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    Characterization of extremely low-frequency electromagnetic sources in conducting media : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University
    (Massey University, 2001) Rumball, Edward Ian
    Physical fields whose sources exist within maritime vessels are of concern to ship-designers and military planners. Among the fields of most significance which have been studied intensively, are those of magnetic, acoustic and pressure sources. New technological developments now require analyses of the underwater electric and magnetic fields of onboard, extremely low-frequency electromagnetic sources. This study investigated methods by which the electromagnetic sources of maritime vessels may be characterised during normal operations in typical coastal environments. It focused on situations where both the sources and field measurement points were located in a common seawater volume. At the electromagnetic frequencies of interest such a medium acts as a thin conducting layer with significant levels of wave reflection and refraction at the media boundaries. To enhance propagation models of the electromagnetic fields over short ranges, the initial investigations aimed to characterise key parameters of the conducting media in shallow-water conditions Conductivity values of seawater can be readily established by conventional methods. However, in the case of the seabed media, direct conductivity measurements are usually highly variable along horizontal and vertical sections due to aeons of land erosion, and the long-term effects of inshore waves and currents. Procedures are described which show how electromagnetic theory and indirect measurement techniques may be used to infer the characteristic values of key seabed parameters in shallow-water areas. This element of the study utilised both analytical and numerical electromagnetic models, and the efficacy of each in this context was examined. Subsequent phases of the study analysed the nature of the electromagnetic sources. In some situations the sources were regarded as point dipoles, and in others they were assumed to have a finite length. Techniques were developed to characterise the dipole moment, length and the location of a typical ship-like source, when each is treated as an electric current dipole. This information was used in turn to demonstrate the likely accuracy in ranging operations on extremely low-frequency, electromagnetic sources over short ranges, and in shallow-water conditions.
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    Characterisation of an interaction involved in viral replication : submitted in partial fulfilment of the requirements of the degree of Doctor of Philosophy, Institute of Fundamental Sciences, Massey University
    (Massey University, 2010) Claridge, Jolyon
    Human rhinoviruses (HRVs) are a major cause of illness worldwide and, as members of Picornaviridae, are closely related to several other human and animal pathogens that exact a large medical and economic cost on society. Viral infections in general are particularly difficult to treat, as viruses co-opt many of the host’s own biochemical pathways, making disabling the virus without harming the host very difficult. Carefully targeted strategies are required and detailed structural information is useful, both to identify new drug targets, and to fully understand interactions. One particular protein expressed by picornaviruses is 3C protease, which is responsible for post-translational processing of the viral capsid. This protease has a cysteine as its active site nucleophile, a functionality not found in eukaryotic proteases. The unusual active site makes 3C an attractive target for pharmaceuticals. Drugs that block the proteolytic action of 3C are currently in clinical trials. In addition to its proteolytic activity, 3C protease also has another function, that of an RNA binding protein. This activity has been shown to be required during replication of the viral RNA genome. In this study, the structure of 3C protease from HRV14 is investigated using NMR and other biophysical techniques. The structural information gained from these studies is used, along with data on 3C protease RNA-binding activity acquired using solution-state NMR and SAXS data, to elucidate a structure of the 3C–RNA complex. In addition, the dynamics of the free protein and of the protein in the presence of a specific inhibitor are investigated by solution-state NMR, and the potential role of dynamics in the function of the protein is explored. Finally, potential allosteric interaction between the RNA-binding and proteolytic functions of 3C is postulated, and further interactions of 3C and the 3C–RNA complex are discussed. It is hoped that a more complete understanding of 3C and its interactions will lead to more effective treatments for picornaviral infections in the future.
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    Computational approaches to the calculation of spectroscopic, structural and mechanical properties of polysaccharide chains : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Massey University
    (Massey University, 2010) Anjukandi, Padmesh
    In this thesis atomistic, statistical mechanical and coarse grained simulation techniques are used to study the properties of biopolymers and in particular the plant polysaccharide pectin. Spectroscopic aspects, structural and conformational behavior, and mechanical properties of the molecule in di erent physical states are addressed. After an introduction to the area and the theoretical techniques utilised herein (chapter 1), chapter 2 deals with the spectroscopic characterisation of pectin. Spectra were obtained theoretically by undertaking complete energy minimisation and Hessien calculations using DFT techniques implemented in Gamess (PC & US) packages. The calculated IR absorptions of di erent pectinic species and oligomers coupled on di erent surfaces were compared with experimental results. Herein, it is con rmed that experimental FTIR studies coupled with DFT calculations can be used as an e ective tool for the characterisation of pectin, and studying chemical coupling of the biopolymer to surfaces. In chapter 3, the properties of single chain polymer systems in controlled solvent conditions were studied using Brownian dynamics simulations, motivated by the formation of secondary structure architectures in biopolymer systems. We focus on the conformational properties of the chain in the presence of an additional torsional potential. New, interesting, and biologically relevant structures were found at the single molecule scale when a torsional potential was considered in the calculations. In chapter 4, results from DFT calculations carried out on single pectin sugar molecules (lengths and the free energies) are incorporated into a statistical mechanical model of polymer stretching, in order to obtain the force-extension behaviour of a single molecule pectin. This captures a good deal of the phenomenology of the single molecule stretching behavior of pectin. Chapter 5 summarises the conclusions of the work and nally chapter 6 suggests direction for further work.
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    Magnetic resonance spectroscopy and imaging as applied to the forestry sector : a thesis submitted to Massey University in partial fulfilment for the degree of Doctor of Philosophy
    (Massey University, 2003) Meder, Albert Roger
    The forestry sector in New Zealand ranks as the third largest export earner. The individual industries within the forestry sector have, in some cases, grown up on the basis of institutionalised knowledge, sometimes without a full understanding of the underlying fundamental physico-chemical relationships and the changes that occur during wood material processing. At the same time the commercial pressures of operating within the forestry sector have resulted in demand for more uniform, high quality, fit-for-purpose product, faster throughput and less downgrade from what is becoming a lower quality feedstock as harvest ages decline. In the 21st century, the forestry sector is being transformed into an "engineered ligno-cellulosic materials processor" and this in turn is requiring a more sophisticated knowledge of the material feedstock and the processes involved in wood products manufacture. The aim of this work was to use magnetic resonance techniques to explore aspects of ligno-cellulosic materials processing at points along the value-added process chain, namely drying, chemical modification (preservation) and re-engineering (gluing) of wood products. Magnetic resonance mini-imaging studies of the water transport during the drying of radiata pine boards rave shown differences in the directional movement of water within the wood structure. These effects show a dependence on the surface area to volume ratio of timber and the orientation of the annual rings with respect to the larger drying face. Narrow, flat-sawn boards exhibit anomalous drying behaviour in terms of water mass transport, whereas thicker boards display more conventional core-shell drying behaviour. These restrictions to flow have been further investigated using diffusion tensor imaging via a modified pulsed field gradient spin-echo sequence to elucidate the nature of anisotropic diffusion in wood. The direction of least restriction to self-diffusion is in the longitudinal direction, as would be expected with it being the direction of active transport within a tree stem, whereas the direction of greatest restriction to self-diffusion is in the radial direction, with the higher density latewood acting as a barrier. Preservation of radiata pine sapwood with novel boron-based preservatives has been investigated using magnetic resonance imaging to determine the penetration and retention of the incipient compounds. An apparent anomaly in retention for trimethylborate-treated Pinus radiata sapwood was investigated by 11B MAS NMR spectroscopy of excised sections of latewood and earlywood, which showed hydrolytic decomposition of trimethyl borate to form boric acid. The rate of hydrolysis of trimethylborate was monitored by 11B MAS NMR spectroscopy and was shown to occur very rapidly in the latewood (within 24 hours), and over a longer time scale of several days in the earlywood. The resulting publication has reported some of the first published 11B MRI images. Magnetic resonance spectroscopy has provided (in conjunction with separate mass spectrometry studies) mechanistic evidence for the accelerated curing of phenol-resorcinol formaldehyde resols, using ammonia in combination with the conventional paraformaldehyde hardener - a process known as GreenWeldTM. Carbon-13 and nitrogen-15 NMR spectroscopy has shown evidence of both benzylamine and aniline type bridging structures formed during cure, compared to only methylene structures being formed under conventional curing conditions. Poly(vinyl acetate) emulsion polymer adhesive has also been examined using NMR spectroscopic methods, with particular focus on the effect of addition of aluminium chloride, which is often commercially added to PVAc formulations as a crosslinking agent. Multinuclear magnetic resonance spectra obtained during the cure of AlCl3 modified PV Ac adhesive, shows a low frequency 27 Al shift of ca. 3 ppm suggesting a local change in environment as the aluminium changes from a solvated to a covalently bonded octahedral environment. Finally, as a preliminary study, a new device for measuring uniaxial extension of visco-elastic solids was trialled on poly(vinyl acetate) hydrogels to study the effect of addition of aluminium chloride on the visco-elastic properties of the adhesive. A similar, manually operated device was used to obtain NMR spectroscopic data during compression of the gel. These studies have shown that addition of aluminium chloride as a crosslinking agent, in fact produces a cured adhesive with fewer crosslinks than the corresponding unmodified adhesive, but with increased resistance to shear-induced creep.
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    Spin-dependent electronic and transport properties of unconventional conductors : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University, Palmerston North, New Zealand
    (Massey University, 2010) Ingenhoven, Philip Christopher
    In this thesis we present three different aspects of spin and spin-dependent transport properties in novel materials. Spurred by the prospect of spintronic devices, which use the spin degree of freedom of electrons instead of, or combined with, the charge degree of freedom, we analyse the spin properties of quantum wires, organic conducting polymers and sheets of graphene. First, we examine a quantum wire that is embedded in a two dimensional electron gas. We consider the Rashba spin-orbit coupling, and include the effect of interaction between the conduction electrons. We construct an analytically solvable low-energy theory for the wire, and explore the interaction between two magnetic impurities in the wire. We find that both the spin-orbit coupling and the electron-electron interaction have an effect on the magnetic interaction, and find the magnetic interaction to be tunable by an electric field. Next, we study an organic conducting polymer, which is contacted to magnetised ferromagnetic leads. In semiconducting organic polymers the current is transported by spinful polarons and spinless bipolarons. We simulate the transport through the system, including both types of charge carriers, and find the current to be insensitive to the presence of bipolarons. In addition, we find the bipolaron density to depend on the relative magnetisation of the ferromagnetic contacts. This constitutes an optical way of measuring the spin accumulation in conducting polymers. Finally, we investigate the optical conductivity of graphene. Symmetry arguments indicate the existence of two kinds of spin-orbit coupling in the two dimensional lattice, but there is no consensus about the actual strength of these couplings. We calculated the microwave optical conductivity of graphene including both possible spin-orbit interactions. We find the low frequency dependence of the optical conductivity to have a unique imprint of the spin-orbit couplings. This opens a possibility to experimentally determine both couplings separately.
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    A dynamic light scattering investigation into the dynamics of non ideal ternary polymer solutions : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University
    (Massey University, 2004) Nash, William
    Dynamic light scattering has been used to investigate three different non ideal ternary polymer systems. The three systems investigated were sodium caseinate and xanthan aqueous solutions, guar and dextran aqueous solutions and dextran and pullulan aqueous solutions. All solutions have been investigated at a temperature of 25°C. Sodium caseinate and xanthan aqueous solutions with total polymer concentrations ranging from 0.01% w/w to 0.15% w/w and ratios of sodium caseinate of x = 1:3, 1:2, 2:1, and 3:l have been investigated. Guar and dextran aqueous solutions with total polymer concentrations ranging from 0.01% w/w to 0.06% w/w at a ratio of guar to dextran of 1:6 have been investigated. Dextran and pullulan aqueous solutions with total polymer concentrations ranging from 1% w/w to 10% w/w with ratios of dextran to pullulan of 1:3, 1:1, and 3:l have been investigated. The solution concentrations have been chosen to fall in the semi-dilute range, while still being miscible. Three different methods of analysis have been applied to resolve the field autocorrelations function into a sum of decaying exponentials; CONTIN, CONTIN multiq, and a Kohlrausch-Williams-Watts fit. These resulting decay rates have been interpreted using the theoretical method outlined by Sun and Wang. The CONTIN multiq method provided the best overall fit to the data. The Sun and Wang method has not provided results which are consistent with those reported elsewhere in the literature. Additional theoretical effort must be applied to interpret the results from dynamic light scattering on these novel non-ideal systems.
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    The development of a spectrometer for portable NMR systems : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University
    (Massey University, 2006) Dykstra, Robin
    Nuclear Magnetic Resonance (NMR) is a relatively complex technique and normally requires expensive equipment. However, with advances in computing, electronics and permanent magnet technologies, NMR is becoming more feasible as a non-invasive tool for industry. The strength of NMR is its ability to probe at the molecular level and hence gain information about molecular structure, organisation, abundance and orientation. This thesis describes the development of an instrumentation platform technology that is compact and therefore portable. It has been produced to aid the development of NMR based tools or sensors for research and industry and will lead to a series of low cost, portable NMR systems for the non-destructive testing of materials such as polymer composites, rubber, timber, bricks and concrete. The instrumentation is largely electronics based and consists of a series of modules that can be interconnected to produce a solution. The first of two main modules is called the system core. What is common to all NMR applications is the generation of precisely timed signals, the capturing of signals and the processing/display of data. This has been implemented by developing a general purpose Digital Signal Processor (DSP) based instrumentation and control module that uses a Universal Serial Bus interface to communicate with a host computer. A graphical user interface is provided by an application running under Windows® XP. The second main module is a radio frequency transceiver that has been developed using digital receiver technology. The signals, after some amplification, are digitized with a 14-bit, 62.5MH.z analogue to digital converter. The sampled signal is then mixed digitally with synthesized sine and cosine functions to generate lower frequency quadrature outputs which are then digitally filtered and decimated before being passed onto the DSP for further processing and storage. A direct digital synthesizer with an analogue output is used to generate any required excitation signals. All synthesizers have phase and frequency hopping capabilities and are phase locked to each other and the DSP. The system was designed to interface to a range of NMR probes. The type of probe is determined by the intended application and each probe has specific requirements such as the type of radio frequency power amplifier, duplexer and preamplifier needed. This results in a number of instrumentation variations and a modular instrument enclosure was used to cater for these variations. The instrument was first configured for an NMR probe called the NMR-MOUSE. Tests were performed with this probe to verify the correct operation and performance of the instrument. The instrument was then reconfigured for a new probe called the NMR-MOLE and further testing was performed. This probe was still undergoing development and had not been previously tested. Finally, a dedicated compact instrument measuring 360 x 240 x 55 mm and weighing 3.6 kg was developed for the NMR-MOUSE probe.
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    Squeezing atoms using a confinement potential : a thesis presented in fulfillment of the requirements for the degree of Master of Science in Mathematical Physics, Massey University, Albany, New Zealand
    (Massey University, 2010) Coxe, Julianne Neilson
    Understanding the complexities of the interior of planets and stars requires the help of analyzing the effects of high pressures on certain elements believed to be found within. The Hartree-Fock method uses the Schr¨odinger equation, Kummer’s differential equations and a confinement potential to simulate an atom being squeezed to high pressures. The Hartree-Fock method was used to calculate the total energies of atoms. After being compared to Gaussian03 and VASP, the results were deemed accurate. It was also observed that the pressure versus density data closely approximated those pairs found in outer space in the interiors of, for example, Jupiter.
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    Investigations of the behaviour of pectin in casein micelle systems and their analogues : thesis presented for the degree of Doctor of Philosophy in Physics
    (Massey University, 2009) Cucheval, Aurelie Suzanne Bernadette
    Firstly, the effect of pectin on acid milk gels in concentrated, quiescent systems was investigated by passive microrheology using two complementary techniques: diffusive wave spectroscopy (DWS) and multiple particle tracking (MPT). DWS, by allowing probing the mechanical properties of the network at high frequency, gave information on its microstructure. The addition of high methoxyl pectins was shown to change the network structure which has been explained by bridging of the casein micelles by the polymer as the system was undergoing acidification. On the other hand, the presence of low methoxyl pectin in the acid milk gel was shown to have no effect on the microstructure of the network at low concentration of polymer (0.1%w/w) which has been attributed to the sensitivity of this low DM pectin to calcium: LM pectin are trapped by calcium and not able to interact with casein micelles anymore. Multiple particle tracking was used to probe the effect of pectin on the heterogeneity of the system by following the distribution of the displacements of added micro beads at a given time lag during the gelation using the Van Hove distribution. Furthermore, the surface chemistry of the probes was modified in an attempt to control their location in the system. Finally, the mean square displacements of the casein micelles obtained by DWS and, of k-casein coated particles obtained by MPT were shown to give good agreement for the same acid milk system. Having established that the interaction between casein micelles and low methoxyl pectin is prevented by the pectin sensitivity to calcium, the effect of the pectin fine structure was investigated on the interaction between k-casein and pectin by surface plasmon resonance (SPR). The amount of pectin binding on a k-casein coated gold surface was shown to be strongly dependant on the pectin fine structure. It was concluded that small negative patches on the pectin backbone, likely to comprise of around two consecutive unmethylesterified galacturonic acid, are the most effective for pectin binding to k-casein. The effect of the direct interaction between pectin and k- casein on ‘calcium-free casein micelle mimics’ in pectin solution was then investigated using coated latex beads. A pectin structure with a limited number of negative patches on its backbone was also shown to limit the potential for destabilization via bridging.
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    On the zero-point energy of elliptic-cyliindrical and spheroidal boundaries : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Theoretical Physics at Massey University, New Zealand
    (Massey University, 2009) Kitson, Adrian Robert
    Zero-point energy is the energy of the vacuum. Disturbing the vacuum results in a change in the zero-point energy. In 1948, Casimir considered the change in the zeropoint energy when the vacuumis disturbed by two parallelmetal plates. The plates disturb the vacuum by restricting the quantum fluctuations of the electromagnetic field. Casimir found that the change in the zero-point energy implies that the plates are attracted to each other. With the recent advances made in the experimental verification of this remarkable result, theoretical interest has been rekindled. In addition to the original parallel plate configuration, several other boundaries have been studied. In this thesis, two novel boundaries are considered: elliptic-cylindrical and spheroidal. The results for these boundaries lead to the conjecture that zero-point energy does not change for small deformations of the boundary that preserve volume. Assuming the conjecture, it is shown that zero-point energy plays a stabilizing role in quantum chromodynamics, the leading theory of the strong interaction.