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 6 of 6 for “"Enhanced sampling methods"”.
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Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions
… they can be applied. </p> <p>Current simulation methods used to accomplish this task, such as the grand canonical and Gibbs ensemble Monte Carlo methods, employ the concept of particles insertion and deletion moves or requires the knowledge of at least one point at coexistence. These types of …
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Enhanced sampling methods and their application in the study of molecular permeation in gram-negative bacteria
… This approach allowed to connect the results of enhanced sampling MD methods with current blockages in single channel experiments.All these results together show that multiscale MD techniques can offer an exhaustive view on the mechanism of molecular diffusion through pores, helping to understand …
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Toward accurate free energy calculations in biomolecular simulation: advances in Markov model reweighting and expanded ensemble method
… with experimental data and developing 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 …
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Memory and fluctuations in chemical dynamics
… liquid-solid interfaces. Specifically, I employ enhanced sampling methods to study a model system of carbon monoxide at a water/platinum interface. Using these methods, I show that the local coordination number around a CO molecule plays a crucial role in the transition states of the …
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Modeling cellular metabolism in multiple scales
… catalytic residues in the active site. This enhanced and updated methodology will provide the community with an intuitive and interactive interface, that can be easily applied to large macroolecular complexes. Beyond the study of protein:ligand interactions, in order to analyze specific …
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Theoretical and computational investigations into structure-function relationships of biomolecular machines at atomic resolution
… be covered computationally. Employing advanced sampling techniques and theoretical modeling, we investigate the mechanism of three exemplary molecular machines in the following. Transcription termination factor Rho is a key factor in bacterial gene expression and regulation. An essential …