with\r\nthe efficiency of MD."^^ . "2024" . . . . . . . "Kai"^^ . "Riedmiller"^^ . "Kai Riedmiller"^^ . . . . . . "Predicting Hydrogen Atom Transfer in Collagen (PDF)"^^ . . . "main.pdf"^^ . . . "Predicting Hydrogen Atom Transfer in Collagen (Other)"^^ . . . . . . "indexcodes.txt"^^ . . . "Predicting Hydrogen Atom Transfer in Collagen (Other)"^^ . . . . . . "lightbox.jpg"^^ . . . "Predicting Hydrogen Atom Transfer in Collagen (Other)"^^ . . . . . . "preview.jpg"^^ . . . "Predicting Hydrogen Atom Transfer in Collagen (Other)"^^ . . . . . . "medium.jpg"^^ . . . "Predicting Hydrogen Atom Transfer in Collagen (Other)"^^ . . . . . . "small.jpg"^^ . . "HTML Summary of #35153 \n\nPredicting Hydrogen Atom Transfer in Collagen\n\n" . "text/html" . .