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 162 for “"energy landscape"”.
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Methods of single-molecule energy landscape reconstruction with optical traps
… protein are unfolded and refolded. The effective energy landscape of a biomolecule can be reconstructed from the force and position data, providing insight into its structure and regulatory functions. We have developed new experimental and analytical methods to reconstruct energy landscapes by …
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Fast Protein and RNA Folding on a Rough Energy Landscape
… is a new signature for downhill folding. The energy landscape of engineered RNA hairpin was also explored using temperature tuning method, which provides insight into the order of stem- and loop-formation in short RNA hairpins.
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Physical models of protein folding within the energy landscape theory
The energy landscape theory of protein fol9.ing is based on a statistical description of a protein's complex potential energy surface. Individual folding events are sampled from an ensemble of possible routes on the landscape. The theory suggests that the landscape of a protein can be described as …
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Energy landscape statistics and coarsening in liquids: a relaxation mode analysis
Energy landscape, the high dimensional energy surface in the configuration space, has been widely applied to interpret slow processes that occur over a long time scale, such as slow relaxations of supercooled liquids approaching the glass transition. Despite extensive simulation studies, …
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Application of the Statistical Energy Landscape Theory to Protein Structure Prediction
… methods to narrow this gap. Using ideas from the energy landscape theory first introduced by Bryngelson and Wolynes, and database analysis, we have designed statistical mechanical energy functions for protein structure prediction by threading and simulated annealing molecular dynamics methods. …
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K-means landscapes: exploring clustering solution spaces using energy landscape theory
… performance. We present the application of energy landscape theory to the K-means cost function to elucidate its topography, which we deduce from K-means landscapes described in terms minima and transition states. We analyse K-means landscapes for Fisher’s Iris dataset, the glass …
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Development Of New Algorithms For Exploring The Potential Energy Landscape Of Chemical Reactions
… ab initio or density functional theory potential energy surfaces.</p> <p> The final two chapters of this thesis focus on the development of a new path optimization framework, the Variational Reaction Coordinate (VRC) method. This framework seeks to improve upon the “chain of states” methods, which …
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Direct energy landscape sampling of the homogeneous nucleation and crystal growth of a model liquid
… 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 temporal …
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The Energy Landscape of Associative Memory Energy Functions and Their Application to Ab Initio Protein Structure Prediction
… dependent on a few statistical properties of the energy landscape. These include the gap in energy between the native basin and the ensemble of misfolded states and the variance in energy of the unfolded states. This insight may be used to design model energy functions for ab initio prediction. In …
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Molecular Simulation Studies of Physical Aging and Rejuvenation in Polymer Glasses
This thesis provides the potential energy landscape description of mobility enhancement that follows deformation of polymer glasses. We show that there are two mechanisms which dictate the mobility enhancement – fold-catastrophe mechanism which reduces the barrier between the minima; and …
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Energy Landscaping - On the Relationship between Functionality and Sequence Mutations for Multifunctional Biomolecules
… of as being guided by a folding funnel on the energy landscape, which is based around the native structure. However, more recently, various biomolecules have been associated with multifunnel energy landscapes, where each funnel exhibits a distinct structural ensemble and function. This work …
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Modeling intrinsically disordered proteins ; a comprehensive study of [alpha]-synuclein
… where each structure corresponds to an energy minimum on a complex energy landscape. The number of structures in the resulting ensemble is related to the resolution in which one wishes to view the energy landscape of the protein. We demonstrate that this approach leads to new insights …
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Protein-DNA interaction, random walks and polymer statistics
… diffusion in a sequence-dependent rough energy landscape. I demonstrate that, despite the landscape's roughness, rapid search can. be achieved if one-dimensional sliding is accompanied by three-dimensional diffusion. I estimate the range of the specific and nonspecific DNA-binding energy …
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Higher Order Structure in the Energy Landscapes of Model Glass Formers
… the behaviour of supercooled liquids and their energy landscapes is well established and widely accepted. Understanding this link would be a key step towards resolving many of the mysteries and controversies surrounding the glass transition. Therefore the study of glassy energy landscapes is an …
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Thermodynamic signatures for hexapeptides with propensity for phase separation and amyloid formation
… collective behaviour properties in the potential energy landscape of monomers and dimers of IDPs. The landscapes of short hexapeptide sequences are explored here. Some of these hexapeptides are chosen to encode aromatic–aromatic and cation–aromatic interactions that are known to drive phase …
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Experimental Interrogation Of One-Dimensional Excitons In Cadmium Selenide And Cadmium Telluride Quantum Nanostructures
… and therefore increase the exciton binding energy as compared to bulk and quantum well structures. In this thesis, excitons in single one-dimensional CdSe and CdTe QWs were investigated using a combination of optical microscopy techniques. My work indicates that excitons in single quantum …
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Understanding long timescale phenomena in atomic systems from accelerated molecular simulation methods
… the crossing by thermal activation of large energy barriers, which represent transition states separating two stable or metastable states of a system. Therefore, we propose two methods to simulate the escape of a system from a metastable state to a transition state, which, when repeated, …
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Learning Generalizable Systems by Learning Composable Energy Landscapes
… certain forms of generalization by estimating energy landscapes over possible predictions for each task, with accurate predictions assigned lower energy. This modeling choice formulates prediction as a search process on the energy landscape, enabling zero-shot generalization to new constraints …
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Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation
… in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very …
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Multilevel frameworks for studying protein energy landscapes
… approaches (Chapter 2) to analyse protein energy landscapes. A key development is the lwONIOM library (Chapter 3), a freely accessible, multilevel, multicentre tool enabling accurate and efficient analysis of complex proteins over extended timescales. Applied to the bovine pancreatic …
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