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 21 for “"Statistical thermodynamics"”.
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Statistical thermodynamics of virus assembly
Experiments show that MgSO4 salt has a non-monotonic effect as a function of MgSO4 concentration on the ejection of DNA from bacteriophage lambda. There is a concentration, N0, at which the minimum amount of DNA is ejected. At lower or higher concentrations, more DNA is ejected. We propose that …
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Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.
… and drive the activation or repression of genes. Statistical thermodynamics has shown to be a promising avenue to describe the binding mechanisms of TFs. Here, I present ChIPanalyser, an R/Bioconductor package that models and predicts binding of TFs to DNA using a statistical thermodynamic …
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Statistical physics of dislocation nucleation by nanoindentation
… by developing analysis methods based on statistical thermodynamics, and are used to evaluate the probability of various atomistic mechanisms. The results of this procedure implicate a critical activation event occurring in a single atomic volume, with an activation enthalpy of a fraction …
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Fluid-phase thermodynamics from molecular-level properties and interactions based in quantum theory
A methodology to predict the thermodynamics of macroscopic fluid systems from quantum chemistry and statistical thermodynamics has been developed. This work extends the group-contribution concepts most utilized in chemical engineering. Computational chemistry software is used to define the …
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Computational Algorithms for Predicting Membrane Protein Assembly From Angstrom to Micron Scale
… systematically, based on the principles of statistical thermodynamics and probabilities and designed using well-structured computational algorithms, up to micron-level molecular architecture of tight junctions, forming a robust prediction with molecular details packed for up to four orders …
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Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale
… systematically, based on the principles of statistical thermodynamics and probabilities and designed using well-structured computational algorithms, up to micron-level molecular architecture of tight junctions, forming a robust prediction with molecular details packed for up to four orders …
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Laser engine simulation using pressure based navier-stokes solver
… Calculation (HPC) based on the the methods of statistical thermodynamics. Two thruster configurations, two laser types (CO₂ and iodide), various laser power levels, and various injection conditions are tested. The results of these tests include the temperature, pressure, velocity and Mach …
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Estimating transcription factor binding properties in human cell lines using statistical methods and genomics datasets
… is an R/Bioconductor package that implements a statistical thermodynamics model for transcription factor binding by leveraging binding motifs, chromatin accessibility and transcription factor concentration. This study aimed to use ChIPanalyser on 135 human transcription factors in the K562 cell …
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Modeling dynamic ruptures with high resolution fault zone physics
… the fault zone and develop a non-equilibrium statistical thermodynamics-based viscoplastic framework for modeling granular systems within the Shear Transformation Zone theory. Thirdly, we present a new hybrid computational algorithm for modeling earthquake ruptures in complex fault zone …
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Computational heterogeneous catalysis applied to steam methane reforming over nickel and nickel/silver catalysts
… reactions taking place during SMR. A detailed statistical thermodynamics framework is developed to allow for the calculation of enthalpies, entropies, and free energies of the surface species at the temperatures and pressures relevant to industrial SMR. The data from the DFT calculations are …
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Hydrogen in aluminum oxide and at the aluminum oxide/aluminum interface: an ab initio thermodynamics and Monte Carlo investigation
… challenging. This thesis utilizes ab initio statistical thermodynamics to resolve the Al₂O₃/Al interface structure and the effect of point defects on the properties of Al₂O₃ and Al₂O₃/Al interface. In the first part, we identify dopants that reduce hydrogen permeability of Al₂O₃ coatings for …
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The role of interfacial and 'entropic' enzymes in transitory starch degradation : a mathematical modeling approach
… is provided by conceptually linking statistical thermodynamics and polymer biochemistry. Each reactant is interpreted as an energy level, transitions between which are constrained by the enzymatic mechanisms. Combinations of in vitro assays of polymer-active CAZymes essential for …
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Fret Studies of DNA Binding By Lambda Cro Variants
… and translation and thus amenable to modeling by statistical thermodynamics. In these cases, the distribution of proteins between monomers and dimers and between nonspecific and specific DNA complexes can be simply predicted from the measured free energy of each of the states. Lambda Cro is …
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Hybrid Carbon Fiber/ZnO Nanowires Polymeric Composite for Stuctural and Energy Harvesting Applications
… the different toms in the simulation box. Proper statistical thermodynamics were employed to relate the dynamics of the molecular model to the macroscale thermodynamic states (pressure, temperature and volume). Per the computed potential energies of the different components of the composite, it …
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The development of h Homogeneous nucleation rate model for thermoplastic foams based on a molecular partition function and Fickian diffusion
… estimates the forward rate of the process. A statistical-mechanical approach was used to create an energy term that is based on a molecular partition function. In this approach, the bulk phase (polymer and blowing, agent mixture) of the system is treated as a regular solution and the potential …
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Improving Thermodynamic Models of Transcription by Combining ChIP and Expression Measurements of Synthetic Promoters
… should be possible.</p><p>State ensemble statistical thermodynamic models are a class of models used to describe combinatorial transcriptional regulation. One way to parameterize these models is measuring the expression of a reporter gene driven by many similar promoters . Models …
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Biomolecular Simulations with Machine Learning Potentials
Computational modelling has become a key component of the drug discovery toolbox. Typically, these tools are driven by empirical forcefields, which are computationally efficient but approximate representations of the true quantum mechanical potential energy surface. Over the last several years, …
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A thermodynamic definition of protein folds
… we propose to model the proteins from a statistical thermodynamic viewpoint based upon their average energetic properties. We show that this model can be used to (1) better characterize the partial unfolding process of proteins, and (2) reclassify the protein fold space from a new …
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Computational modeling of gene expression from regulatory sequences
… and various perturbation experiments, and make statistical inferences from the ensemble about detail regulatory mechanisms of ind. Years of genetic experiments have put forth an assortment of hypotheses about ind regulation. We use our modeling approach to show how a mechanism involving MAPK …
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Adding ammonia during Fischer-Tropsch Synthesis: Pathways to the formation of N-containing compounds
… it was desired to evaluate the kinetics and thermodynamics of the NH₃ decomposition on the Fe(100) surface at relevant temperatures and pressures (by combining the DFT results with statistical thermodynamics) to better understand the role of NHₓ surface species involved in the pathway to the …
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