This thesis is a report of the work I have done over the last five years to study thermodynamic and kinetic aspects of single-molecule behavior in the condensed phase. It is concerned specifically with the development of analytically tractable models of various phenomena that have been observed in experiments on such single-molecule systems as colloids, double-stranded DNA, multi-unit proteins, and enzymes. In fluid environments, the energetics, spatial conformations, and chemical reactivity of these systems undergo fluctuations that can be characterized experimentally in terms of time correlation functions, survival probabilities, mean first passage times, and related statistical parameters. The thesis shows how many of these quantities can be calculated in closed form from a model based on simple Brownian motion, or generalizations of it involving fractional calculus. The theoretical results obtained here have been shown to agree qualitatively or quantitatively with a range of experimental data. The thesis therefore demonstrates the effectiveness of Brownian motion concepts as a paradigm of stochasticity in biological processes.

In this research, a first-principles, non-equilibrium thermodynamic-ensemble approach applicable across all temporal and spatial scales is developed based on steepest-entropy-ascent quantum thermodynamics (SEAQT). The SEAQT framework provides an equation of motion consisting of both reversible mechanical dynamics and irreversible relaxation dynamics, which is able to describe the evolution of any state of any system, equilibrium or non-equilibrium. Its key feature is that the irreversible dynamics is based on a gradient dynamics in system state space instead of the microscopic mechanics of more traditional approaches. System energy eigenstructure and density operator (or ensemble probability distribution) describe the system and system thermodynamic state, respectively. Extensive properties (i.e., energy, entropy, and particle number) play a key role in formulating the equation of motion and in describing non-equilibrium state evolutions. All the concepts involved in this framework (i.e., eigentstructure, density operator, and extensive properties) are well defined at all temporal and spatial scales leading to the extremely broad applicability of SEAQT. The focus of the present research is that of developing non-equilibrium thermodynamic models based specifically on the irreversible part of the equation of motion of SEAQT and applying these to the study of pure relaxation processes of systems in non-equilibrium states undergoing chemical reactions and heat and mass diffusion. As part of the theoretical investigation, the new concept of hypo-equilibrium state is introduced and developed. It is able to describe any non-equilibrium state going through a pure relaxation process and is a generalization of the concept of stable equilibrium of equilibrium thermodynamics to the non-equilibrium realm. Using the concept of hypo-equilibrium state, it is shown that non-equilibrium intensive properties can be fundamentally defined throughout the relaxation process. The definition of non-equilibrium intensive properties also relies on various ensemble descriptions of system state. In this research, three SEAQT ensemble descriptions, i.e., the canonical, grand canonical, and isothermal-isobaric, are derived corresponding, respectively, to the definition of temperature, chemical potential, and pressure. To computationally and not just theoretically permit the application of the SEAQT framework across all scales, a density of states method is developed, which is applicable to solving the SEAQT equation of motion for all types of non-equilibrium relaxation processes. In addition, a heterogeneous multiscale method (HMM) algorithm is also applied to extend the application of the SEAQT framework to multiscale modeling. Applications of this framework are given for systems involving chemical kinetics, the heat and mass diffusion of indistinguishable particles, power cycles, and the complex, coupled reaction-diffusion pathways of a solid oxide fuel cell (SOFC) cathode. / Ph. D.

published_or_final_version / Mechanical Engineering / Doctoral / Doctor of Philosophy

No description available.

No description available.

The thermodynamic properties of chloride, nitrate and nitrite AFm hydrates have been determined. Investigations of solid solutions and thermodynamic calculations on the influence of these anions on mineralogical changes in cement paste were performed and compared with experiments. To calculate volume changes, densities of principal crystalline phases occurring in cement were critically assessed and tabulated, in some cases with addition of new data. Database was obtained by calculating densities from crystallographic data and unit cell contents. In hydrated cements, anion sites in AFm phase are potentially occupied by OH, SO₄ and CO₃ ions. C1, NO₃ or NO₂ ions readily displace hydroxide, sulfate and carbonate in the AFm structures. Nitrates and nitrites do not have ability to displace chloride from the Friedel’s salt (C1-AFm) though. The binding power of AFm for nitrite/nitrate/chloride was calculated and confirmed experimentally at 25°C. It was observed that presence of chloride, nitrate or nitrite alters the AFm/Aft balance and thereby affect the specific volume of paste solids. It was found that the success of nitrite as a corrosion inhibitor for protection of embedded steel arises from its “smart” behaviour. AFm normally stores and sequesters nitrite. If chloride ingress occurs in service, the AFm undergoes ion exchange, gaining chloride and forming Friedel’s salt, while releasing soluble nitrite ions to the pore fluid. As a result, the aqueous ratio of [NO₂^-]/[C1^-] increases and remains within the passivation range for steel.

Student Number : 0009716H - MSc dissertation - School of Molecular and Cell Biology - Faculty of Science / Positive charges play an important role in the active site of a variety of proteins including alpha class GST. The presence of Arg15 at the subunit interface between the H- and Gsite of hGST A1-1 was shown to be important for the catalytic function of the enzyme, thus providing an electrostatic potential in the G-site. This electrostatic potential favours ionisation and activation of GSH bound to hGST A1-1. Although much is known regarding the catalytic function of GSTs, little is known of the effect of Arg15 on the binding of glutathione conjugates and nonsubstrate ligands. Others (Matulis and Lovrien, 1998) have pointed out that binding of the nonsubstrate ligand ANS is accomplished via ion pair formation with a charged residue such as Arg. Therefore, in order to evaluate the importance of the positive charge provided by the side chain of Arg15 in the active site of hGST A1-1 protein engineering techniques were employed to generate an R15L variant. The variant does not display a detectable difference in the secondary or tertiary structural content relative to the wild type hGST A1-1 protein. The catalytic activity of the R15L variant is, however, substantially reduced indicating local tertiary structural changes at and possibly near the active site. In the presence of ANS the fluorescence spectra of the variant R15L protein had a significantly lower intensity relative to wild type protein indicating either increased exposure of hydrophobic surface area at the Hsite and/or reduced number of ANS molecules bound (i.e., reduced affinity). Although ANS is displaced by GSO3 - in the wild type protein, no such displacement is observed for the R15L variant protein. Isothermal titration calorimetry experiments for GSO3 - and ANS binding to R15L indicated that the variant protein binds GSO3 - more tightly (higher affinity) than ANS (lower affinity). The above information, taken together, argues in favour of both molecules (ANS and GSO3 -) occupying the active site of R15L simultaneously. Despite the fact that there is no experimental crystal structure of hGST A1-1 complexed with either of the ligands, the placement of ANS was argued (Dirr et al., 2005) to be at the H-site and of GSO3 - at the G-site of the protein. The binding of ANS is both enthalpically and entropically favourable over the temperature range investigated (5 to 25°C) indicating expulsion of water molecules from the active site as well as the lack of a localised C-terminal #1;9 helix. The hydrophobic character of both the ligand and the site which accommodates it (H-site) contribute favourably towards the reaction enthalpy. ANS is conformationaly more constrained than GSO3 - when found free in solution, thus exhibiting more favourable conformational entropy change upon binding to R15L variant. The binding of GSO3 - is enthalpically favourable but entropically opposed. The expulsion of water molecules from the G-site, which accommodates GSO3 -, is insufficient to compensate for the loss of conformational entropy of both the ligand and C-terminal #1;9 helix, which becomes localised upon binding. However, favourable enthalpic contributions arise from the formation of hydrogen bonds, salt links and van der Waals contacts between the R15L variant and the ligand and the C-terminal #1;9 helix. Arg15 forms a salt link with Glu104 of the neighbouring domain and therefore provided an ideal opportunity to evaluate the role of Arg15 and its impact on interdomain stability. Conformational stability and unfolding studies of the R15L variant, monitored via fluorescence, indicated that the variant deviates from the model of a two-state transition. There are no stable thermodynamic intermediate(s) observed, but the increase in the mvalue is an indicator of a transition state which is more stable against urea relative to the wild type protein. Kinetically (Wallace et al., 1998b), the wild type hGST A1-1 follows a three-state unfolding transition where the kinetic intermediate is defined as having undergone conformational changes at the domain-domain interface and the C-terminal region. The substitution of Arg15 with Leu may have impacted on the packing of the native form of the variant R15L relative to the wild type GST A1-1, thus rendering the R15L protein more stable against urea. Arg15, therefore, may have an important role at the interdomain interface of GSTs.

Submitted in fulfillment of the academic requirements for the Masters of Applied Science (Chemistry), Durban University of Technology, Durban, South Africa, 2016. / In this work, the thermodynamic properties for the binary mixtures containing the ionic liquid (IL): 1-ethyl-3-methylimidazolium ethyl sulphate ([EMIM] [EtSO4]) were calculated. The binary systems studied were {pyridine (Py) or ethyl acetoacetate (EAA) or thiophene (TS) + [EMIM] [EtSO4]}. The results were interpreted in terms of the intermolecular interactions between the (pyridine + IL), (ethyl acetoacetate + IL), and (thiophene + IL) molecules. The physical properties: density, speed of sound, and refractive index were measured for the binary mixtures over the complete mole fraction range using an Anton Paar DSA 5000 M vibrating U- tube densimeter and an Anton Paar RXA 156 refractometer, respectively. The measurements were done at T = (298.15, 303.15, 308.15, 313.15, and 318.15) K and at p = 0.1 MPa. The experimental data was used to calculate the derived properties for the binary mixtures namely:- excess molar volume (V E ), isentropic compressibility (ks), molar refractions (R) and deviation in refractive index (Δn). For the binary mixtures, (Py or EAA or TS + IL), V E was negative throughout the whole composition range which indicates the existence of attractive intermolecular interaction between (pyridine + IL) and (ethyl acetoacetate + IL) for (thiophene + IL), V E was negative at low mole fraction of thiophene and became positive at high mole fraction of thiophene. For the binary mixtures (pyridine + IL), (ethyl acetoacetate + IL), ks was positive indicating that the binary mixtures were more compressible than the ideal mixture. For the binary mixture (thiophene + IL) ks was negative at low thiophene composition and positive at high composition indicating that the binary mixture was less compressible than the ideal mixture at low thiophene composition and more compressible at high composition of thiophene. The molar refraction, R, is positive for the (Py or EAA or TS + IL) binary systems at T = (298.15 – 318.15) K, molar refraction decreases as the organic solvent composition increases. For the binary mixture (pyridine + [EMIM] [EtSO4]), Δn is negative at mole fractions < 0.75 of pyridine and positive at mole fractions >0.75 at all temperatures and decreases with an increase in temperature. For the binary system (ethyl acetoacetate + [EMIM] [EtSO4]), Δn values are positive over the entire composition range and at all temperatures and increases with an increase in temperature. Δn values for the (thiophene + IL) system are negative for mole fractions of thiophene < 0.62 and becomes positive for mole fractions of thiophene > 0.62 and Δn increases with an increase in temperature. The Redlich-Kister smoothing equation was used successfully for the correlation of V E and Δn data. The Lorentz- Lorenz equation gave a poor prediction of V E , but a good prediction of density or refractive index. / M

A calorimeter was constructed for the determination of heat capacities of solids from 1.5 to 84 K. Results from this and other calorimeters are discussed, on bis(adiponitrile)copper(I) nitrate and tetramethylammonium trichloromanganate(II) ("TMMC") from 1.5 to 300 K, and on β-modification metal-free, copper(II), and nickel(II) phthalocyanines from under 5 to 80 K. Bis(adiponitrile)copper(I) nitrate has not-very-pronounced heat capacity maxima at 51 and 63 K. The total molar anomalous entropy change is estimated as between 1/2 R1n2 and R1n2. A previous assertion by X-ray crystallographers (Bull.Chem.Soc. Japan, <strong>32</strong>, 1221 (1959)) that the nitrate ions are disordered among four orientations at room temperature is not supported by these results or by consideration of structure factors or of the potential field on the nitrate ions. The TMMC heat capacity results are consistent with those given in Solid State Comm., <strong>15</strong>, 1185 (1974) and Phys.Rev. B, <strong>12</strong>, 5858 (1975). The anomalous molar entropy change associated with the monoclinic-hexagonal transition at 126 K is estimated as R1n2.8, of which 1/3 occurs between 124 and 127 K; it is suggested that the NC₄ tetrahedra undergo twofold disordering and that the H atoms also undergo some disordering. The heat capacities of the copper and nickel phthalocyanines are surprisingly different from each other, especially below 25K, where the former is markedly lower except for two first-order transitions at about 9-13K with a total molar entropy change of not less than approximately R1n4. Magnetic and Schottky anomalies are, apparently, not involved in either material; perhaps the transitions in copper phthalocyanine involve disordering of the copper ions among four positions in the plane of each molecule. Below 8 K, the heat capacities of copper and metal-free (but not nickel) phthalocyanine apparently obey the T³ law.

M.Ing. (Engineering Management) / The turbo-generator unit is very important equipment for electric power production, which has a high rate of failure. As the capacity increases, condition monitoring and fault diagnostic play a crucial role to guarantee safe operation and cost efficiency. The Eskom generator fleet is fast approaching the end of the original designed life. Also in view of the recent constrained reserve margin, outage downtime, maintenance costs, resource management, and maintenance inherent problems, a systematic approach is required to optimise scheduled time-based maintenance to improve reliability and availability. The subject of turbo machine condition monitoring requires the development of new technologies to diagnose the turbo-generator problems. Condition is an underlying factor in the performance of machines. It is also an important predictor of future performance that the machine is in a good condition and will be reliable and perform better. It provides a reference for maintenance engineers on the current condition of the turbo-generator. Trends in condition monitoring can be used to determine whether turbo-generators are being maintained and that are meeting their expected service lives or whether their performance is deterioration faster than expected. In the industry, traditional maintenance philosophies have taken two approaches; the first approach is to perform fixed time interval maintenance, where the system engineers take advantage of relaxed production cycles to fully inspect all aspects of the turbo-generator. The second route is for engineers to simply react to the generator failure as and when it happens. All too many utilities operate largely in the reactive run-to-failure mode. The old phrase, “if it aren’t broken don’t fix” is perennial run to failure argument. Nonetheless, making use of today’s technology, a new scientific methodology is becoming popular to maintenance management. For the purpose of investigating the management of condition-based monitoring and diagnostic technology to optimise timed-based maintenance of large turbo-generators, Eskom Units installed with condition monitoring techniques were considered. The minidissertation culminated in the compilation of case histories based on Eskom turbo-generator fleet where the technology is being rolled out. The literature survey looked at current industry practices in areas such as total productive maintenance (TPM), technology management and support systems, return on investment (ROI) and maintenance management to compare what Eskom is doing to what in others in the field are doing. There is no research work currently that has been done that links maintenance to maintenance technology deployment enablers. The research incorporates a number of operational experiences where some Eskom turbo-generator units continue to operate with a known fault. Regular maintenance interventions introduce faults into the machine due to human error, the opening of units and the handling of components. Attention is given to the impact of two-shifting or cyclic operation on turbo-generators that were originally designed for base load condition. The time–based maintenance of these units is not taking advantage of condition monitoring information. Also, the installed condition monitoring techniques fall short of addressing twoshifting monitoring requirements. A number of lessons were learnt from the implementation of the condition-based maintenance technology on Eskom generator fleet. The theory of maintenance management underscores establishment of a good relationship between system engineers, maintenance personnel and the technology provider which is key to success of the technology. It further indicates that this relationship must go deeper than the mere technology provider and the end user of the technology service agreement. The maintenance engineers are taking key business decision for the well-being of machines and maintenance technology needs to demonstrate that it is creating value for the business. From the people perspective attention is required to staff motivation and providing balanced job satisfaction, whilst ensuring that employees feel part of an integrated organisation maintenance strategy rather than of being under thread of disempowered by the technology. A myriad of considerations have been identified to affect the effective execution of conditionbase maintenance strategy on Eskom generator fleet. There are multiple dashboards or standards indicators that can be used for maintenance management improvement. It has been established that the success of the implementation of condition-based maintenance rests in the concept of total productive maintenance approach. Within the ambit of TPM, the entire process of maintenance must be managed on the basis of maintenance programmes plan, which will have function of connecting the various maintenance programmes.