Global ETD Search
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 17 of 17 for “"Markov State Models"”.
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MARKOV STATE MODELS AND THEIR APPLICATIONS IN PROTEIN FOLDING SIMULATION, SMALL MOLECULE DESIGN, AND MEMBRANE PROTEIN MODELING
… dissertation is focused on the application of Markov State Models on protein folding and designing of small drug-like molecules, as well as application of computational tools on the study of biological processes. The central focus of protein folding is to understand how proteins obtain their …
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Efficient sampling of protein conformational dynamics and prediction of mutation effects.
… elucidate the kinetics of molecular simulations, Markov State Models (MSMs) have proven their ability to extract both kinetic and thermodynamic properties of long-timescale motions using ensembles of shorter MD simulation trajectories. In this dissertation, we have implemented an MSM path-entropy …
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Computational investigation of early events in plant growth signaling
… in their fully phosphorylated forms and built Markov state models from those simulations in order to examine the behavior of features characteristic of active protein kinases. We find that the BAK1 kinase domain displays local unfolding of the αC helix, while the BRI1 αC helix also unfolds, …
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Machine learning of molecular conformations, kinetics and beyond
… I build a deep-learning based model termed “State-free Reversible VAMPnets” (SRVs) to learn slow CVs that govern the dominant kinetics of the system. By comparing SRVs with the existing kernel based method, I show that SRVs are more accurate, less sensitive to feature selection and feature …
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Toward accurate free energy calculations in biomolecular simulation: advances in Markov model reweighting and expanded ensemble method
… Populations (BICePs) framework to reweight Markov state models constructed from extensive MD trajectories against nuclear magnetic resonance (NMR) measurements. Applied to ten linear and cyclic beta-hairpin peptide mimics, BICePs refines Karplus parameters for scalar couplings and reweights …
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COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
… of exchange between distinct conformational states (i.e. folding and unfolding, binding and unbinding). The above studies are typically done using different, but complementary approaches. Alchemical methods, including free energy perturbation (FEP) and thermodynamic integration (TI), have …
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Computational methods to design biophysical experiments for the study of protein dynamics
… this purpose, molecular dynamics simulations and Markov state models of protein conformational dynamics are utilized to rank sets of labeled residue-pairs in terms of their ability to capture the conformational dynamics of the protein. The applications of our experimental study design methodology …
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Probing Nucleation Mechanisms of Gas Hydrates via Molecular Simulations
… Molecular Dynamic (MD) simulations along with Markov State Models (MSMs). The investigation of the nucleation behavior of mixed CH<sub>4</sub>/H<sub>2</sub>S hydrates within bulk aqueous solutions reveals the roles of different guest species in the hydrate formation process and the impacts of …
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Molecular mechanisms of neurotransmitter transport in neurons
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01
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Markov state modeling of binding and conformational changes of proteins
… in their sequences of events. The theory of Markov state models (MSMs) provides the theoretical framework in which all these cases can be modeled. For this purpose, MSMs are estimated in this work from MD data, and rate equation models, which are related to MSMs, are inferred from …
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Understanding Chromatin Organization and Dynamics with Coarse-Grained Modeling
… relevant timescales. We have developed CG models and toolkits to facilitate modeling chromatin and related proteins. We have also applied CG protein and DNA models to study chromatin folding and phase separation. In Chapter 1, we begin with an overview of the hierarchical scales of genome …
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Activation mechanisms of non-class A G protein-coupled receptors
… introduced by adaptive sampling, we construct Markov State Models and reweigh the probabilities of the sampled free energy landscapes. These approaches allow us to reconstruct the full activation landscape for each of these proteins and recover the thermodynamics and kinetics associated with …
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Computational dissection of nitrate transport mechanism
"Nitrogen is an essential nutrient in plants and a major driving force for crop yields and food production. Annually, about 110 million tonnes of nitrogenous fertilizers are applied globally to enhance crop yields. However, over half of the nitrogen added to the soil is lost to the environment, …
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Molecular Simulation of Mutation Effects on Protein Folding and Function
… data. From these datasets, kinetic network models called Markov state models (MSMs) can be constructed to infer long timescale dynamics from ensembles of short trajectories. These models can be analyzed in a human interpretable way and make physics-based connections to experimental …
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Machine learning of molecular motifs in soft supramolecular systems
L'abstract è presente nell'allegato / the abstract is in the attachment
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Chemical selectivity principles of translocation catalysis by membrane transporters
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-05-01