Knowledge on cysteine oxidation state and disulfide bond connectivity is of great importance to protein chemistry and 3-D structures. This research is aimed at finding the most relevant features in prediction of cysteines oxidation states and the disulfide bonds connectivity of proteins. Models predicting the oxidation states of cysteines are developed with machine learning techniques such as Support Vector Machines (SVMs) and Associative Neural Networks (ASNNs). A record high prediction accuracy of oxidation state, 95%, is achieved by incorporating the oxidation states of N-terminus cysteines, flanking sequences of cysteines and global information on the protein chain (number of cysteines, length of the chain and amino acids composition of the chain etc.) into the SVM encoding. This is 5% higher than the current methods. This indicates to us that the oxidation states of amino terminal cysteines infer the oxidation states of other cysteines in the same protein chain. Satisfactory prediction results are also obtained with the newer and more inclusive SPX dataset, especially for chains with higher number of cysteines. Compared to literature methods, our approach is a one-step prediction system, which is easier to implement and use. A side by side comparison of SVM and ASNN is conducted. Results indicated that SVM outperform ASNN on this particular problem. For the prediction of correct pairings of cysteines to form disulfide bonds, we first study disulfide connectivity by calculating the local interaction potentials between the flanking sequences of the cysteine pairs. The obtained interaction potential is further adjusted by the coefficients related to the binding motif of enzymes during disulfide formation and also by the linear distance between the cysteine pairs. Finally, maximized weight matching algorithm is applied and performance of the interaction potentials evaluated. Overall prediction accuracy is unsatisfactory compared with the literature. SVM is used to predict the disulfide connectivity with the assumption that oxidation states of cysteines on the protein are known. Information on binding region during disulfide formation, distance between cysteine pairs, global information of the protein chain and the flanking sequences around the cysteine pairs are included in the SVM encoding. Prediction results illustrate the advantage of using possible anchor region information.

No description available.

The thin film technology is of great importance in modern society and is a key technology in wide spread applications from electronics and solar cells to hard protective coatings on cutting tools and diffusion barriers in food packaging. This thesis deals with various aspects of thin film processing and the aim of the work is twofold; firstly, to obtain a fundamental understanding of the sputter deposition and the reactive sputter deposition processes, and secondly, to evaluate sputter deposition of specific material systems with low friction properties and to improve their performance.From studies of the reactive sputtering process, two new methods of eliminating the problematic and undesirable hysteresis effect were found. In the first method it was demonstrated that an increased process pressure caused a reduction and, in some cases, even elimination of the hysteresis. In the second method it was shown that sufficiently high oxide content in the target will eliminate the hysteresis. Further studies of non-reactive magnetron sputtering of multi-element targets at different pressures resulted in huge pressure dependent compositional gradients over the chamber due to different gas phase scattering of the elements. This has been qualitatively known for a long time but the results presented here now enable a quantitative estimation of such effects. For example, by taking gas phase scattering into consideration during sputtering from a WS2 target it was possible to deposit WSx films with a sulphur content going from sub-stoichiometric to over-stoichiometric composition depending on the substrate position relative the target. By alloying tungsten disulphide (WS2) with carbon and titanium (W-S-C-Ti) its hardness was significantly increased due to the formation of a new titanium carbide phase (TiCxSy). The best sample increased its hardness to 18 GPa (compared to 4 GPa for the corresponding W-S-C coating) while still maintaining a low friction (µ=0.02) due to the formation of easily sheared WS2 planes in the wear track.

Abstract Glutaredoxins (Grx) are small thiol disulphide oxidoreductases with a conserved active site sequence -CXXC/S- and a glutathione (GSH) binding site. They catalyze the reduction of protein disulphides, preferring protein-GSH mixed disulphides as substrates. The accumulation of protein-GSH mixed disulphides has been observed during oxidative stress, where they may serve both a regulatory and an antioxidant function by protecting the enzymes from irreversible oxidation. Once oxidative stress has been removed the GSH-protein mixed disulphides are reduced by GSH or, more efficiently, by Grx. The present study showed for the first time that Grx1 and Grx2 can be detected in healthy human lung. Highly specific expression of Grx1 was observed in alveolar macrophages, but it could also be detected from sputum supernatant. Grx1 levels in alveolar macrophages were lower in selected inflammatory diseases than in control lung samples. Grx1 was also mainly negative in the fibrotic areas in usual interstitial pneumonia, an aggressive fibrotic lung disease. Overall, the present study suggests that Grx1 is a potential redox modulatory protein regulating the intracellular as well as extracellular homeostasis of glutathionylated proteins and GSH not only in healthy lung, but also in inflammatory and fibrotic lung diseases. In order to study the mechanism of action of glutaredoxins in vitro, a new real-time fluorescence-based method for measuring the deglutathionylation activity of glutaredoxins using a glutathionylated peptide as a substrate was developed. The first reaction intermediate in the deglutathionylation reaction was shown to be exclusively Grx-GSH mixed disulphide and this specificity was solely dependent on the unusual γ-linkage present in glutathione. The study also demonstrated the role of conserved residues in the proximity of proposed GSH binding site to the GSH binding specificity of E. coli Grx1. Opening the binding groove and removing charged residues enabled Grx to form more readily mixed disulfides with other molecules besides GSH. Different members of the PDI family showed considerably lower activity levels compared to glutaredoxins and, in contrast to the glutaredoxin-GSH mixed disulphide, the only intermediate in the PDI catalysed reaction was PDI-peptide mixed disulphide.

This thesis work contains electrical transport and low frequency (1/f) noise measurements in ultrathin graphene and Molybdenum disulphide (MoS2) field effect transistors (FET). From the measurements, We mainly focus on the origin of disorder in both the materials. To address the orgin of disorder in graphene, we study single and bilayer graphene-FET devices on SiO2 substrate. We observe that both conductivity and mobility are mainly determined by substrate induced long range, short range, and polar phonon scattering. For further confirmation, we fabricate suspended graphene devices which show extremely high mobility. We find that, in contrast to substrate-supported graphene, conductivity and mobility in suspended graphene are governed by the longitudinal acoustic phonon scattering at high temperature and the devices reach a ballistic limit at low temperature. We also conduct low frequency 1/f noise measurements, known to be sensitive to disorder dynamics, to extract more information on the nature of disorder. The measurements are carried out both in substrate-supported and suspended graphene devices. We find that 1/f noise in substarted graphene is mainly determined by the trap charges in the SiO2 substrate. On the other hand, noise behaviour in suspended graphene devices can not be explained with trap charge dominated noise model. More-over, suspended devices exhibit one order of magnitude less noise compared to graphene on SiO2 substrate. We believe noise in suspended graphene devices probably originate from metal-graphene contact regions. In the second part of our work, We present low temperature electrical transport in ultrathin MoS2 fields effect devices, mechanically exfoliated onto Si/SiO2 substrate. Our experiments reveal that the electronic states in MoS2 are localized well up to the room temperature over the experimentally accessible range of gate voltage. This manifests in two dimensional (2D) variable range hopping (VRH) at high temperatures, while below ~ 30 K the conductivity displays oscillatory structures in gate voltage arising from resonant tunneling at the localized sites. From the correlation energy (T0) of VRH and gate voltage dependence of conductivity, we suggest that the charged impurities are the dominant source of disorder in MoS2. To explore the origin of the disorder, we perform temperature dependent I - V measurements at high source-drain bias. These measurements indicate presence of an exponentially distributed trap states in MoS2 which originate from the structural inhomogeneity. For more detailed investigation, we employ 1/f noise which further confirms possible presence of structural disorder in the system. The origin of the localized states is also investigated by spectroscopic studies, which indicate a possible presence of metallic 1T-patches inside semiconducting 2H phase. From all these evidences, we suggest that the disorder is internal, and achieving high mobility in MoS2 FET requires a greater level of crystalline homogeneity.

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Hydrogen is a clean and sustainable form of carrier of energy that can be used in mobile and stationary applications. At present hydrogen is produced mostly from fossil sources. Solar photoelectrochemical processes are being developed for hydrogen production. Storing hydrogen can be done in three main ways: in compressed form, liquid form and by chemical bonding. Near term spaceport operations are one of the prominent applications for usage of large quantities of liquid hydrogen as a cryogenic propellant. Efficient storage and transfer of liquid hydrogen is essential for reducing the launch costs. A Two Stage Reverse Turbo Brayton Cycle (RTBC) CryoCooler is being developed at University of Central Florida. The cryocooler will be used for storage and transport of hydrogen in spaceport and space vehicle application. One part in development of the cryocooler is to reduce the friction and wear between mating parts thus increasing its efficiency. Tribological coatings having extremely high hardness, ultra-low coefficient of friction, and high durability at temperatures lower than 60 K are being developed to reduce friction and wear between the mating parts of the cryocooler thus improving its efficiency. Nitrides of high-melting-point metals (e.g. TiN, ZrN) and diamond-like-carbon (DLC) are potential candidates for cryogenic applications as these coatings have shown good friction behavior and wear resistance at cryogenic temperatures. These coatings are known to have coefficient of friction less than 0.1 at room temperature. However, cryogenic environment leads to increase in the coefficient of friction. It is expected that a composite consisting of a base layer of a hard coating covered with layer having an ultra-low coefficient of friction would provide better performance. Extremely hard and extremely low friction coatings of titanium nitride, molybdenum disulphide, TiN/MoS2 bilayer coatings, DLC and DLC/MoS2 bilayer coatings have been chosen for this application. TiN film was deposited by reactive DC magnetron sputtering system from a titanium target and MoS2 film was deposited by RF magnetron sputtering using a MoS2 target. Microwave assisted chemical vapor deposition (MWCVD) technique was used for preparation of DLC coatings. These composite coatings contain a solid lubricating phase and a hard ceramic matrix phase as distinctly segregated phases. These are envisioned as having the desired combination of lubricity and structural integrity. Extremely hard coatings of TiN and DLC were chosen to provide good wear resistance and MoS2 was chosen as the lubricating phase as it provides excellent solid lubricating properties due to its lamellar crystal structure. This thesis presents preparation; characterization (SEM and XRD), microhardness and tribological measurements carried out on TiN and TiN/MoS2 coatings on aluminum and glass substrate at room temperature. It also presents initial development in preparation of DLC coatings.

My work presents a novel approach to fabricate binder free three-dimensional carbon nanotubes/sulfur (3DCNTs/S) hybrid composite by a facile and scalable method increasing the loading amount from 1.86 to 8.33 mg/cm2 highest reported to date with excellent electrochemical performance exhibiting maximum specific energy of ~1233Wh/kg and specific power of ~476W/kg, with respect to the mass of the cathode. Such an excellent performance is attributed to the fact that 3DCNTs offers higher loading amount of sulfur, and confine polysulfide within the structure. In second part of the thesis, molybdenum disulfide (MoS2) is typically studied for three electrochemical energy storage devices including supercapacitors, Li-ion batteries, and hybrid Li-ion capacitors. The intrinsic sheet like morphology of MoS2 provides high surface area for double layer charge storage and a layered structure for efficient intercalation of H+/ Li+ ions. My work demonstrates the electrochemical analysis of MoS2 grown on different substrates including copper (conducting), and carbon nanotubes. MoS2 film on copper was investigated as a supercapacitor electrode in three electrode system exhibiting excellent volumetric capacitance of ~330F/cm3 along with high volumetric power and energy density in the range of 40-80 W/cm3 and 1.6-2.4 mWh/cm3, respectively. Furthermore, we have developed novel binder-free 3DCNTs/ MoS2 as an anode materials in half cell Li-ion batteries. The vertically oriented morphology of MoS2 offers high surface area and active electrochemical sites for efficient intercalation of Li+ ions and demonstrating excellent electrochemical performance with high specific capacity and cycling stability. This 3DCNTs/ MoS2 anode was coupled with high surface area southern yellow pine derived activated carbon (SYAC) cathode to obtain hybrid 3DCNTs/ MoS2 || SYAC Li-ion capacitor (LIC), which delivers large operating voltage window of 1-4.0V with excellent cycling stability exhibiting capacitance retention of ~80% after 5000 cycles.

4 Abstract Purinergic P2X receptors are membrane ion channels activated by extracellular ATP. There are seven isoforms of mammalian P2X receptors designated as P2X1-7, which according to their structure represent a specific family of ligand gated ionic channels, with extraordinary structural/functional properties. The P2X receptor consists of three subunits and each subunit has two transmembrane domains. Crystalographic data demonstrate that ionic channel pore is situated between the second transmembrane domains. Crystal structure of P2X4 receptor from the zebrafish (Danio rerio) is available in both open and closed state of the channel and the exact structure of ATP binding site is solved. The aim of this thesis was to study the structure-function relationships in a model of recombinant P2X4 receptor of the rat. By employing the point mutagenesis and electrophysiological recording, the functional importance of conserved cysteine residues in the ectodomain and amino acid residues which form the extracellular vestibule was investigated. All ten cysteins were substituted one by one with alanine or threonine and ATP-induced currents were measured from HEK293T cells expressing wild type (WT) and mutated P2X4 receptors. The results indicate that C116A, C126A, C149A and C165A mutations disrupt two disulfide bonds...

The production of large area, high quality two-dimensional (2D) materials using chemical vapour deposition (CVD) has been an important and difficult topic in contemporary materials science research, after the discovery of the diverse and extraordinary properties exhibited by these materials. This thesis mainly focuses on the CVD synthesis of two 2D materials; bilayer graphene and monolayer tungsten disulphide (WS2). Various factors influencing the growth of each material were studied in order to understand how they affect the quality, uniformity, and size of the 2D films produced. Following this, these materials were combined to fabricate 2D vertical heterostructures, which were then spectroscopically examined and characterised. By conducting ambient pressure CVD growth with a flat support, it was found that high uniform bilayer graphene could be grown on the centimetre scale. The flat support provides for the consistent delivery of precursor to the copper catalyst for graphene growth. These results provide important insights not only into the upscaling of CVD methods for growing large area, high quality graphene and but also in how to transfer the product onto flexible substrates for potential applications as a transparent conducting electrode. Monolayer WS2 is of interest for use in optoelectronic devices due to its direct bandgap and high photoluminescence (PL) intensity. This thesis shows how the controlled addition of hydrogen into the CVD growth of WS2 can lead to separately distributed domains or centimetre scale continuous monolayer films at ambient pressure without the need for seed molecules, specially prepared substrates or low pressure vacuum systems. This CVD reaction is simple and efficient, ideal for mass-production of large area monolayer WS2. Subsequent studies showed that hexagonal domains of monolayer WS2 can have discrete segmentation in their PL emission intensity, forming symmetric patterns with alternating bright and dark regions. Analysis of the PL spectra shows differences in the exciton to trion ratio, indicating variations in the exciton recombination dynamics. These results provide important insights into the spatially varying properties of these CVD-grown TMDs materials, which may be important for their effective implementation in fast photo sensors and optical switches. Finally, by introducing a novel non-aqueous transfer method, it was possible to create vertical stacks of mixed 2D layers containing a strained monolayer of WS2, boron nitride, and graphene. Stronger interactions between WS2 on graphene was found when swapping water for IPA, likely resulting from reduced contamination between the layers associated with aqueous impurities. This transfer method is suitable for layer by layer control of 2D material vertical stacks and is shown to be possible for all CVD grown samples, a result which opens up pathways for the rapid large scale fabrication of vertical heterostructure systems with large area coverage and controllable thickness on the atomic level.