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 69 for “"Energy Landscapes"”.
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Sampling Configurational Energy Landscapes
… by these surfaces, traditionally termed energy landscapes. When studying molecular systems, it is important to be able to quantify measures of similarity or difference between a pair of structures generated from an energy landscape. These measures are needed to make predictions of the …
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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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Accelerated sampling of energy landscapes
In this project, various computational energy landscape methods were accelerated using graphics processing units (GPUs). Basin-hopping global optimisation was treated using a version of the limited-memory BFGS algorithm adapted for CUDA, in combination with GPU-acceleration of the potential …
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Visualising Energy Landscapes Through Manifold Learning
Potential energy surfaces (PESs) or landscapes provide a conceptual framework for structure prediction, and a detailed understanding of their topological features is necessary to develop efficient methods for their exploration. The ability to visualise these surfaces is essential, but the high …
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Exploring Downhill Protein Folding Free Energy Landscapes
… protein folding, i.e., folding with the free energy barrier comparable to the thermal energy kBT, is investigated by combining laser induced temperature-jump kinetics measurements and Langevin dynamics simulations. A kinetic and thermodynamic survey of multiple WW domain mutants is performed …
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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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Modeling rough energy landscapes in defected condensed matter
… We also calculate the migration mechanisms and energy barriers for the most relevant PDC species in Fe-H. Our results demonstrate the essential role of hydrogen-vacancy interactions in mediating the formation and migration of PDCs, and the relevance of these crystalline defects to the problem of …
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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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Probing Spin Glass Energy Landscapes with 1/f Noise
… and to the understanding of the underlying energy barrier distribution. Analysis of our measurements provides the first explicit determination of the evolution of the spin-glass energy barrier distribution as a function of film thickness and temperature. By fabricating samples of multiple …
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Energy Landscapes of Hybrid Potentials Based on NMR Data
… into the biomolecualr simulations within the energy landscape framework, is presented. It enhances the simulations of proteins, membrane proteins in particular, in terms of producing experimentally compatible structures and orientations when the atomistic force fields do not necessarily …
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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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Analysing First Passage Time Distributions of Large Ill-Conditioned Energy Landscapes
… kinetics of competing pathways on multifunnel energy landscapes. Multifunnel landscapes are associated with molecular switches and multifunctional materials, and are expected to exhibit multiple relaxation time scales. Energy landscapes, consisting of local minima connected by transition …
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On the complexity of energy landscapes: algorithms and a direct test of the Edwards conjecture
When the states of a system can be described by the extrema of a high-dimensional function, the characterisation of its complexity, i.e. the enumeration of the accessible stable states, can be reduced to a sampling problem. In this thesis a robust numerical protocol is established, capable of …
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Using Data-Driven Models to Understand Transition Metal Catalyst Energy Landscapes and Metal-Organic Framework Stability
… intermediates on the methane-to-methanol energy landscape, linear free energy relationships (LFERs) that are invoked during HTVS to simplify catalyst screening cannot be readily used. As an alternative approach, the absence of universal scaling relations between intermediate energetics …
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Application and Development of Molecular Dynamics Methods to Examine the Energy Landscapes of Protein Folding and Transient Protein -Protein Complexes
… last to break. Computation of the docking free energy, by taking into the account the electrostatic, van der Waals, and entropic contributions, matched well with the experimental value. Extensive structure and sequence based evolutionary analyses of the cytochrome c2 revealed the conservation of …
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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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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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Disordered systems and quantum algorithms: from spin glasses to neural networks
… 5000-qubit processor that explores deeper energy landscapes and reduces annealing time by up to 85% compared to traditional forward annealing. To address the challenge of exponentially small energy gaps, we introduce a new framework that uses cyclic quantum annealing to efficiently sample …
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Stirred spin glass models of in vivo protein folding
… glasses and proteins is that both have complex energy landscapes with multiple energy minima and barriers. The approach to equilibrium in such systems has been previously studied. We present here a ""stirred"" spin glass whose equilibrium is constantly being perturbed by a possibility for …
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Entropy functions and rare events in disordered systems by transfer matrix calculations and Monte Carlo sampling
… In a similar way, I studied the minimum free-energy distribution of RNA secondary structures over ensembles of random sequences. Furthermore I investigated the dynamics of different Monte Carlo algorithms in complex energy landscapes and the connection to static properties.
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