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 8 of 8 for “"Enhanced sampling techniques"”.
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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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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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Multiscale Analysis of Macromolecular Systems
… to current state-of-the-art experimental techniques. The relevant dynamics in complex macromolecular systems correspond to timescales longer than what can be sampled using MD with standard computational resources. In addition, even if Boltzmann-distributed sampling can be achieved, the …
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Computational modeling and simulation of ligand-gated ion channels
… in different functional states. Moreover, enhanced sampling techniques can be used to characterize the conformational transitions between different functional states in these proteins. In this work, after a brief introduction (Chapter 1), two studies --- each focused on a different …
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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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Phase transitions in soft matter: From colloidal suspensions to biomolecular condensate regulation
… interfaces. By employing advanced computational techniques, we elucidate the underlying mechanisms driving these phase transitions, contributing to a deeper understanding of water's fundamental properties, such as the surface tension, or the interfacial arrangement of molecules. Another highly …
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Interactions of Proteins with Membranes: Insights from Molecular Dynamics Simulations
… of paramount importance. However, experimental techniques such as X-ray crystallography and cryo-electron microscopy often struggle to capture the full conformational landscape of membrane proteins due to their complex interactions with lipid bilayers and their dynamic nature. These limitations …
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Microscopic description of gas permeation and delivery pathways in biological macromolecules
… with their surroundings within a medium requires techniques that provide both atomic spatial and small temporal resolutions. To fulfill these purposes, I have employed molecular dynamics (MD) simulation to characterize delivery pathways of O2, NO and CO2 in aerobic respiratory terminal oxidases …