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Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 4 of 4 for “"Alchemical free energy calculations"”.
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Biomolecular Simulations with Machine Learning Potentials
… of the true quantum mechanical potential energy surface. Over the last several years, machine learned forcefields have emerged as a powerful paradigm, replacing manual parametrisation with a purely data driven approach and learning to reproduce the outputs of more expensive electronic …
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Computational approaches for drug design at the Protein-Protein interface
… further developed to perform replica-exchange alchemical free energy calculations using the Bennett Acceptance Ratio non-biased estimator. These simulations are in general shown to be very accurate and show promise in generating hypotheses for novel high-affnity oligoamide compounds.
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Computational investigation of early events in plant growth signaling
… exchange umbrella sampling scheme together with alchemical free energy calculations and conventional molecular dynamics simulations, we examine the mechanisms through which brassinosteroid binding to the BRI1 extracellular domain induces association with the BAK1 extracellular domain. We find …
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Toward accurate free energy calculations in biomolecular simulation: advances in Markov model reweighting and expanded ensemble method
… enhanced sampling methods for reliable free energy landscapes. In Chapter 2, we present the Bayesian Inference of Conformational Populations (BICePs) framework to reweight Markov state models constructed from extensive MD trajectories against nuclear magnetic resonance (NMR) …