Browsing by Subject "entropy"
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Item Estimation of Velocity Distribution and Suspended Sediment Discharge in Open Channels Using Entropy(2011-08-08) Cui, HuijuanIn hydraulics, velocity distribution is needed to determine flow characteristics, like discharge, sediment discharge, head loss, energy coefficient, moment coefficient, and scour. However, the complicated interaction between water and sediment causes great difficulties in the measurement of flow and sediment discharge. Thus, the development of a method which can simulate the velocity distribution and sediment discharge in open channels is designable. Traditional methods for the estimation of velocity distribution, such as the Prandtl-von Karman logarithmic velocity and of sediment concentration distribution, such as the Rouse equation, are generally invalid at or near the channel bed and are inaccurate at the water surface. Considering the limitations of traditional methods, entropy based models have been applied, yet the assumption on the cumulative distribution function made in these methods limits their application. The objective of this research is to develop an efficient method to estimate velocity distribution and suspended sediment discharge in open channels using the Tsallis entropy. This research focuses on a better-organized hypothesis on the cumulative probability distribution function under more applicable coordinates, which should be transformable in different dimensions. Velocity distribution and sediment distribution are derived using the Tsallis entropy under the hypothesis that the cumulative probability distribution follows a non-linear function, in which the value of the exponent is shown to be related to the width-depth ratio of channel cross-section. Three different combinations of entropy and empirical methods for velocity and sediment concentration distribution are applied to compute suspended sediment discharge. Then advantages and disadvantages of each method are discussed. The velocity distribution derived using the Tsallis entropy is expected to be easy to apply and valid throughout the whole cross-section of the open channel. This research contributes to the application of entropy theory and shows its advantages in hydraulic engineering.Item The impact of protein fluctuations on molecular recognition(2008-12-05) anthony C manson; Dr. Wlodek Bujalowski; Dr. Werner Braun; Dr. Montgomery Pettitt; Dr. Mary MoslenThe effect of protein fluctuations on molecular recognition is poorly understood. Prediction of useful properties such as binding affinity using rigid structures has produced sporadic success. Although attempts have been made to model the effect of\r\nconformational fluctuations, capturing the impact of backbone relaxation has remained\r\nparticularly elusive. In order to investigate these effects, a series of surface exposed\r\nAla/Gly mutants were designed in the flexible RT loop of the C-terminal SH3 domain of\r\nSEM5. One set of mutations was designed to perturb the ensemble of accessible\r\nconformations in the unbound ensemble while leaving the interaction surface with the\r\nligand unchanged. The other set was designed to perturb both the interaction surface as\r\nwell as the ensembles of bound and free conformations. The effects of these mutations\r\nwere investigated by generating random conformations of the RT loop and performing\r\nprincipal component analysis to organize the randomly generated conformational states\r\ninto a coherent landscape. To predict the effect of these mutations, we developed a\r\nstatistical mechanical technique using a simplified energy function that only applied the\r\neffects of excluded volume and implicit solvation. This energy function was utilized to\r\nweight an ensemble of conformational states from which aggregate thermodynamic\r\nproperties could be derived. The computed effects of the mutations on the binding\r\naffinity agreed with experimentally determined values (R= 0.97) from isothermal titration\r\ncalorimetry. The results indicate that the bound state of SEM5 SH3 domain contains a\r\nconsiderable repertoire of conformational variants of the high-resolution structure and\r\nthat the determinants of binding cannot be elucidated from the static structure of the\r\nbound complex.\r\nItem Investigation of combustive flows and dynamic meshing in computational fluid dynamics(Texas A&M University, 2005-02-17) Chambers, Steven B.Computational Fluid Dynamics (CFD) is a ?eld that is constantly advancing. Its advances in terms of capabilities are a result of new theories, faster computers, and new numerical methods. In this thesis, advances in the computational ?uid dynamic modeling of moving bodies and combustive ?ows are investigated. Thus, the basic theory behind CFD is being extended to solve a new class of problems that are generally more complex. The ?rst chapter that investigates some of the results, chapter IV, discusses a technique developed to model unsteady aerodynamics with moving boundaries such as ?apping winged ?ight. This will include mesh deformation and ?uid dynamics theory needed to solve such a complex system. Chapter V will examine the numerical modeling of a combustive ?ow. A three dimensional single vane burner combustion chamber is numerically modeled. Species balance equations along with rates of reactions are introduced when modeling combustive ?ows and these expressions are discussed. A reaction mechanism is validated for use with in situ reheat simulations. Chapter VI compares numerical results with a laminar methane ?ame experiment to further investigate the capabilities of CFD to simulate a combustive ?ow. A new method of examining a combustive ?ow is introduced by looking at the solutions ability to satisfy the second law of thermodynamics. All laminar ?ame simulations are found to be in violation of the entropy inequality.