Utilization of amorphous metallic alloy has received much attention for use in numerous microelectronic and electrochemical devices since they provide unique electrical, thermal conductivity, and magnetic properties. To develop these functional properties, it is essential to understand the amorphous structure and the property relationships. First principles calculations provide insight into the structure, thermodynamic stability, electronic and magnetic properties of amorphous alloys. For Ru- and Co-based alloys, the thermodynamic stability was examined by calculating the mixing energy along with those of crystalline counterparts. The amorphous RuP, CoP, RuB, and CoB alloys, become energetically more favorable than their crystalline counterparts at moderate P(B) content. The atomistic structures have well-defined local structures depending on the atomic size ratio and electronic interactions between constituent elements. Their local ordering is attributed to strong p-d hybridization, which contributes to stabilizing the Ru(Co)-P(B) alloys. Surface segregation of P(B) and interfacial adhesion with copper were also studied. Li-X (X: Si, Ge, and Sn) were examined when 1 or 2 Li atoms are inserted into the interstitial sites. Li insertion in the tetrahedral site, which is the most preferable site in the diamond matrix, causes outward displacement and charge localization around the X neighbors, thereby weakening of the covalent bonds leading to destabilization of the host matrix. We present the energetics, structure, electronic and mechanical properties of crystalline and amorphous Li-X (X: Si, Ge, Sn, and Si+Sn) alloys. Our calculations show that the incorporation of Li leads to disintegration of the tetrahedrally-bonded X network into small clusters of various shapes. Electronic structure analysis highlights that the charge transfer leads to weakening or breaking of X bonds with the growing splitting between s and p states, and consequently the Li-X alloys softens with increasing Li content. / text

The purpose of the work is to show how to employ the experimental data from geocryology and soil physics for thermodynamic calculations of gas hydrate phase equilibria by taking into account pore water behavior in sediments. In fact, thermodynamic calculation is used here to determine the amount of non-clathrated pore water content in sediments in equilibrium with gas and hydrate phases. A thermodynamic model for pore water behavior in sediments is developed. Taking into account the experimental water potential data, the model calculations show good agreement with the experimentally measured unfrozen water content for different pressure and temperature conditions. The proposed thermodynamic model is applied for calculations of three-phase equilibria: multicomponent gas phase (methane, natural gas, etc.) – pore water in clay, sand, loamy sand, etc. – bulk (or pore) hydrate. As a result, correlations have been established between unfrozen and non-clathrated water content in natural sediments.

This thesis presents several ways to understand transports of air and water masses in the atmosphere and ocean, and the transports of energy that they imply. It presents work using various kinds of observations as well as computer simulations of the atmosphere and oceans. One of the main focuses is to identify similarities and differences between models and observations, as well as between different models. The first half of the thesis applies Lagrangian methods to study flows in the atmosphere and oceans. Part of the work focuses on understanding how particles follow the currents in the Baltic Sea and how they disperse. It is suggested that the commonly used regional ocean model for the Baltic Sea, RCO, underestimates the transport and the dispersion of the particles, which can have consequences for studies of e.g. biogeochemistry as well as for operational use. A similar methodology is used to study how particles are transported between the tropics and mid-latitudes by the large-scale atmospheric circulation. It is found that the mass transport associated with northbound and southbound particles can cancel in the zonally averaged circulation, and we propose that the degree of cancellation depends on the method of averaging. The latter half of the thesis focuses on Eulerian stream functions and specifically a thermodynamic stream function that combines the zonal and meridional circulations of the atmosphere into a single circulation. The results are used to study the inter-annual variability of the intensity and thermodynamic properties of the global atmospheric circulation. A significant correlation to ENSO variability is found both in reanalysis and the EC-Earth coupled climate model. It is also shown that a set of models from the CMIP5 project show a slowdown of the atmospheric circulation as a result of global warming and associated changes in near-surface moisture content and upper-level radiative cooling. / Denna avhandling presenterar olika metoder för att studera datormodeller av atmosfä- ren, haven, och klimatsystemet. Metoderna använder såväl Lagrangeska synsätt dvs att betrakta atmosfären eller haven som individuella partiklar i rörelse, som Eulerska synsätt där atmosfären och haven ses som gas eller vätska i rörelse. I artikel 1 sjö- sätts ett antal “surface drifters” i Östersjön som driver fritt med havsströmmarna och vars hastighet mäts av satelliter. Genom att modellera Lagrangeska partiklars rörelser i Östersjön och jämföra med dessa “surface drifters” kan det visas att datormodeller kan underskatta både medelhastigheten av partiklarna samt deras utbredning. I ar- tikel 2 simuleras luftmassornas rörelser mellan tropikerna och mellanbreddgraderna (∼ 45◦N/S). Ett medelvärde över all longituder tenderar att ignorera betydande mass- och energitransporter mellan tropikerna och mellanbredderna, och dessa kvantifieras i detalj i artikel 2. Artiklarna 3 och 4 presenterar en metod för att studera atmosfärens storskaliga rörelser utifrån ett termodynamiskt perspektiv där luftmassornas värme och fukt studeras. Det visas att variationer ytvattentemperatur vid ekvatorn i Stilla havet kan få atmosfären att, i ett globalt medelvärde, bli fuktigare och varmare samtidigt som masstransporter- na saktar ner. På samma sätt visas att en global uppvärmning till följd av ökade utsläpp av växthusgaser kan få atmosfären att bli varmare, fuktigare och att masstransporterna kan sakta ner. / <p>At the time of the doctoral defence the following papers were unpublished and had a status as follows: Paper 3: In press; Paper 4: Manuscript.</p> / BalticWay

No description available.

<p>While a number of different proteomic, genomic, and computational approaches exist for the characterization of drug action, each of the experimental approaches developed to date has both strengths and weaknesses. Currently, there is no one "perfect" assay for drug mode-of-action studies. A protocol that could assay all the proteins in the proteome for both direct and indirect binding interactions of drugs would greatly facilitate studies of drug action. Recently, the SPROX (stability of proteins from rates of oxidation) technique was developed as a chemical modification- and mass spectrometry-based strategy for detecting protein-ligand interactions by monitoring the change in thermodynamic stability of proteins upon ligand binding. This is accomplished by monitoring the denaturant dependent oxidation of globally protected methionine residues. The SPROX technique has been interfaced with bottom-up proteomics methods to allow for the proteome-wide analysis of protein-ligand interactions. However, the strategy has been limited by the need to detect and quantify methionine containing peptides in the bottom-up proteomics experiment. </p><p>The work in this dissertation is focused on evaluating the current SPROX protocol, developing modifications to improve proteome coverage, and applying the SPROX platform to two different drug mode-of-action studies. Three main strategies were employed to improve protein coverage. First, a chemo-selective isolation of un-oxidized methionine containing peptides was employed to enrich for methionine containing peptides, and it was found to produce a ~2-fold improvement in proteomic coverage. Second, a pre-fractionation strategy involving the use of isoelectric focusing was employed to decrease sample complexity prior to LC-MS/MS analysis and it was found to generate a ~2-3 fold improvement in proteomic coverage, however when combined with the methionine enrichment strategy the improvement was ~6-fold as the benefits of both were additive. Third, a tryptophan modification strategy was developed that could ultimately expand the number of useful peptides in proteome-wide SPROX experiments to include those that contain tryptophan. Also, investigated was the use of several different mass spectrometer systems (including a bench-top quadrupole and orbitrap system and two different quadrupole time-of-flight systems) in the SPROX protocol. The results of these studies indicate that there is a significant advantage in proteome coverage when faster mass spectrometers are used. The use of high energy collision dissociation (HCD) in the orbitrap system was also more advantageous than the use of collision induced dissociation (CID) in the Q-ToF systems. Regardless of the mass spectrometer used, the major source of error in the SPROX experiment was found to be the random error associated with the LC-MS/MS analysis of isobaric mass tagged peptides. This random error was found to yield a false discovery rate of between 3 and 10% for "hit" peptides in the SPROX experiment. </p><p>The above improvements in the SPROX protocol were used in two protein-ligand binding experiments. One set of experiments involved studies on two small molecules with a specific anti-cancer phenotype in human colon cancer cells. These studies identified 17 proteins as potential "hits" of these two small molecules. After preliminary validation of these proteins, approximately 50% were eliminated as false positives and one protein, p80/nucleophosim, showed consistent data indicating a destabilizing interaction with both small molecules. The destabilization is indicative of an indirect interaction with the small molecules that would be mediated through a protein-protein interaction network. In another set of experiments the breast cancer drug, tamoxifen, and its main, active metabolite, 4-hydroxy tamoxifen, were assayed for binding to the proteins in a yeast cell lysate to better understand its adverse effects on yeast cells. The results of these studies identified ~80 proteins as potential "hits" of these two drugs. After preliminary validation of these proteins, approximately 30% were eliminated as false positives and one protein, SIS1, type II Hsp40, showed consistent data indicative of a direct binding interaction.</p> / Dissertation

The Mo-Ni-Re system is one of the important subsystems of the Ni based superalloys engineered for use in high temperature applications. Considering the contradictions among previously reported information, the present study was devoted to the complete experimental determination of the phase equilibria in the Mo-Ni-Re system, structural characterization of its intermetallic phases and thermodynamic modeling of the system with the help of the CALPHAD method. The experimental investigation of phase equilibria was carried out with the help of equilibrated alloys and phase diagrams of the Ni-Re and Mo-Ni-Re system (at 1200°C and 1600°C) were proposed. In comparison with previous investigations, the Ni-Re phase diagram determined during the present study showed significant difference in terms of homogeneity domains, freezing ranges and peritectic reaction temperature. The 1200°C isothermal section of the Mo-Ni-Re system proposed during the present study showed large extension of the Mo-Re σ phase and Mo-Ni δ phase in the ternary region. In addition, presence of two previously unknown ternary phases was also observed. The isothermal section of the Mo-Ni-Re system at 1600°C also showed large extension of σ phase in the ternary region whereas extension of the Mo-Re χ phase in both isothermal sections was restricted to narrow composition range. The presence of the ternary phases observed in the 1200°C isothermal was not evidenced in 1600°C isothermal section. On the other hand, partial investigations of phase boundaries in the Mo-Ni and Mo-Re binary systems and determination of liquidus projection of the Mo-Ni-Re system was also carried out. The liquidus projection of the Mo-Ni-Re system proposed during present study also showed largely extended primary crystallization fields of the Mo-Re σ phase and Re solid solution in the ternary region. Since isothermal sections of the Mo-Ni-Re system showed largely extended homogeneity domain of σ, structural characterization of the Mo-Ni-Re σ with particular emphasis on determination of site occupancy trends as a function of composition was carried out by combined Rietveld refinement of the X-ray and neutron diffraction data. The experimental results gathered during the present study along with the information available in the literature were used as input for thermodynamic modeling of the Mo-Ni-Re system. The thermodynamic description of the Mo-Re system was taken from literature whereas thermodynamic modeling of the Mo-Ni, Ni-Re and Mo-Ni-Re system was carried out during the present study with the help of the CALHAD method.Keywords: Mo-Ni; Mo-Re; Ni-Re; Mo-Ni-Re; phase diagram; isothermal section; structural characterization; thermodynamic modeling; CALPHAD method

Cities interact with and rely on energy in complex ways. Fundamentally cities rely upon high quality energy and outputs of low quality for their very existence. The energy flows and transformations enabling cities are tied to physical limits imposed by thermodynamics. Understanding of these limits and the relationships among energy and cities, it is revealed herein, is of vital importance to the sustainability of cities. Four contributions to this understanding are provided. The first articulates how the thermodynamic forces driving cities, together with the dynamic environment within which cities reside, stipulates what type of activities within cities are sustainable. Second, a model depicting the scaling relationship between urban energy use and economic output is devised, and it’s fit to historical data demonstrated via nonlinear regression. By differentiating between energy used to grow and energy used to maintain economic output the model illustrates how reductions in these values on a per dollar basis abets growth while the reverse delays growth, or stops it altogether when energy needs for maintenance become too high. Third, an exergy network conceptualization of cities is developed that reveals the structure of the exergy flows in a city. The topology of the network drastically alters the city’s ability to maximize usefulness of imported energy as well as alter that variability in the amount of usefulness extracted. Finally, the resilience of cities with respect to energy is presented by considering the energy storage and buffer capacity of the urban metabolism. The city of Toronto is shown to have adequate flexibility in food and transport fuels to withstand operation for days without undue interruption of typical activities. Together these differing aspects of the open non-equilibrium details of cities establish an improved prescription of the sustainable city.

Cities interact with and rely on energy in complex ways. Fundamentally cities rely upon high quality energy and outputs of low quality for their very existence. The energy flows and transformations enabling cities are tied to physical limits imposed by thermodynamics. Understanding of these limits and the relationships among energy and cities, it is revealed herein, is of vital importance to the sustainability of cities. Four contributions to this understanding are provided. The first articulates how the thermodynamic forces driving cities, together with the dynamic environment within which cities reside, stipulates what type of activities within cities are sustainable. Second, a model depicting the scaling relationship between urban energy use and economic output is devised, and it’s fit to historical data demonstrated via nonlinear regression. By differentiating between energy used to grow and energy used to maintain economic output the model illustrates how reductions in these values on a per dollar basis abets growth while the reverse delays growth, or stops it altogether when energy needs for maintenance become too high. Third, an exergy network conceptualization of cities is developed that reveals the structure of the exergy flows in a city. The topology of the network drastically alters the city’s ability to maximize usefulness of imported energy as well as alter that variability in the amount of usefulness extracted. Finally, the resilience of cities with respect to energy is presented by considering the energy storage and buffer capacity of the urban metabolism. The city of Toronto is shown to have adequate flexibility in food and transport fuels to withstand operation for days without undue interruption of typical activities. Together these differing aspects of the open non-equilibrium details of cities establish an improved prescription of the sustainable city.

The aim of this experimental study is to investigate the inhibitive properties of polyglycol and polyglycol+KCl aqueous solutions on hydrate formation, which causes serious fluid flow problems, especially during deepwater drilling operations. As the petroleum industry continues to search oil in deeper and deeper seas, the possibility of facing hydrate problems during drilling operations increases because of the suitable conditions for hydrate formation. The main goal of this study is to investigate the hydrate inhibition capacity (thermodynamic and/or kinetic inhibition) of polyglycol and KCl which are mainly used in drilling fluids for shale inhibition and wellbore stability. A high pressure hydrate forming reactor is used to form and dissociate methane hydrate from aqueous solutions of polyglycol and polyglycol+KCl. In total 10 experiments were carried out, 5 of them with 0%, 1%, 3%, 5% and 7 % by volume of polyglycol solutions (Group-A experiments). The remaining 5 experiments (Group-B) had 8% by weight of KCl in solution in addition to the same polyglycol concentrations of Group-A experiments. Among the two chemicals tested for their hydrate inhibiting potentials, polyglycol did not exhibit any thermodynamic inhibition capacity while KCl was observed to have the ability of hydrate inhibition thermodynamically. On the other hand, increase in polyglycol concentration at constant KCl concentration (Group-B) increases the hydrate formation depression capacity of KCl. Polyglycol inhibits methane hydrate formation kinetically. The higher the polyglycol concentration in aqueous solution, the lower is the initial rate of methane hydrate formation (corresponding to first 15 minutes of hydrate formation). On the other hand, there exists a slower change of methane hydrate formation rate as polyglycol concentration increases.

Time- and rate-dependent materials such as polymers, bituminous materials, and soft materials clearly display all four fundamental responses (i.e. viscoelasticity, viscoplasticity, viscodamage, and healing) where contribution of each response strongly depends on the temperature and loading conditions. This study proposes a new general thermodynamic-based framework to specifically derive thermo-viscoelastic, thermo-viscoplastic, thermo-viscodamage, and micro-damage healing constitutive models for bituminous materials and asphalt mixes. The developed thermodynamic-based framework is general and can be applied for constitutive modeling of different materials such as bituminous materials, soft materials, polymers, and biomaterials. This framework is build on the basis of assuming a form for the Helmohelotz free energy function (i.e. knowing how the material stores energy) and a form for the rate of entropy production (i.e. knowing how the material dissipates energy). However, the focus in this work is placed on constitutive modeling of bituminous materials and asphalt mixes. A viscoplastic softening model is proposed to model the distinct viscoplastic softening response of asphalt mixes subjected to cyclic loading conditions. A systematic procedure for identification of the constitutive model parameters based on optimized experimental effort is proposed. It is shown that this procedure is simple and straightforward and yields unique values for the model material parameters. Subsequently, the proposed model is validated against an extensive experimental data including creep, creep-recovery, repeated creep-recovery, dynamic modulus, constant strain rate, cyclic stress controlled, and cyclic strain controlled tests in both tension and compression and over a wide range of temperatures, stress levels, strain rates, loading/unloading periods, loading frequencies, and confinement levels. It is shown that the model is capable of predicting time-, rate-, and temperature-dependent of asphalt mixes subjected to different loading conditions.