Two different air-water interfacial flows are studied including plunging wave breaking and flow past a vertical surface-piercing circular cylinder using complementary CFDShip-Iowa version 6 including Cartesian grid solver and orthogonal curvilinear grid solver. The plunging wave-breaking process for impulsive flow over a bump in a shallow water flume has been simulated using the exact experimental initial and boundary conditions. The overall plunging wave breaking process is described with major wave breaking events identified: jet plunge, oblique splash and vertical jet. These major events repeat up to four times before entering the chaotic breaking. The simulations show a similar time line as the experiments consisting of startup, steep wave formation, plunging wave, and chaotic wave breaking swept downstream time phases. Detailed wave breaking processes, including wave profile at maximum height, first plunge, entrapped air bubble trajectories and diameters, kinetic, potential, and total energy, and bottom pressures are discussed along with the experimental results. The simulations show differences and similarities with other experimental and computational studies for wave breaking in deep water and sloping beaches. The geometry and conditions in the present study are relevant to ship hydrodynamics since it includes effects of wave-body interactions and wave breaking direction is opposite to the mean flow. Large-eddy simulation with the Lagrangian dynamic subgrid-scale model has been performed to study the flow past a surface-piercing circular cylinder for Re and Fr effect. The flow features near the air-water interface show significant changes with different Reynolds numbers from sub-critical to critical regime. It is shown that the interface makes the separation point more delayed for all regime of Re. Remarkably reduced separated region below the interface is observed for critical Re regime and it is responsible for much reduced wake and recirculation region behind the cylinder and it recovers in the deep flow. At different Fr, significant changes are shown on the air-water interface structures. At lower Fr, relatively smaller bow waves are observed in front of the cylinder with Kelvin waves behind the cylinder and small amount of free-surface roughness and turbulence are also seen in the wake region. For higher Fr, the bow wave increases remarkably with the larger wake region and deeper depression and it breaks with similar features of plunging breakers. Much more small air-water interface structures including splashes and bubbles are observed behind the cylinder. It is hard to distinguish the Kelvin waves behind the cylinder due to much larger free-surface oscillations and turbulence. As Fr increases, the Kelvin wave angle decreases and deeper and narrower depression region behind the cylinder are observed. The flow features around the cylinder are significantly changed due to this cavity region behind the cylinder.

Seminario para optar al título de Ingeniero Comercial, Mención Administración / Desde inicios de la revolución industrial, las prácticas y avances tecnológicos han impactado en nuestros hábitos de consumo y producción, pero también en el medio ambiente de una manera sin precedentes. Actualmente el problema medio ambiental y social ha derivado en lo que se conoce como desarrollo sostenible, en donde se propone que los sistemas sociales y ambientales tengan la misma o más importancia que los sistemas económicos, provocando un cambio de paradigma que invita a analizar las formas en cómo las economías producen y consumen bienes y servicios. Bajo esta lógica es que desde el legislativo chileno se intenta poner al día a los estándares internacionales en la materia y se han generado varios instrumentos legislativos para controlar las emisiones y en general, el desperdicio y daño que se genera por nuestra cultura del extraer, producir, comprar y desechar. La ley REP en Chile además de formalizar la industria del reciclaje, es una invitación al desarrollo más profundo de prácticas de uso de productos. Es el primer paso para desarrollar el tema de la gestión y uso adecuados de materiales en nuestra economía. Entendamos que el reciclaje es el último paso de los ciclos técnicos, y no, como se podría pensar, la solución al problema de residuos. Antes del reciclaje debemos reducir, prolongar el uso, reutilizar/redistribuir, remanufacturar/reacondicionar nuestros productos para una correcta valorización de los materiales, horas hombres y energía contenidas en él durante todo su ciclo de vida. Esta investigación tiene como objetivo describir los factores de éxito para la adopción y establecimiento de la circularidad dentro de nuestra economía y la ley REP, como parte de esta y no como finalidad para el problema de residuos, para definir cuáles son los puntos débiles de nuestros sistemas técnicos y sociales, además, establecer focos de innovación. Las principales conclusiones son el desarrollo de indicadores medio ambientales para las organizaciones cualquiera sea su giro, además de la incorporación de estas métricas a áreas de alto impacto en el comportamiento organizacional, como los sistemas de incentivos. Esta información debe ser transparentada y reportada como organización para poder guiar la toma de decisiones a nivel social respecto a este tema, entendiendo los principios de disponibilidad y comparación como motor de prácticas como la eco innovación y eco diseño. Además, establecemos el problema como ético: debemos hacernos cargo del impacto de nuestras acciones para asegurar el principio de intergeneracionalidad y cuidado de nuestros ecosistemas. / 2018-12

Circular dichroism (CD) spectra were obtained for bacteriophage T4 lysozyme and three of its mutants in the presence and absence of colloidal silica nanoparticles. Mutant lysozymes were produced by substitution of the isoleucine at position 3 with tryptophan, cysteine and leucine. Each substitution resulted in an altered structural stability, quantified by a difference in free energy of unfolding from the wild type. CD spectra recorded in the absence of colloidal silica agreed with x-ray diffraction data in that the mutants and wild type showed similar secondary structures. CD spectra of protein-nanoparticle complexes recorded after contact for 90 minutes showed significant differences from those recorded in the absence of nanoparticles, and these differences varied among the proteins. The percentage of a-helix lost in these proteins upon adsorption to silica nanoparticles was also recorded as a function of time by CD. For a 1:2 protein to particle mixture, different kinetic behaviors were observed among the proteins. The more unstable the protein, the greater the rate and extent of secondary structure loss upon adsorption. For a 1:1 protein to particle mixture, only results recorded with the tryptophan mutant were significantly different from the other variants. The kinetic data recorded for the 1:2 protein to particle ratio was evaluated using two different protein adsorption models. Both models allow proteins at an interface to exist in two different states: state 1 molecules retain their native conformation, while state 2 molecules lose a certain amount of their native secondary structure and occupy more surface area than state 1 molecules. The main difference between these two models is that one allows state 2 molecules to be adsorbed directly from solution, while the other requires that state 2 molecules be generated by surface-induced conversion of state 1 molecules. The former model showed a better fit to the data than the latter from a least squares comparison. Both models indicated that proteins of lower thermal stability have a greater tendency to adopt state 2 on silica. / Graduation date: 1997

Graduation date: 1994

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 228-251).

To understand protein stability and the mechanism of protein folding, it is essential that we gain a better understanding of the ensemble of conformations that make up the denatured state of a protein. The primary goal of the research described here was to see what we might learn about the denatured state using fluorescence. To this end, tryptophan was introduced at five sites in Ribonuclease Sa (RNase Sa): D1W, Y52W, Y55W, T76W, and Y81W. The fluorescent properties of the denatured states of these five proteins were studied and compared to the fluorescent properties of eight model compounds: N-acetyl-tryptophan-amide (NATA), N-acetyl-Ala-Trp-Ala-amide (AWA), N-acetyl-Ala-Ala-Trp-Ala-Ala-amide (AAWAA), and five pentapeptides based on the sequence around the original tryptophan substitutions in RNase Sa. Regardless of the denaturant, λmax for the proteins and model compounds differed very little, 349.3 ± 1.2 nm. However, significant differences were observed in the fluorescence intensity at λmax (IF), suggesting that IF is more sensitive to the immediate environment than λmax. The differences in IF are due in part to quenching by neighboring side chains. More importantly, IF was always significantly greater in the protein than in its corresponding pentapeptide, indicating that the protein exerts an effect on the tryptophan, which cannot be mimicked by the pentapeptide models. Acrylamide and iodide quenching experiments were also performed on the model compounds and proteins. Significant differences in the Stern-Volmer quenching constant (KSV) were also observed between the proteins and between the proteins and their corresponding pentapeptides. Importantly, the KSV for the protein was always less than in its corresponding pentapeptide. These data along with the IF data show that non-local structure in the unfolded state influences tryptophan fluorescence and accessibility. In summary, these and our other studies show that fluorescence can be used to gain a better understanding of the denatured states of proteins.

This thesis concerns the circular epistemology of Hegel's Phenomenology of Spirit and Science of Logic. I argue that these works can be read as epistemologies based on the dialectical structure of their progression. Furthermore, I claim that this dialectical structure is circular. I hold that the epistemology of these works is circular not only because it is anti-foundational, self-justifying, and presuppositionless, but also in these works one instance of knowledge depends on the next for its justification and so on, until the last instance of knowledge returns to the first. Hegel sharply attacks Reinhold in The Difference Between Fichte's and Schelling's System of Philosophy, but changes his mind in the Science of Logic to embrace elements of Reinhold's philosophy. I argue that, through this circular epistemological reading of the Phenomenology of Spirit and the Science of Logic, we can account for Hegel's changing view. / McAnulty College and Graduate School of Liberal Arts; / Philosophy / MA; / Thesis;

Structure-specific recognition of nucleic acids is a promising method to reduce the size of the recognition unit required to achieve the necessary selectivity and binding affinity for small molecules. It has been demonstrated recently that G-quadruplex DNA structures can be targeted by organic cations in a structure-specific manner. Structural targets of quadruplexes include the planar end surfaces of the G-tetrad stacked columns as well as four grooves. The significant structural differences between quadruplex DNA and duplex DNA make quadruplex DNA a very attractive target for highly selective, structure-specific drug design. We have used a variety of biophysical techniques including circular dichroism, surface plasmon resonance, thermal melting and absorbance spectroscopy to investigate small molecules that can selectively bind to the ends of human telomeric DNA as well as the ends of the G-quadruplex structure formed by the purine-rich promoter region of the c-MYC oncogene. We have also screened a library of heterocyclic diamidines, and identified one that binds selectively in the grooves of human telomeric quadruplex DNA. This compound is an excellent starting point for the design of new anti-cancer and anti-parasitic compounds with high affinity and selectivity for human telomeric DNA.

It has been shown that heterocyclic diamidines, a class of minor groove binders, are promising antimicrobial agents. These compounds bind none covalently to the minor groove of A/T rich regions of the kinetoplast DNA and kill the parasite. The mechanism of action of these compounds is not well understood, yet many hypotheses have been proposed. One of the methods that improve the specificity is cooperative binding. Since there are many binding sites available in k-DNA thus the cooperativity in adjacent binding sites is desirable. A library of compounds has been scanned and few of those compounds identified that are able to bind to two adjacent A/T binding sites separated by a single G. Many biophysical methods such as isothermal titration calorimetry, surface Plasmon resonance, circular dichroism and thermal melting have been used to explore the thermodynamic profiles and binding mode of these compounds. The pulsed field gradient NMR was used to investigate the structural changes to the DNA sequence upon binding of the minor groove binders and find a correlation between their biological difference and structural changes. The molecular dynamics was applied to look at the interaction of some of the heterocyclic diamidines to the DNA with more details and predict the unknown structures.

The present study aims to explore dynamical behavior of the fluid- elastic vibration of a single cylinder and three cylinders in shear flow by numerical simulations. This paper investigates the effects of the shear parameter, mass ratio, and spacing(P/D) on fluid-elastic vibration of the cylinders. Continuity equation and momentum equations are solved alternatively using a CFD package, Fluent 6.3.26. Dynamic meshing techniques together with the cylinder motion equations are employed in the simulation. Under different flow conditions, flow types, and cylinder motion models, lock-in and fluid-elastic vibration are studied. The results show that motion and flow types of a single cylinder in uniform flow are in agreement with the previous studies in literatures. In shear flow, however, as the shear parameter increases, the fluid-elastic vibration of the cylinder is induced, and thus amplitude of the cylinder increases considerably. Further, three cylinders in the shear flow are studied. Three cylinders arrangements (classified as side-by-side, tandem ,and stagger) and the distance between cylinders are the factors to cause fluid-elastic vibration. Compared with the single cylinder motion, three cylinders motion¡¦s critical flow velocity is smaller than that of the single cylinder motion, which means two cylinders motion are more subject to fluid-elastic vibration.