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 10 of 10 for “"minimum free energy"”.
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Application of Semi-Grand Canonical Monte Carlo (SGMC) methods to describe non-equilibrium polymer systems
… I assert that thermodynamic consistency and energy minimization is an integral part of this endeavor; reliable analyses of structure and properties are built upon the foundation of a minimum-free-energy ensemble of configurations that reproduces the experimental results. This project …
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Correlating antisense RNA performance with thermodynamic calculations
… a correlation between the expression level and minimum free energy to enable the design of specific asRNA fragments. The thermodynamics of asRNA and mRNA hybridization were computed based on the fluorescent protein reporter genes. Three different fluorescent proteins (i) green fluorescent …
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Entropy functions and rare events in disordered systems by transfer matrix calculations and Monte Carlo sampling
… distribution. 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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Molecular design of interfacial modifications to alter adsorption/desorption equilibria at fluid-adjoining interfaces
… used the SPC/E water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time …
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Graphical methods in RNA structure matching
… important because producing non-coding RNA is an energy intensive process, and in the absence of strong selection one would expect it to disappear.</p> <p>RNA families with common functions have specifically conserved structural motifs, which are directly related to the functional roles of RNA in …
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Deep Learning for Human MicroRNA Precursor Prediction: A Systematic Literature Review
… them all. This study proposes that entropy, minimum free energy, stem-loop structures, sequence information, and secondary structures are essential in miRNA prediction. This study's limitations stemmed from insufficient datasets to train the model to avoid over or under-fitting. Finally, …
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On the fidelity of translation
… essential for the aminoacylation. The calculated minimum free energy pathway suggested a two-step binding mechanism, which consists of a fast initial binding of triphosphate, followed by a slow binding of the nucleoside. In the slow nucleoside binding step, a conserved histidine stabilizes the …
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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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The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
… realistic glycobiological condensed phase free energy computation. Ab-initio pucker free energy surfaces/volumes of !-Ribofuranose and !-Glucopyranose in vacuum and in water were computed. These are the first converged Hartree-Fock/MM free energy simulations for these carbohydrates …
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Computational studies of the structure, dynamics, and catalysis of the hepatitis delta virus ribozyme
… ribozyme was further investigated using QM/MM free energy simulations to include conformational sampling and entropic effects. Umbrella sampling simulations were combined with a finite temperature string method to generate the multidimensional free energy surface underlying the self-cleavage …