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Item The disordered- and ordered-state structures of κ-carrageenan : an X-ray scattering, molecular dynamics, and density-functional theory study : 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, 2022) Westberry, Benjaminκ-carrageenan is a biopolymer extracted from marine algae. It exists in aqueous solution, at high temperatures and/or low salt concentrations as a ‘disordered-state’, and at low temperatures and in the presence of certain salts as an ‘ordered-state’. The transition between disordered- and ordered-states involves molecular structural changes, which are essential to its interesting viscoelastic properties that are routinely exploited in a plethora of applications. Despite this, the molecular conformations of the disordered- and ordered-states, as well as the details of the transitional pathway connecting them, remain a source of contention. While decades of research have amassed a vast trove of information on the disorder-order transition, an atomistic understanding of the structure in solution has remained elusive. This study takes advantages of recent advances in computational capabilities in order to simulate κ-carrageenan solutions on length scales of ∼10 nm over μs time scales, and thus develop atomistic models of the disordered- and ordered-states. Both models are used to calculate wide-angle X-ray scattering profiles, and these are subsequently validated by comparison to data obtained at a synchrotron facility. The models will be further explored using density functional theory to calculate their expected optical rotation behaviour, which finds that the formation of double-helices from single chains is able to explain the increase in optical rotation measured experimentally when transitioning from the disordered to ordered-state. Structural analysis of both experimentally-verified models find the disordered-state to have a significant amount of residual helical secondary-structure, whereas the ordered-state is mostly double-helical. Crucially, simulations show that the ordered-state arises spontaneously from the so-called disordered-state at a rate dependant on salt concentration, without prior uni-molecular changes. The findings of this research are the most detailed model of the disorder-order transition to-date, and demonstrate that the existing paradigm of a ‘coil-to-helix’ transition is in need of revision.Item Use of X-ray to identify contaminants in pelleted seed lots for biosecurity : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science (Agricultural Science) at Massey University, Manawatū, New Zealand(Massey University, 2019) Wang, YufanThousands of tonnes of seed, of which around 10% is pelleted, comes into New Zealand through international trade every year. However, this trade also brings potential risks to New Zealand biosecurity. Pelleted seeds can contain contaminants, including seeds other than the crop species in the seed lot and inert matter; both may cause negative effects on crop growth or bring pests and diseases. A reliable method is necessary to inspect seed lots for the contaminants. The conventional way to inspect for contaminants in pelleted seeds is to separate the seeds from pellets and inspect visually. However, this is a time consuming and potentially health damaging procedure. A faster and safer non-invasive inspection method is needed urgently. X-ray imaging systems have the potential to non-invasively identify contaminants in seed lots. 2-D X-ray was firstly applied in this research to determine if the system could separate non-target seeds such as weed seed from naked crop “target” seeds, since if 2-D X-ray cannot separate non-target seeds from naked target seeds, there is little chance to separate seeds that are pelleted. In this research, three target species were used. These were beet (Rapistrum, Ranunculus and spinach as contaminants), carrot (Polygonum, Chenopodium and Solanum as contaminants) and lettuce (Sonchus and Lapsana as contaminants), because of their high contamination rates in imported seed lots. Seed shape parameters: dimensions, form, circularity, roughness and intensity, were used to characterize seeds for further comparison. The results showed Ranunulus can be separated from beet by dimensions and intensity; Rapistrum can be separated by elongation, circularity and intensity; spinach was hard to separate from beet. In the carrot group, Chenopodium and Solanum can be separated from carrot by either dimensions, elongation or circularity, while Polygonum cannot be separated from Carrot. For contaminants in lettuce, Sonchus can be separated from lettuce by dimensions and intensity; Lapsana can be separated by elongation and circularity. However, all the separation above was based on mean values, seeds with extreme sizes would limit the effects of shape parameters in seed separation. Determining if pelleting seeds can also be separated using the same parameters was the next important step for determining if 2-D X-ray can be used for pelleted seed inspection. However, little literature can be found regarding specific pelleting materials and pelleting procedures, as they are held by the seed companies. Therefore, protocols for pelleting the relatively small numbers of pelleted seed for research are needed. During several trials on seed pelleting, Methocel™ and gypsum was identified as suitable pelleting materials. The vortex mixer was identified as the best equipment for pelleting using a one-by-one adding method, which was feasible for pelleting both tiny-seeds and small-quantities seeds. The seeds pelleted showed a uniform and well-rounded appearance. However, when applying the same 2-D X-ray for seed separation, the seed projections were hard to be extracted for further analysis, because of the poor differentiation between seeds and pellets. This research explored the potential of using 2-D X-ray to separate naked non-target seed from naked target seeds by seed shape parameters. The outcomes confirmed that the mean values of shape parameters can separate contaminants from target seeds, however at the extreme ends of the range seed parameters overlap will limit the value of the shape parameters. Pelleting seeds under laboratory conditions can also be realized by using vortex mixer as equipment and using Methocel™ and gypsum as pelleting materials. Nonetheless, 2-D X-ray was not a reliable tool to detect pelleted seeds, since it is hard to separate seed projections from pellets with images only from a top view. 3-D X-ray could potentially be applied in future research because of its higher resolution than 2-D X-ray. In addition, 3-D X-ray images enable analysts to analyze seeds from different angles other than one fixed angle, which makes the analysis free from image overlap problems. Although research on 3-D X-ray for seed separation is at its beginning, it is potentially useful for pelleted seed analysis.Item 'Only the darkness knows who I am' : discourses on x-rays in the shadow clinic and how visualizing shadows contributes to the possibilities of aesthetic empathy in the perception of the body in x-ray : a thesis presented in partial fulfilment of the requirements for the degree of PhD in Visual and Material Culture at Massey University, Wellington, New Zealand(Massey University, 2012) Clark, EmilyThis thesis examines the discourses of x-ray images as they exist on-line. Throughout my research I apply both the stance of both the privileged flâneur/euze and the badaud(s) that have been identified as an ideological manifestation of the mass media since the early 20th century and established as characterisations of Euro-Western modernity (Shaya 2006). By examining specific case studies gathered from the resources of the World Wide Web, my thesis has worked to establish the existence of what I have called “The Shadow Clinic”. It applies methodologies that incorporate both subjective and objective viewpoints assigned to examine and provide analysis for, identifying an ‘empathic vision’ that might exist in the examination of clinical visual material. I have also investigated the possibilities of bringing to these images an empathic vision that incorporates both an aesthetic and semiotic analysis of the image along with an appraisal of the images’ effectiveness through narratives and responses. The basic premise is that images are powerful and demanding and the perspective of medical imaging technologies works like all other images to change our perception of ourselves as well as of our understanding of the world. Using the metaphorical, allegorical and physical entity of shadows as a visually potent, literally complex and politically charged manifestation, the methodological stance moves in between giving importance to the physical manifestation — or the quantifiable — and meta-physical — or qualitative. Limited but unhindered by not being a radiologist, the authorial perspective is one of examination and analysis (rather than diagnostic) of images that have strongly impacted upon the visual world since the last century. Such images continue to produce concurrent social and cultural ambiguities — ambiguities that persistently exist between what is revealed and what is concealed. Using the concept of “The Shadow Clinic”, this thesis demonstrates some of the plethora of discourses emergent through the visibility of x-ray imagery on–line and in addition to the more conservative approach of using medical material through the publication of academic papers and research, the space of the World Wide Web is the space of the marketing, pedagogy, palliation and ministration. I have studied the workings of the Shadow Clinic, through the texts on the historical and political machinations of the Clinic by Foucault and Illich, as well as social and cultural theorist who concentrate on the place of empathic vision and clinical perspectives. This thesis particularly concentrates on the engagement with the aesthetic of empathy through visualization, and focuses on how shadows do the work of accentuating proximity and remoteness, the Body and embodiment.