The present work, briefly described below, consists of implementation of several quantum algorithms in an NMR Quantum Information Processor. Game theory gives us mathematical tools to analyze situations of conflict between two or more players who take decisions that influence their welfare. Classical game theory has been applied to various fields such as market strategy, communication theory, biological processes, foreign policies. It is interesting to study the behaviour of the games when the players share certain quantum correlations such as entanglement. Various games have been studied under the quantum regime with the hope of obtaining some insight into designing new quantum algorithms. Chapter 2 presents the NMR implementation of three such algorithms. Experimental NMR implementation given in this chapter are: (i) Three qubit ‘Dilemma’ game with corrupt sources’. The Dilemma game deals with the situation where three players have to choose between going/not going to a bar with a seating capacity of two. It is seen that in the players have a higher payoff if they share quantum correlations. However, the pay-off falls rapidly with increasing corruption in the source qubits. Here we report the experimental NMR implementation of the quantum version of the Dilemma game with and without corruption in the source qubits. (ii) Two qubit ‘Ulam’s game’. This is a two player game where one player has to find out the binary number thought by the other player. This problem can be solved with one query if quantum resources are used. This game has been implemented in a two qubit system in an NMR quantum information processor. (iii) Two qubit ‘Battle of Sexes’ game. This game deal with a situation where two players have conflicting choices but a deep desire to be together. This leads to a dilemma in the classical case. Quantum mechanically this dilemma is resolved and a unique solution emerges. The NMR implementation of the quantum version of this game is also given in this chapter. Quantum adiabatic algorithm is a method of solving computational problems by evolving the ground state of a slowly varying Hamiltonian. The technique uses evolution of the ground state of a slowly varying Hamiltonian to reach the required output state. In some cases, such as the adiabatic versions of Grover’s search algorithm and Deutsch-Jozsa algorithm, applying the global adiabatic evolution yields a complexity similar to their classical algorithms. However, if one uses local adiabatic evolutions, their complexity is of the order √N (where N=2n) [37, 38]. In Chapter 3, the NMR implementation of (i) the Deutsch-Jozsa and the (ii) Grover’s search algorithm using local adiabatic evolution has been presented. In adiabatic algorithm, the system is first prepared in the equal superposition of all the possible states which is the ground state of the beginning Hamiltonian. The solution is encoded in the ground state of the final Hamiltonian. The system is evolved under a linear combination of the beginning and the final Hamiltonian. During each step of the evolution the interpolating Hamiltonian slowly changes from the beginning to the final Hamiltonian, thus evolving the ground state of the beginning Hamiltonian towards the ground state of the final Hamiltonian. At the end of the evolution the system is in the ground state of the final Hamiltonian which is the solution. The final Hamiltonian, for each of the two cases of adiabatic algorithm described in this chapter, are constructed depending on the problem definition. Adiabatic algorithms have been proved to be equivalent to standard quantum algorithms with respect to complexity [39]. NMR implementation of adiabatic algorithms in homonuclear spin systems face problems due to decoherence and complicated pulse sequences. The decoherence destroys the answer as it causes the final state to evolve to a mixed state and in homonuclear systems there is a substantial evolution under the internal Hamiltonian during the application of the soft pulses which prevents the initial state to converge to the solution state. The resolution of these issues are necessary before one can proceed for the implementation of an adiabatic algorithm in a large system. Chapter 4 demonstrates that by using ‘strongly modulated pulses’ for creation of interpolating Hamiltonian, one can circumvent both the problems and thus successfully implement the adiabatic SAT algorithm in a homonuclear three qubit system. The ‘strongly modulated pulses’ (SMP) are computer optimized pulses in which the evolution under the internal Hamiltonian of the system and RF inhomogeneities associated with the probe is incorporated while generating the SMPs. This results in precise implementation of unitary operators by these pulses. This work also demonstrates that the strongly modulated pulses tremendously reduce the time taken for the implementation of the algorithm, can overcome problems associated with decoherence and will be the modality in future implementation of quantum information processing by NMR. Quantum search algorithm, involving a large number of qubits, is highly sensitive to errors in the physical implementation of the unitary operators. This can put an upper limit to the size of the data base that can be practically searched. The lack of robustness of the quantum search algorithm for a large number of qubits, arises from the fact that stringent ‘phase-matching’ conditions are imposed on the algorithm. To overcome this problem, a modified operator for the search algorithm has been suggested by Tulsi [40]. He has theoretically shown that even when there are errors in implementation of the unitary operators, the search algorithm with his modified operator converges to the target state while the original Grover’s algorithm fails. Chapter 5, presents the experimental NMR implementation of the modified search algorithm with errors and its comparison with the original Grover’s search algorithm. We experimentally validate the theoretical predictions made by Tulsi that the introduction of compensatory Walsh-Hadamard and phase-flip operations refocuses the errors. Experimental Quantum Information Processing is in a nascent stage and it would be too early to predict its future. The excitement on this topic is still very prevalent and many options are being explored to enhance the hardware and software know-how. This thesis endeavors in this direction and probes the experimental feasibility of the quantum algorithms in an NMR quantum information processor.

Branched chain amino acids are classified as essential amino acids since their biosynthetic routes or pathways are restricted only to micro-organisms, fungi and plants. Given their unique distribution, the enzymes of the branched chain amino acid biosynthetic pathway are ideal targets for the development of herbicides, anti-bacterials and potentially antifungal agents. Acetohydroxy acid synthase (AHAS) catalyses the firs step in the biosynthesis of branched chain amino acids. AHAS activity had been first identified in extracts of E. coli as early as in 1958 by Brown and Umbarger . Ever since its discovery, AHAS have been found to exist in all eubacteria, archaebacteria, algae, yeast and plants. The enzymatic properties of prokaryotic and eukaryotic AHASs have been thoroughly investigated. A single isoform of the enzyme is known to exist in all organisms except in enterobacteria which have three isoforms of the enzyme. Activity of the three isoforms of E. coli AHAS (I, II and III) have been studied using various biochemical and biophysical methods. AHAS enzyme expressed in bacteria and yeast are heterotetrameric composed two large catalytic and two small regulatory subunits. While much has been learnt from the structure of the catalytic subunits (yeast and Arabidopsis thaliana) and the regulatory subunits (regulatory subunit of E. coli AHAS III) in isolation, the structural properties of the holoenzyme remain unexplored. AHAS is unique from the point of view that it exhibits a striking domain organization in the catalytic subunit and also in the regulatory subunits. Thus understanding the nature of protein – protein interactions both as domain – domain interactions within the subunit as well as protein – protein interactions across subunits is crucial to understanding the structural basis for the activity and regulation of this important enzyme. Of these, understanding the structural basis for the interaction between the regulatory and the catalytic subunits within the holoenzyme is paramount. The poor solubility and the intrinsic instability of the proteins have hampered the efforts to structurally characterize any of the AHAS holoenzymes. An active AHAS I construct has been created by Vyazmensky et. al., where the catalytic and the regulatory subunit have been expressed together as a single chain separated by a flexible linker. While this single chain construct is catalytically active, there have been no reports of successful crystallization of this single chain AHAS I enzyme. The crystallographically determined structure of the catalytic subunit of yeast and A. thaliana AHAS has shown that the protein is composed of three independently folded domains, α, β and γ. More importantly the polypeptide sequence of the catalytic subunits of AHAS across all species is largely conserved. This indicates that the overall tertiary folds of the catalytic subunit would be alike. The unique domain architecture of the AHAS catalytic subunit and the relatively small size of the regulatory subunit forms the basis for implementation of a novel strategy, in which structural interactions between the domains (catalytic site as well as the non catalytic site interactions) as well as structural interactions between the domains of the catalytic and the regulatory subunit of E. coli AHAS I can be explored in an incremental manner. Initiation of structural characterization of the individual domains of the catalytic subunit of E. coli AHAS I and understanding the structural basis of the interaction between the domains of the catalytic and the regulatory subunits of the protein, using solution NMR methods, forms the theme for this study. The domains of the catalytic subunit (ilvB) of E.coli AHAS I were identified based on the similarity in the sequence of this subunit with the yeast protein and the structural information of the yeast protein. The individual domains of the ilvB protein (ilvBα, ilvBβ and ilvBγ) and ilvN, the regulatory subunit of AHAS I, were cloned, expressed and purified for structural studies. The problem of poor expression and solubility profiles of the AHAS proteins was circumvented with the help of a novel cytb5 fusion system developed in our laboratory during the course of this study. The high expression levels of the fusion protein in minimal medium enabled the preparation of isotopically (15N, 13C/15N, 2H/13C/15N) enriched samples of the proteins in a cost effective manner. The cytb5 fusion system has provided very uniform and reliable expression of these proteins without accumulation of any protein in the insoluble fraction. From the structure of the catalytic subunit of yeast AHAS it is known that the α and γ domains of the protein interact to form the active site. The two domains provide group specific interaction sites for anchoring the co-factor TPP in an appropriate conformation for catalysis. The β domain on the other hand does not directly participate in the ormation of the active site but anchors the co-factor FAD which in turn plays a structural role in enzyme catalysis. In the present study we employed biochemical and biophysical methods to establish the structural integrity of the individually expressed domains of the catalytic subunit (ilvB) and the regulatory subunit of AHAS I. Reactions catalyzed by enzymes formed by assembling different domain and subunits indicate that the proteins when reconstituted in vitro form a catalytically competent complex. Formation of S-acetolactate, the product of the reaction catalyzed by the AHAS I holoenzyme, has been confirmed using colorimetric as well as spectroscopic methods such as CD and NMR. Multinuclear, multidimensional NMR methods have been utilized to obtain sequence specific assignments of apo - ilvBβ (non FAD bound form). Preparation of an NMR amenable sample of ilvBβ proved to be the rate limiting step due to the predisposition of the protein to undergo aggregation at concentrations required for solution NMR studies. However, careful screening of large number of buffer conditions enabled us to establish an optimum sample condition where the protein was soluble, stable and free of aggregation and hence suitable for NMR studies. Uniformly enriched 15N, 13C/15N, and 2H/13C/15N samples of ilvBβ were prepared to obtain sequence specific assignments and secondary structural information. From the secondary chemical shifts of backbone 13Cα atoms and short and medium range NOEs the secondary structure of the non FAD bound (apo) form of ilvBβ has been determined. Using chemical shift mapping methods, the residues of the ilvBβ domain that are involved in FAD binding have been identified. The distribution of the secondary structural elements and the residues that are involved in binding the co-factor FAD were found to be conserved for the E. coli and yeast proteins. This suggests that the tertiary Fold of the FAD binding β domain of the catalytic subunit of E. coli AHAS is identical to that in the yeast protein. The interaction between the individual domains of ilvB and ilvN (the regulatory subunit) has been investigated using spectroscopic methods. Changes in CD spectra indicate that ilvN interacts with ilvBα and ilvBβ domains of the catalytic subunit and not with the ilvBγ domain. NMR chemical shift mapping methods has shown that ilvN binds close to the FAD binding site in ilvBβ and proximal to the intra-subunit ilvBα/ilvBβ domain interface. The implication of this interaction and the role of the regulatory subunit on the activity of the holoenzyme are discussed.

No description available.

The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K+ channel KcsA are discussed.

I investigated how land use and human activities affect the sources and cycling of carbon (C) in subtropical rivers. Annually rivers receive a large amount of terrestrial C, process a portion of this C and return it to the atmosphere as CO2. The rest is transported to the ocean. Land use and human activities can affect the sources and fate of terrestrial C in rivers. However, studies on these effects are limited, especially in the humid subtropics. I combined measurements of the partial pressure of dissolved CO2 (pCO2), C isotopes (13C and 14C) and solid-state 13C nuclear magnetic resonance (NMR) to study C cycling in three subtropical rivers in Texas, two small rivers (Buffalo Bayou and Spring Creek) and a midsized river (the Brazos). My pCO2 data show that small humid subtropical rivers are likely a large source of atmospheric CO2 in the global C cycle. My measurements on pCO2, C isotopic and chemical composition of dissolved inorganic C (DIC) and particulate organic C (POC) revealed four types of effects of land use and human activities on river C cycling. First, oyster shells and crushed carbonate minerals used in road construction are being dissolved and slowly drained into Buffalo Bayou and the lower Brazos and may be a source of river CO2 released to the atmosphere. Second, river damming and nutrient input from urban treated wastewater stimulate algal growth and reduce CO2 evasion of the middle Brazos. Third, urban treated wastewater discharge is adding old POC to the middle Brazos and decomposition of the old POC adds to the old riverine DIC pool. Fourth, agricultural activities coupled with high precipitation enhance loss of old organic C (OC) from deep soils to the lower Brazos, and decomposition of the old soil OC contributes to the old CO2 evaded. I document for the first time the river C cycling effects of the use of carbonate minerals in construction and the riverine discharge of urban wastewater. Results presented here indicate the need to study disturbed river systems to better constrain the global C budget.

Concrete, due to its low cost, durability and fire resistance, is one of the world’s most widely used construction materials. Concrete is typically reinforced with steel bars and welded wire mesh. Since the cost of steel is increasing and steel corrosion is a significant contributor to structural failure, it is advantageous to find an alternative replacement reinforcement material which can not only replace the steel, but also resist corrosion. Over the past few decades, polymeric fibres have been used as concrete reinforcement. The chemical bond between the polymeric fibre and the cementitious matrix is an important factor in the fibre’s performance as a concrete reinforcement. Despite the great importance of the chemical bonding at the polymeric fibre/concrete interface, the chemical bonding at the interface is not well understood. To investigate the chemical interactions between polymeric materials and concrete, model systems of polymeric powder/white cement and polymeric fibre/white cement were chosen, where white cement was chosen for its suitability for nuclear magnetic resonance (NMR) experiments. The chemical interactions between poly(ethylenevinyl acetate) (EVA), poly(ether imide) (PEI), and poly(vinylidene fluoride) (PVDF) polymeric powders were studied via 13C NMR spectroscopy. It was found that EVA admixture undergoes hydrolysis in a cementitious matrix and follows a pseudo-second order kinetics model up to 32 days of cement hydration. PEI was also found to undergo hydrolysis at the imide functional group in a cementitious matrix. PVDF powder undergoes dehydrofluorination in the cementitious environment, producing a brown coloured polymer which is a result of conjugation of the polymer backbone. The interfacial transition zone between fluoropolymeric powder/white cement and steel and polymeric fibres (high density polyethylene/polypropylene, poly(vinyl alcohol), PEI, PVDF, and Nylon 6.6) was studied at short range using 19F, 27Al, and 43Ca NMR spectroscopy and at long range using the scanning electron microscopy/energy dispersive spectroscopy method. It was concluded that the chemistry of polymeric fibres themselves can alter the surrounding interfacial transition zone such that the calcium silicate hydrate favours a tobermorite or jennite-like structure, which could contribute to a strong or weak interface.

Nuclear magnetic resonance (NMR) spectroscopy was used to determine the structure of transmembrane (TM) segment IX of the Na+/H+ exchanger isoform 1 (NHE1) in dodecylphosphocholine micelles. Studying isolated TM segments in this fashion constitutes a well-established "divide and conquer" approach to the study of membrane proteins, which are often extremely difficult to produce, purify, and reconstitute in full-length polytopic form. A similar approach was combined with NMR spin relaxation experiments to determine the peptide backbone flexibility of NHE1 TM VII. The combined NMR structural and dynamics studies are consistent with an important role for TM segment flexibility in the function of NHE1, a protein involved in apoptosis and myocardial disease. The study of the rhomboid protease system is also described from two perspectives: 1) I attempted to produce several TM constructs of the substrate spitz or a related construct and the production and purification are described in detail; and 2) I present coarse-grained molecular dynamics simulation results for the E. coli rhomboid ecGlpG and a spitz TM construct. Spitz appears to preferentially associate with rhomboid near TMs 1 and 3 rather than the proposed substrate gate at TM 5. The two proteins primarily interact at the termini of helices rather than within the hydrocarbon core of the bilayer. Finally, I present a detailed analysis of coarse-grained molecular dynamics simulations of the fibroblast growth factor receptor 3 TM domain dimerization. Specifically, algorithms are described for analyzing critical features of wild-type and G380R mutant constructs. The G380R mutation is the cause of achondroplasia, the most common form of human dwarfism. The results suggest that the proximity of a residue to the dimer interface may impact the severity of the mutant phenotype. Strikingly, heterodimer and mutant homodimer constructs exhibit a secondary dimer interface which may explain the increased signaling activity previously reported for the G380R mutation--the helices may rotate with the introduction of G380R. The unifying theme of this work is the 'study of membrane proteins' using complementary techniques from structural biology and computational biochemistry.

In this thesis the synthesis and full characterization of a new bulky diphosphine, tetrakis-(2,6-diisopropylphenyl)diphosphine, are described. This compound displays facile oxidation and a thorough investigation of its redox properties has been studied by combining solution electrochemical techniques such as cyclic voltammetry (CV) and rotating disk electrode (RDE) voltammetry, with spectroscopic methods such as electron paramagnetic resonance (EPR) and Simultaneous Electrochemical Electron Paramagnetic Resonance (SEEPR) spectroscopy over a wide temperature range. Density functional theory (DFT) calculations were carried out to aid in structural characterization of the radical cation that is produced and to provide computed hyperfine splitting (HFS) constants for comparison with experimental results. For comparison to this species with bulky aromatic substituents, similar studies were conducted that have identified the previously unreported radical cation of tetrakis-tert-butyldiphosphine with a bulky aliphatic substituent that provides even higher steric pressure than the 2,6-diisopropylphenyl group. DFT calculations are reported, as is full characterization with fluid and frozen-solution EPR spectroscopy. Further CV and EPR (SEEPR) studies are reported that led to the identification of radical cations of tris(2,6-diisopropylphenyl)arsine and bis(2,4,6-triisopropylphenyl)(2,6-diisopropylphenyl)phosphine. DFT calculations are reported, as is full characterization with fluid and frozen-solution EPR spectroscopy. / xix, 172 leaves : ill (some col.) ; 29 cm

Glass materials surround us, impacting our lives on a daily basis, whether geologically deposited by volcanic activity or synthesized in large volume by industry. These amorphous oxide materials are vastly important due to their variety of applications including solid electrolytes, cookware, and storage of high-level nuclear waste. Although they are used for different applications, one common characteristic of these materials is the absence of long-range periodic order. This makes it difficult to use traditional solid-state characterization methods such as x-ray and neutron diffraction to study glass structure. Nuclear magnetic resonance (NMR), is ideally suited to study materials that exhibit short-range non-periodic order as it probes directly at a nucleus of interest and is sensitive to its local structural environment. This ability of solid-state NMR is illustrated by revealing local structural features in various oxide materials presented in this thesis. Within is a compilation of studies looking at basic borates, followed by borovanadates and complex borosilicate glasses. A multinuclear application of using quantum chemical calculations, single and double resonance methods and charge-balance models are discussed to deconvolute the complex structures of these disordered materials. This is followed by a study of a difficult low-gamma nucleus, 73Ge, (once considered “impossible” for solid-state NMR) which is explored for future material studies by looking at 73Ge NMR of crystalline and glassy germanates. 73Ge chemical shifts were related to coordination environments and quadrupolar coupling constants were related to bond length distortions.

Glass materials surround us, impacting our lives on a daily basis, whether geologically deposited by volcanic activity or synthesized in large volume by industry. These amorphous oxide materials are vastly important due to their variety of applications including solid electrolytes, cookware, and storage of high-level nuclear waste. Although they are used for different applications, one common characteristic of these materials is the absence of long-range periodic order. This makes it difficult to use traditional solid-state characterization methods such as x-ray and neutron diffraction to study glass structure. Nuclear magnetic resonance (NMR), is ideally suited to study materials that exhibit short-range non-periodic order as it probes directly at a nucleus of interest and is sensitive to its local structural environment. This ability of solid-state NMR is illustrated by revealing local structural features in various oxide materials presented in this thesis. Within is a compilation of studies looking at basic borates, followed by borovanadates and complex borosilicate glasses. A multinuclear application of using quantum chemical calculations, single and double resonance methods and charge-balance models are discussed to deconvolute the complex structures of these disordered materials. This is followed by a study of a difficult low-gamma nucleus, 73Ge, (once considered “impossible” for solid-state NMR) which is explored for future material studies by looking at 73Ge NMR of crystalline and glassy germanates. 73Ge chemical shifts were related to coordination environments and quadrupolar coupling constants were related to bond length distortions.