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.
Results
Showing 1 to 20 of 34 for “"Enhanced Sampling"”.
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Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions
… To circumvent these difficulties, non-Boltzmann sampling methods such as the umbrella sampling and Wang-Landau sampling techniques, have been employed to study these phase transitions. </p> <p>Vapor-solid and liquid-solid phase transitions were studied using a combination of hybrid Monte Carlo …
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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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Multiscale Analysis of Macromolecular Systems
… In addition, even if Boltzmann-distributed sampling can be achieved, the definition of good reaction coordinates quantifying the progress of the reaction is non-trivial because of the high degrees of freedom of the system. My doctoral dissertation focuses on these two interrelated issues: …
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Dynamic Molecular Mechanisms and Drug Design of Important Therapeutic Targets
… respectively, through improved enhanced sampling. Here, molecular mechanisms of small molecule and peptide mediated activation of important therapeutic targets have been uncovered using powerful computational techniques (including GaMD, LiGaMD, Pep-GaMD, molecular docking and …
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Structural Dynamics and Electrostatic Properties of the VEGF and PIM-1 Oncogenic Promoter G-Quadruplexes from Polarizable Molecular Dynamics Simulations
… specificity. Here, we employed conventional and enhanced sampling molecular dynamics simulations on two oncogenic GQ structures with the Drude polarizable force field to gain crucial insights into structural and electrostatic properties contributing to overall GQ stability and potential …
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Atomistic insights into the structure, dynamics, and regulation of integral membrane proteins
… Emad Tajkhorshid, MD simulations—integrated with enhanced sampling, structural modeling, and free energy calculations—were employed to investigate conformational dynamics, lipid modulation, and domain coupling mechanisms in membrane protein systems. In the first study, we present a complete …
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Machine learning of molecular conformations, kinetics and beyond
… I present a deep-learning based accelerated sampling framework termed “Molecular Enhanced Sampling with Autoencoders” (MESA) that utilizes high-variance collective variables (CVs) to guide sampling. By applying the framework on some molecular systems, I show its efficiency for exploring …
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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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Development of Computational Antibiotic Screening Platform Across Bacterial Outer Membrane Proteins
… all-atom and coarse-grained molecular modeling, enhanced sampling techniques, and a parallel computing environment to maximize the performance. We further demonstrate the efficacy of this platform with a comprehensive study of a benchmark case. Key findings include free energy profile, …
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Accelerated simulations and computer-aided drug design of membrane proteins
… that provides simultaneous unconstrained enhanced sampling and free energy calculations. GaMD has been successfully applied to study physical pathways and mechanisms of protein folding and ligand binding of important membrane proteins. Based on the principles of GaMD, Ligand GaMD (LiGaMD) …
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Forensic applications of raman spectroscopy
… and extended using the development of novel sampling techniques and task-specific instrumentation described in this thesis. The phenomenon of Raman scattering, enhanced Raman scattering and their relevance in forensic investigations was reviewed. Particular emphasis was placed on current …
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Mechanistic insights into how collective effects mediate the T cell response
… that the risk of autoimmunity increases through enhanced sampling of rare epitopes and activation of cross-reactive T cells. These results provide a potential explanation for why persistent infections often trigger autoimmune diseases. To further understand the emergence of the quorum threshold, …
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Molecular Mechanisms of Protein Self-Assembly and Aggregation
… fibrillar surfaces using a specially designed enhanced sampling scheme, which allows us to obtain enthalpy-driven binding thermodynamics consistent with experiments and to propose major polar binding modes. In the second part of the thesis, Chapters 6 and 7, we model the aggregation of two …
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Enhancing Robustness of Neural Network Interatomic Potentials through Sampling Methods and Uncertainty Quantification
… (UQ) techniques, introduction of novel data sampling strategies, and development of structural similarity analysis algorithm to extract physical insights from diverse data sets. First, we examine the efficacy of UQ for single deterministic neural networks, demonstrating that a Gaussian …
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Decoding the Sequence-Dependent Properties of Intrinsically Disordered Proteins
… tau transfer to microtubules. Next, we use enhanced sampling techniques to determine a membrane-assisted fibril forming pathway for the IDP α-synuclein, which gives us insight to Parkinson’s disease specific fibril formation.
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Gas migration inside proteins: Mechanism, characterization, and applications
… a molecular dynamics methodology called locally-enhanced sampling and a novel volumetric oxygen accessibility map method, applied to the hydrogenase enzyme, that gas molecules make their way not through static channels, but through well-defined ""pathways"", which are completely defined by the …
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Kinetics of Disordered Proteins and their Interactions
… dynamics are poorly understood. I performed enhanced sampling simulations of both an sdAb designed using a sequence-matching method as well as one developed with a structural approach to better understand their conformational space and provide information to improve selectivity and …
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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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Novel applications and methods for the computer-aided understanding and design of enzyme activity
… of reactivity. Leveraging a computational enhanced sampling technique called transition interface sampling, we show that trajectories sampled in such a manner as to selectively visit the conformations predicted to be characteristic of reactivity exhibit rate constants many orders of …
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Role of the colonic lymphoglandular complex in mucosal immunity in swine
… experimental methodology might help to confirm enhanced sampling capacity of the LGC versus absorptive mucosa.</p>
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