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 16 of 16 for “"Free energy barriers"”.
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A multiscale model for the oxide ion conducting and proton conducting solid oxide cells
Solid oxide cells (SOCs) are high-efficiency energy conversion devices under high temperature. However, the key reaction mechanisms governing the overall performance of SOCs are not well understood. Here, we develop a multiscale model combining density functional theory calculations, transition …
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Structural Transitions in Self-Assembled Lipid Systems Driven by Induced Curvature: From Cell -Penetrating Peptides to Programmable Vesicles
… broadly enabling and its induction can lower the free energy barriers for a range of different entry mechanisms, such as direct translocation as well as endocytotic pathways. Furthermore, we show that the TAT peptide interacts strongly with actin cytoskeleton, which enhances membrane deformation …
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Barrier Heights and Diffusion Coefficients in Protein Folding
… two-state, all-or-none transition. However, the energy landscape theory of protein folding predicts small and even zero folding free energy barriers (downhill folding) because of partial or complete compensation between large enthalpic and entropic terms as folding proceeds. They have been …
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A Random First Order Theory of Liquid -Glass Transition
… to explain the magnitude and variation of free energy barriers for glassy relaxation. A variety of empirical correlations embodied in the concept of liquid ""fragility"" are shown to be quantitatively explained by such a model. Fragility parameters, the size of heterogeneities, the degree …
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A Random first order theory of liquid-glass transition
… to explain the magnitude and variation of free energy barriers for glassy relaxation. A variety of empirical correlations embodied in the concept of liquid ""fragility"" are shown to be quantitatively explained by such a model. Fragility parameters, the size of heterogeneities, the degree …
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Structural transitions in self-assembled lipid systems driven by induced curvature: from cell-penetrating peptides to programmable vesicles
… broadly enabling and its induction can lower the free energy barriers for a range of different entry mechanisms, such as direct translocation as well as endocytotic pathways. Furthermore, we show that the TAT peptide interacts strongly with actin cytoskeleton, which enhances membrane deformation …
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Direct energy landscape sampling of the homogeneous nucleation and crystal growth of a model liquid
… be activated processes involving the crossing of free-energy barriers. Attempts to capture the entire crystallization process over long timescales with molecular dynamic simulations have met major obstacles because of the temporal constraints of molecular dynamics. Herein, we circumvent this …
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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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Development of a ReaxFF force field for glyphosate and investigation of its abiotic degradation pathways
… sampling method has been used to determine the free energy barriers opposing C-P and C-N bond dissociation. Approximately fifty carbon-phosphorus interaction parameters were fitted against a density functional theory (DFT) derived training set that included configurational energies of glyphosate …
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Transition path sampling in organometallic catalysis: Overcoming the rare event problem in ab initio molecular dynamics
… minima and transition states on the potential energy surface (PES) of a reaction and calculating free energies using the harmonic approximation. Ab initio molecular dynamics (AIMD) is an obvious strategy to address these issues. Within these simulations, the full range of thermally accessible …
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Aromaticity Across States: A Framework for Reactivity and Structure in Organic Systems
… and η6-coordinated arenes retain high free energy barriers, strongly dearomatized η2- and η4-arenes display substantially lower barriers (~20 kcal mol−1), demonstrating that the extent of aromaticity loss, rather than metal binding alone, governs reactivity. The second part examines how …
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Phase Phenomena of Proteins in Living Matter
… conformational changes can occur without costly free-energy barriers. Specific structures are proposed for each phase based on the simulation. To understand the ``quniary'' interaction between cells, we examine the interplay between folding and inter-domain interactions of engineered FiP35 WW …
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Developing methods to construct ring pucker free energy hypersurfaces applied to the analysis of glycosidase enzyme catalytic mechanisms
… of carbohydrate substrates. In this thesis, the free energy of ring puckering is calculated by implementing the Hill-Reilly reduced coordinate pucker description into the sampling enhancing Free Energies from Adaptive Reaction Coordinate Forces (FEARCF) method. FEARCF non-Boltzmann simulations of …
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Machine Learning Force Fields for Modelling Reactions at Complex Interfaces
… that our workflow can be used to determine energy barriers with quantum mechanical accuracy, requiring minimal human supervision. Furthermore, we show that machine learning surrogate modelling not only reduces the computational cost of routine in silico catalytic simulation tasks but also …
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Towards more robust and efficient methods for the calculation of Protein-Ligand binding affinities
… that should be accurate in principle, such as free energy perturbation (FEP) theory, to relatively simple approximations based on empirically derived scoring functions, the counterbalancing demands of speed and accuracy have left us with no completely satisfactory solution thus far. This thesis …
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Enzyme-Catalyzed Phosphoryl Transfer Reactions: Energetics of Transition States and Vanadate Analogues in Aqueous Solution
… are significant contributors to the reaction free energies and activation barriers of organic phosphate hydrolysis reactions. The methanolysis of dimethyl phosphate (DMP) and dimethyl vanadate (DMV) as well as acetyl phosphate (AcP) and acetyl vanadate (AcV) are modeled in aqueous solution to …