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 20 of 23 for “"free energy landscape"”.
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Investigating the Structure and Function of IGP Synthase
… Jarzynskis identity were used to determine the free energy landscape for ammonia conduction through hisF and showed, for the first time, that it was indeed energetically feasible for this ubiquitous enzymatic fold to exploit its barrel structure to transport reaction intermediates. The …
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The conformational landscape of RNA translational regulators and their potential as drug discovery targets
… an ensemble of energetic minima along a free-energy landscape. Knowledge of this structural landscape has become an important goal for understanding its diverse biological functions. In this case, NMR spectroscopy has emerged as an important player in the characterization of RNA …
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Low frequency charge-density wave dynamics
… equilibrium dynamics can be described by a rough free energy landscape with extreme sensitivity of the local details of the landscape to changes in the temperature or current. The nonequilibrium dynamics were directly related to the drive current.
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Inverse design of self-assembling colloids via landscape engineering
… framework capable of rationally manipulating the free energy landscape for self-assembly to derive building blocks that preferentially form into a target aggregate structure. The methodologies derived within are applicable to a wide class of self-assembly systems, both simulated and experimental, …
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The Emergence of Knowledge And The Benefits Of Quorum
… of knowledge with an emergence of a complex free energy landscape, where distinct patterns/memories correspond to distinct free energy minima. Conversely, the Marcus-inverted regime for the environmental degrees of freedom causes such free energy to merge and results in loss of data. We show …
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On the Kinetics of Protein Misfolding and Aggregation
… the dynamics of proteins in the region of the free energy landscape corresponding to protein aggregation. First, a section on Method development describes the extension and elaboration of the previously established kinetic assay relying on quartz crystal microbalance measurements for the study …
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The Systems Biology of the Protein Quality Control
… conformational dynamics using its empirical free-energy landscape (FEL). The FEL model successfully predicts the proteasome behaviors under a variety of conditions both in this and in previous studies and provides important insights into the molecular events and transitions underlying …
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Stochastic Modeling and Simulations of Biological Transport
… However, the actual mechanism of how chemical energy is converted into their directed motion has still remained obscure. Recent experiments on motor proteins have been producing exciting results that have motivated theoretical studies. In order to provide deep insight onto motor protein's …
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Polymer Infiltration Under Extreme Confinement
… the effect of varying cross-section on the free energy landscape of infiltrating polymers. I discover that barriers can be introduced into the infiltration free energy as a result of the large change in free surface area between constrictions and expansions along the length of the capillary. …
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Insights into the Substrate Binding Specificity of Quorum-Quenching Acylase PVDQ
… interaction network analysis, and binding free energy calculations. The main findings are: firstly, results from pKa predictions support the observation that the pKa of the N-terminus of Serβ1 was depressed due to the surrounding residues. Multiple molecular docking studies provided …
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Computational Studies on the Mechanical Properties of Muscle and Blood Clot Elasticity
… protein fibrinogen. These investigations utilize free dynamics MD to verify experimentally observed conformations of proteins, SMD to probe their response to mechanical forces, and adaptive biasing force (ABF) simulations to measure the free energy landscape of tertiary structure transformations. …
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Investigation of physical principles of protein phase transitions
… For Aβ42 on lipid membranes, I quantify the free energy landscape of liquid-liquid phase separation (LLPS) and fibrillation, demonstrating that LLPS serves as a crucial intermediate step in facilitating aggregation. In the P301L variant of tau, I track individual tau molecules and monitor …
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Advances in understanding protein-lipid interactions through biophysical and bioelectronic approaches
… of interest. However, due to the nature of the free energy landscape with respect to protein folding, they can misfold and transform into toxic oligomeric or fibrillar species. In particular, this thesis focuses on a subset of IDPs, namely amyloid-beta 40 and 42, α-synuclein and …
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Molecular structure, hierarchical assembly and stimuli-responsive mechanics of tropoelastin and elastin biomaterials
… unfolding pathways, we analyze the associated free-energy landscape with the Bell-Evans model to interpret temperature-induced phase transitions. We develop a feedback loop between simulation and experiment for predictive biomaterial design, enabling new applications in drug delivery and tissue …
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Mechanochemical Understanding of Metal-Coordinated Polymers Using Simulation and Experiment
… We use metadynamics simulations to show that the free energy landscape of metal-coordination bonds can be related to the macroscopic dynamic relaxation of these bonds in ideal polymer hydrogels as measured through experimental rheology. We then expand beyond single coordination complexes and use …
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Understanding Chromatin Organization and Dynamics with Coarse-Grained Modeling
… while 10n-bp linkers lead to funnel-shaped free energy landscape with a strong folding trend. Within the condensate, the transition rates slow down, while the unfolding and folding rates are comparable. These two studies highlight that the intrinsic physical chemistry properties of chromatin …
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Computational study of the structure and function of membrane transport proteins
… MD simulation and determining the free energy landscape associated with the so called IF–OF transition. Employing the information from the free energy calculations and equilibrium MD simulations from the members of the sugar porter family I present a unified mechanism of transport …
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Energy Landscapes for Protein Folding
… systems, via approaches based on the potential energy landscape (PEL) framework. By applying geometry optimisation techniques, the PEL is discretised into stationary points (i.e.~low-energy minima and the transition states that connect them). Essentially, minima characterise the low-lying …
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Structure & Function of Bacterial Transport Machines in their Cellular Context
… of transport, with cardiolipin providing energy via the proton-motive force. I test this hypothesis through flow cytometry detection of labelled substrate trapped T1SS in a mixed population of cells, by comparing parental MG1655 *Escherichia coli* with a cardiolipin deficient MG1655 …
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Theoretical and computational investigations into structure-function relationships of biomolecular machines at atomic resolution
… mechanism transmitting other form of energy into mechanical force is still unclear. Molecular dynamics simulations, though capable of providing atomic details, are limited in the study of molecular machines owing to the challenge that these machine usually function on a millisecond (or …
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