published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Caribbean-style hybrid concrete-masonry structures consist of a reinforced concrete frame with partially grouted and reinforced infill masonry walls. The infill walls are typically connected to the RC frame with cast-in-place dowel reinforcement along one or more edges of the wall. There is limited guidance in masonry codes to design these types of structures, and their seismic performance has not been characterized with experimental tests. In this work, an experimental program characterized the seismic behavior of hybrid concrete-masonry frames and showed they do not exhibit the typical strut mechanism observed in unreinforced masonry infill structures. In addition, a detailed finite element modeling scheme and calibration methodology was developed for modeling partially grouted masonry. This model includes a novel calibration method to account for the difference in the shear and tensile behavior of bed joints with grouted and ungrouted cells, and a method to account for the contribution of vertical reinforcement to the shear capacity of the bed joints with grouted cells. Finally, simplified models were proposed for use in engineering design. A modification of the TMS 402 strut model for hybrid concrete-masonry was suggested to incorporate the effects of the masonry infill and connections in large models.

The molecular identity of the green emission of polyfluorene is investigated in the view point of the molecular interactions between modeled segments. The semi-empirical quantum methods, ZINDO/S and AM1 (AM1-CIS), are used in combination to provide reasonable explanations for experimental spectroscopic properties of monodisperse fluorene oligomers and fluorene oligomers with a central keto defect in dilute solutions. Applying the same method, the molecular interactions between model segments are found to exist and are significant. However, the spectroscopic property change from the molecular interactions is negligible. In addition, the effects of mechanical stress and multi-defects on fluorene oligomers are investigated. On the other hand, the redox mechanisms proposed for the oxidation of an amphiphilic cyanine (C8S3) J-aggregates immobilized at ITO electrode and the subsequent dehydrogenated dimmer formation during cyclic voltammetry based on analysis of absorption spectra during the process are verified with the combined semi-empirical quantum methods similar to the previous methods. The absorption spectra assigned by experiment for electrochemical species involved in the proposed mechanism show reasonable match to the theoretically estimated absorption energies of the corresponding simplified model systems. In addition, the standard reduction potentials of the fairly large molecules, C8S3 monomer and its dehydrogenated dimer, are pursued with quantum mechanical calculations. The free energy difference between the oxidized and reduced states of the target systems is decomposed to electronic energy, solvation energy and temperature-dependent free energies terms. Based on AM1 ground state geometries and with the corresponding temperature dependent free energies, the electronic energies and the solvation energies are each evaluated by two different methods. The electronic energies are calculated with AM1 method and DFT calculation and, also, the solvation energies are obtained based on the atomic partial charges from AM1 and DFT wavefunctions with continuum dielectric solvent approximation. The four calculation schemes from the combinations of the electronic and solvation energy estimation methods are tested with the redox compounds with various molecular weights and the estimations are compared with the corresponding experimental redox potentials. The relative redox potentials between two different redox systems are found to be reasonably estimated with the four calculation schemes. / text

Making use of linear and homological algebra techniques we study the linearization map between the generalized Burnside and rational representation rings of a group G. For groups G and H, the generalized Burnside ring is the Grothendieck construction of the semiring of G × H-sets with a free H-action. The generalized representation ring is the Grothendieck construction of the semiring of rational G×H-modules that are free as rational H-modules. The canonical map between these two rings mapping the isomorphism class of a G-set X to the class of its permutation module is known as the linearization map. For p a prime number and H the unique group of order p, we describe the generators of the kernel of this map in the cases where G is an elementary abelian p-group or a cyclic p-group. In addition we introduce the methods needed to study the Bredon homology theory of a G-CW-complex with coefficients coming from the classical Burnside ring.

Digital communications have now become a fundamental part of modern society. In communications, channel coding is an effective way to reduce the information rate down to channel capacity so that the information can be transmitted reliably through the channel. This thesis is devoted to studying the mathematical theory and analysis of channel codes that possess a useful diagonal structure in the parity-check and generator matrices. The first aspect of these codes that is studied is the ability to describe the parity-check matrix of a code with sliding diagonal structure using polynomials. Using this framework, an efficient new method is proposed to obtain a generator matrix G from certain types of parity-check matrices with a so-called defective cyclic block structure. By the nature of this method, G can also be completely described by a polynomial, which leads to efficient encoder design using shift registers. In addition, there is no need for the matrices to be in systematic form, thus avoiding the need for Gaussian elimination. Following this work, we proceed to explore some of the properties of diagonally structured lowdensity parity-check (LDPC) convolutional codes. LDPC convolutional codes have been shown to be capable of achieving the same capacity-approaching performance as LDPC block codes with iterative message-passing decoding. The first crucial property studied is the minimum free distance of LDPC convolutional code ensembles, an important parameter contributing to the error-correcting capability of the code. Here, asymptotic methods are used to form lower bounds on the ratio of the free distance to constraint length for several ensembles of asymptotically good, protograph-based LDPC convolutional codes. Further, it is shown that this ratio of free distance to constraint length for such LDPC convolutional codes exceeds the ratio of minimum distance to block length for corresponding LDPC block codes. Another interesting property of these codes is the way in which the structure affects the performance in the infamous error floor (which occurs at high signal to noise ratio) of the bit error rate curve. It has been suggested that “near-codewords” may be a significant factor affecting decoding failures of LDPC codes over an additive white Gaussian noise (AWGN) channel. A near-codeword is a sequence that satisfies almost all of the check equations. These nearcodewords can be associated with so-called ‘trapping sets’ that exist in the Tanner graph of a code. In the final major contribution of the thesis, trapping sets of protograph-based LDPC convolutional codes are analysed. Here, asymptotic methods are used to calculate a lower bound for the trapping set growth rates for several ensembles of asymptotically good protograph-based LDPC convolutional codes. This value can be used to predict where the error floor will occur for these codes under iterative message-passing decoding.

There is a dogma in molecular biology that biological functions of peptides are determined by their structure ("function" code), coded in their primary structure ("structure" code). This work describes a new approach that attempts to elucidate these relationships by peptide topology design based on intriguing conformational properties of pipecolic acid based amino acids--like 1,2,3,4 tetrahydroisoquinoline (Tic). Opioid peptides, owing to the heterogeneity of opioid receptors, display a wide variety of physiological actions. The mu opioid receptor selective octapeptide I (D-Tic-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH₂) is a model compound for topographical modifications induced by sequential substitutions by Tic residue. Thus, the closely related peptides I and II (Gly-D-Tic-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH₂, obtained by coupling Gly residue to I) have contrasting affinities for the mu opioid receptor (IC₅₀ = 1.2 and 278 nM, respectively). Conformational analysis of I and II by means of 1D and 2D ¹H NMR spectroscopy allowed to determine dramatic differences in the side chain orientation of D-Tic in both peptides and to propose features of the bioactive conformation. The extended conformation of I (due to g(-) side chain conformation of D-Tic) is well recognized by the mu receptor in contrast to the folded conformation of II (due to a g(+) side chain conformation of D-Tic¹, that places the aromatic ring on the opposite side of the molecule), which is not. Peptide III (D-Phe-Cys-Tic-D-Trp-Orn-Thr-Pen-Thr-NH₂), featuring replacement of Tyr³ by Tic³, binds very weakly to the mu opioid receptor, due to rotation of the Tic aromatic side chain to the opposite side of the molecule (Tic side chain is in a g(+) conformation again). As these substitutions conserve the conformation of the backbone, constrained cyclic amino acids (picolic acid derivatives) can modify the topography of the peptide in a predictable manner, and (in conjunction with biological data) disclose structural elements of bioactive conformations. The mechanisms of pipecolic acid side chain rotamer selection, will be discussed in the context of design principles.

Vibrio vulnificus are marine bacteria causing fatal septicemia through wound infections or consumption of contaminated seafood. V. vulnificus is an excellent model for the study of surface polysaccharides, as it is capable of synthesizing capsular polysaccharide (CPS), lipopolysaccharide (LPS) and exopolysaccharide (EPS). V. vulnificus strains exhibit a multitude of carbotypes that evolve through unknown mechanisms. CPS is a confirmed virulence factor, but the genetics of its biosynthesis are unknown. The main objective of these experiments was to gain insight into the biosynthesis, regulation and evolution of ATCC 27562 outer surface polysaccharides. A miniTn10 transposon (Tn) system was used for mutagenesis and single insertions were confirmed through Southern analysis. A novel 25 kb CPS biosynthesis locus was identified through sequencing of regions surrounding Tn insertions; a region encoding putative LPS core biosynthetic functions was identified adjacent to the CPS cluster. The CPS locus contained features of O-antigen biosynthetic loci and was unusual in carrying characteristics of both group I and IV capsular biosynthetic loci. Mutations in this region resulted in elimination of CPS and LPS, and both were shown to be dependent on the activity of the polymerase Wzy. Evidence is presented here supporting horizontal transfer (HT) as a contributor to V. vulnificus CPS evolution. CPS regions of V. vulnificus 27562, YJ016 and CMCP6 contain strain specific genes surrounded by conserved regions, suggestive of HT. Moreover, a CPS locus virtually identical to that of 27562 was discovered in Shewanella putrefaciens strain 200. 27562 CPS is distinctive as it contains N-acetylmuramic acid. Genes encoding murA and murB activities were identified within the cluster and shown to be functionally redundant, supporting HT acquisition of this region. A screen of V. vulnificus gDNA library using CPS biosynthesis and transport mutants identified a cyclic diguanylate cyclase, dcpA. dcpA-mediated increase in cyclic diguanylate lead to EPS production, rugosity phenotypes and enhanced biofilm formation. Interestingly, virulence and motility were not affected suggesting complexity of cyclic diguanylate regulation in V. vulnificus, supported by the large number of cyclic diguanylate related proteins in Vulnificus strains.

The first part of the thesis addresses the fatigue performance of concrete bridge decks with GFRP stay-in-place structural forms replacing the bottom layer of rebar. The forms were either flat plate with T-up ribs joined using lap splices, or corrugated forms joined through pin-and-eye connections. The decks were supported by simulated Type III precast AASHTO girders spaced at 1775mm (6ft.). Two surface preparations were examined for each GFRP form, either using adhesive coating that bonds to freshly cast concrete, or simply cleaning the surface before casting. For the bonded deck with flat-ribbed forms, adhesive bond and mechanical fasteners were used at the lap splice, whereas the lap splice of the unbonded deck had no adhesive or fasteners. All the decks survived 3M cycles at 123kN service load of CL625 CHBDC design truck. The bonded flat-ribbed-form deck survived an additional 2M cycles at a higher load simulating a larger girder spacing of 8ft. Stiffness degradations were 9-33% with more reduction in the unbonded specimens. Nonetheless, live load deflections of all specimens remained below span/1600. The residual ultimate strengths after fatigue were reduced by 5% and 27% for the flat-ribbed and corrugated forms, respectively, but remained 7 and 3 times higher than service load. The second part of the thesis investigates the performance of bridge deck overhangs reinforced by GFRP rebar. Overhangs of full composite slab-on-girder bridge decks at 1:2.75 scale were tested monotonically under an AASHTO tire pad. Five tests were conducted on overhangs of two lengths: 260mm and 516mm, representing scaled overhangs of 6ft. and 8ft. girder spacing, respectively. The 260mm overhang was completely reinforced with GFRP rebar while the 516mm overhang consisted of a GFRP-reinforced section and a steel-reinforced section. The peak loads were approximately 2 to 3 times the established equivalent service load of 24.3kN, even though the overhangs were not designed for flexure according to the CHBDC but rather with lighter minimum reinforcement in anticipation of shear failure. The failure mode Abstract ii of each overhang section was punching shear. The steel-reinforced overhang section exhibited a greater peak load capacity (13.5%) and greater deformability (35%) when compared to the GFRP-reinforced overhang section. / Thesis (Master, Civil Engineering) -- Queen's University, 2013-09-17 18:54:18.131

This thesis is concerned with the deposition of nanoparticle films onto boron-doped diamond and tin-doped indium oxide (lTO) surfaces and the characterisation of the films using electron microscopy, powder diffraction methods and quartz crystal microbalance (QCM) data. The redox behaviour of the porous films was examined using cyclic voltammetry in various media to investigate potential electroanalytical applications. TiOz (anatase) mono-layer films were immobilised onto an inert boron-doped diamond substrate. Cyclic voltammetry experiments allowed two distinct steps in the reduction - protonation processes to be identified that are consistent with the formation of Ti(III) surface sites accompanied by the adsorption of protons. Preliminary data for electron transfer processes at the reduced TiOz surface such as the dihydrogen evolution process and the 2 electron - 2 proton reduction of maleic acid to succinic acid are discussed. Novel multi-layer TiOz films were deposited with a variety of organic binder molecules onto ITO substrates. The redox reactivity of Cuz+ with 1,4,7,10- tetraazacyclododecane- 1,4,7, IO-tetrayl- tetrakis (methyl-phosphonic acid) in solution and immobilised on an electrode surface are investigated. The influences of film thickness, scan rate, and pH on the electrochemistry of immobilised pyrroloquinoline quinone was investigated with two possible electron transport processes observed. The thickness of TiOz phytate films was found to change the shape of the resulting cyclic voltammograms dramatically. Computer simulation and impedance spectroscopy allowed insights into the diffusion of electrons to be obtained. 1, 1 ~Ferrocenedimethanol was employed as an adsorbing redox system to study the voltammetric characteristics of carboxymethyl-y-cyclodextrin films and evidence for two distinct binding sites is considered. The apparent transport coefficients for dopamine and Ru(NHJ)6J+ are estimated for TiOz Nafion® films. The electrochemical processes in biphasic electrode systems for the oxidation of water-insoluble N,N-didodecyl-N;N~diethyl-benzene-diamine (DDPD) pure and dissolved in di-(2-ethyl-hexyl)phosphate (HDOP) immersed in aqueous electrolyte media are described. Transfer of the anion from the aqueous electrolyte phase into the organic phase accompanies the oxidation of pure DDPD. In the presence of HOOP, oxidation is accompanied by proton exchange. The electrochemically driven proton exchange process occurs over a wide pH range. Organic microdroplet deposits of OOPD in HDOP at basal plane pyrolytic graphite electrodes are studied using voltammetric techniques and compared to the behaviour of organic microphase deposits in mesoporous Ti02 thin films. Two types of Ti02 thin film electrodes were investigated, (i) a 300-400 nm film on ITa and (ii) a 300-400 nm film on ITa sputter-coated with a 20 nm porous gold layer. The latter biphasic design is superior. Titanium carbide (TiC) nanoparticies were deposited onto ITa electrodes. Partial anodic oxidation and formation of novel core-shell TiC-Ti02 nanoparticies was observed at applied potentials positive of 0.3 V vs. SCE. Significant thermal oxidation of TiC nanoparticies by heating in air occurs at 250 °c leading to coreshell TiC-Ti02 nanoparticies, then Ti02 (anatase) at ca. 350 °c, and Ti02 (rutile) at temperatures higher than 750 °c. The electrocatalytic properties of the core-shell TiC-Ti02 nanoparticulate films were surveyed for the oxidation of hydroquinone, ascorbic acid, dopamine and nitric oxide (NO) in aqueous buffer media. Mono- and multi-layer Ce02 deposits on ITa are shown to be electrochemically active. A reduction assigned to a Ce(IV/III) process has been observed and followup chemistry in the presence of phosphate discovered. The interfacial formation of CeP04 has been proven and effects of the deposit type, pH and phosphate concentration on the process analysed. The electrochemistry of multi-layer Ce02 nanoparticulate films in organic solvent is shown to be more stable.

Transmissible spongiform encephalopathies (TSEs) are a group of fatal, neurodegenerative diseases that can affect both humans and animals. TSEs can be sporadic, familial, or acquired diseases. The prion hypothesis states that a misfolded form of the host glycoprotein, PrPC, acts as the infectious agent in TSE disease. The misfolded form, PrPSc, is increased in β-sheet content, detergent insoluble and partially resistant to proteinase K (PK) digestion. Based on the prion hypothesis, most current post-mortem diagnostic tests rely on the presence of PrPSc as indicative of TSE disease. However, recently experimental cases of TSE disease have been identified where no PrPSc deposition is evident. One example of this is a murine transgenic model of Gerstmann Sträussler Scheinker (GSS) disease. GSS is a familial TSE disease, caused by a number of different mutations in human PrP including a point mutation from proline to leucine at residue 102. A murine model of GSS disease, produced through gene-targeting, contains the same point mutation at the equivalent residue, 101, in murine PrP. These mice do not develop spontaneous disease during their lifespan, but when inoculated intra-cerebrally with either human P102L GSS (101LL/GSS) or hamster 263K scrapie (101LL/263K); develop a clinical disease and vacuolar TSE-related pathology. Upon biochemical and immunohistochemical analysis, the brain tissues of these clinically ill mice contain little or no detectable PrPSc. However titration experiments have previously shown infectivity titres of 107-109IU/g of brain tissue. Standard PK digestion (at 37°C), NaPTA precipitation and isolation of PrPSc through detergent insolubility and differential centrifugation all confirmed the observation of little or no detectable PK-resistant PrP (PrP-res) in the 101LL/GSS and 101LL/263K brain tissues, despite the high levels of TSE infectivity. The presence of PrPSc and/or TSE infectivity in the spleen during disease pathogenesis is dependent upon TSE agent strain and host species. Previous studies utilising wild-type mice infected with ME7, have shown that the levels of infectivity observed in spleen tissue are 2- 3log10 lower than those observed in the brain tissue of the same mice. However, experiments conducted as part of this thesis showed that sub-passage of both the brain and spleen tissue from clinically ill 101LL/GSS and 101LL/263K mice into 101LL mice by intra-cerebral inoculation result in short incubation periods, indicating that infectivity levels were similarly high in both tissues. Biochemical analysis of the primary spleen tissue identified the presence of PrP-res, albeit at lower levels than those observed in wild-type spleens infected with a standard laboratory TSE strain, ME7 or 79A. However, the presence of PrP-res indicates that the spleen has a role in disease pathogenesis, which will require further investigation. Additionally, the spleen tissue maintains the discrepancy between PrP-res and TSE infectivity that is observed in the brain tissue of these models and further questions the prion hypothesis. As little or no PrP-res was detectable in the brain tissues of 101LL/GSS and 101LL/263K mice by standard biochemical and immunohistochemical techniques, it was hypothesised that an in vitro amplification technique, protein misfolding cyclic amplification (PMCA) could amplify PrPSc to detectable levels. A series of optimisation experiments were performed to produce a reliable positive control for amplification of mouse PrPSc from a standard laboratory mouse TSE strain, 79A or ME7, with a normal wild-type mouse brain homogenate substrate. While a wide range of technical and experimental conditions were investigated, consistent and reproducible amplification of mouse PrPSc was not achieved and therefore amplification of PrPSc from 101LL/GSS and 101LL/263K tissues could not be performed as interpretation of results would be complicated without the presence of a positive control. Previous research has shown that while other commercial assays, e.g. TeSeE (BioRad), identified tissues from these models as borderline positive or negative for TSE disease, one TSE diagnostic assay, the IDEXX HerdChek kit, that utilises the Seprion ligand, identified both the brain and spleen tissue from 101LL/GSS and 101LL/263K clinical mice as positive for TSE disease. In order to identify if TSE infectivity is associated with the target of the Seprion ligand, brain tissue homogenates from 101LL/GSS, 101LL/263K and a positive control wild-type/79A homogenate were depleted of the Seprion ligand target utilising a PAD-beads kit (Microsens Biotechnologies), which incorporates the Seprion ligand as the capture agent, in combination with magnetic beads. Upon inoculation, a single depletion of the homogenates produced no significant reduction in incubation period to clinical disease in either the depleted homogenates or the wash buffers produced, in comparison to a non-depleted brain homogenate. This result indicates that a single depletion with the Seprion ligand, did not remove enough of the aggregated protein to significantly alter the level of infectivity in the depleted homogenate and that any infectious agent, which was initially bound to the Seprion ligand due to non-specific interactions, was then released during the wash steps of the procedure. Proteomic differences between all components produced during a single depletion of an infected brain homogenate, wild-type/79A, or a normal uninfected brain homogenate were assessed to potentially identify the target of the Seprion ligand. In conclusion, these murine models of TSE disease, 101LL/GSS and 101LL/263K, which contain both high infectivity levels with little or no PrP-res in the brain tissue and similar high levels of infectivity with low levels of PrP-res in the spleen, questions the accepted correlation between levels of infectivity and PrP-res or PrPSc as proposed by the prion hypothesis. It is hypothesised that either an alternative form of PrP, which has not yet been identified is the infectious agent in these disease models, or that the TSE infectious agent is a component which associates with PrPSc rather than being PrPSc itself. The eventual identification of the infectious agent present in these unusual disease models will increase our understanding of these diseases, potentially offer improved diagnostics for infectivity, and perhaps identify novel therapeutic targets.