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 14 of 14 for “"Path Sampling"”.
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Thermal cis-trans isomerization of azobenzene studied by path sampling and QM/MM stochastic dynamics
… is tracked by analyzing complete dynamical pathways between stable states. The suitability of this description is validated by using two test systems, pure azo benzene and a derivative with electron donating and electron withdrawing substituents (“push-pull” azobenzene). Each system is …
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Transition path sampling in organometallic catalysis: Overcoming the rare event problem in ab initio molecular dynamics
… time scale limitation by adapting Transition Path Sampling (TPS) for use in organometallic chemistry. TPS is a novel Monte Carlo technique to focus an MD simulation on a reactive event. We present new algorithms to generate initial reactive trajectories for TPS and a novel trajectory …
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Finite Sample Bounds and Path Selection for Sequential Monte Carlo
… in the estimation of normalizing constants using path sampling. In the final chapter of this thesis, we develop automatic methods for choosing sequences of distributions that provide low-variance path sampling estimators. These approaches are motived by properties of the theoretically optimal, …
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Computing the energetic component of the charge-transfer symmetry factor
… response and to test the accuracy of transition path sampling (TPS) for the calculation of activation energies. Activation energies from transition path sampling (10.2 kJ/mol) agree within statistical uncertainty with reference calculations (UI: 15.2 kJ/mol; MT: 15.7 kJ/mol) and are lower than …
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Path manipulation strategies for rendering dynamic environments.
The current work introduces path manipulation as a tool that extends bidirectional path tracing to reuse paths in the temporal domain. Defined as an apparatus of sampling and reuse strategies, path manipulation reconstructs the subpaths that compose the light transport paths and addresses the …
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The Dynamics of Dehydrogenases - A Phase Space Odyssey
… effects from first principles, using transition path sampling and centroid molecular dynamics. This method allows for the calculation of kinetic isotope effects without the assumptions necessitated by transition state theory or free energy perturbation methods. It was found that this method could …
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Computational Approaches for Understanding and Redesigning Enzyme Catalysis
… The approach combined statistical mechanical path sampling algorithms and machine learning methods to identify the structural characteristics of enzyme-substrate complexes primed for successful conversion of substrate to product, which were then energetically stabilized by mutating KARI. A …
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Artificial intelligence and protein engineering : information theoretical approaches to modeling enzymatic catalysis
… static molecular structures. Using computational sampling techniques, especially rare-event sampling methods like Transition Path Sampling, we can now generate large datasets of reactive and non-reactive enzyme trajectories. However, due to the high dimensionality of phase space, as well as the …
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Sampling Configurational Energy Landscapes
… similar orientations to allow an interpolated pathway to be generated between them which can be used to identify the transition states between the pair which is a key limiting step in discrete path sampling. The efficiency of the transition state search is strongly dependent on the quality of …
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Large scale simulation and analysis to understand enzymatic chemical mechanisms
… function of up to 6 dimensions, along a reaction path determined through a combination of knowledge from physical organic chemistry, local energetic optimizations, and experimental information. The activation barriers were converted to reaction rates and simulated with mass action kinetics. The …
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Ensemble methods in computational protein and ligand design : applications to the Fc[gamma] immunoglobulin, HIV-1 protease, and ketol-acid reductoisomerase systems
… is also presented, in which the transition path ensemble is explored using transition path sampling. We find that this ensemble approach is better able to predict relative enzyme activities and suggests a conserved, dynamic mechanism for catalysis. The results and analysis presented herein …
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Theoretical and computational investigations into structure-function relationships of biomolecular machines at atomic resolution
… be covered computationally. Employing advanced sampling techniques and theoretical modeling, we investigate the mechanism of three exemplary molecular machines in the following. Transcription termination factor Rho is a key factor in bacterial gene expression and regulation. An essential …
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Competitive Nucleation in Nanoclusters
… relative to the metastable state. A multiple path maximum likelihood analysis, (MPMLA), is developed to extract accurate reaction coordinates to the different phases. The results show that the linear combination of size and surface area of a given component is the accurate variable that …
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Energy Landscapes for Protein Folding
… of the physical environment, employing enhanced sampling strategies, and improving computing code and hardware. While significant advances have been made in these areas, for numerous systems a large spatiotemporal gap between experiment and simulations still exists, due to the limited time and …