Efficient image-based rendering

Recent advancements in real-time ray tracing and deep learning have significantly enhanced the realism of computer-generated images. However, conventional 3D computer graphics (CG) can still be time-consuming and resource-intensive, particularly when creating photo-realistic simulations of complex or animated scenes. Image-based rendering (IBR) has emerged as an alternative approach that utilizes pre-captured images from the real world to generate realistic images in real-time, eliminating the need for extensive modeling. Although IBR has its advantages, it faces challenges in providing the same level of control over scene attributes as traditional CG pipelines and accurately reproducing complex scenes and objects with different materials, such as transparent objects. This thesis endeavors to address these issues by harnessing the power of deep learning and incorporating the fundamental principles of graphics and physical-based rendering. It offers an efficient solution that enables interactive manipulation of real-world dynamic scenes captured from sparse views, lighting positions, and times, as well as a physically-based approach that facilitates accurate reproduction of the view dependency effect resulting from the interaction between transparent objects and their surrounding environment. Additionally, this thesis develops a visibility metric that can identify artifacts in the reconstructed IBR images without observing the reference image, thereby contributing to the design of an effective IBR acquisition pipeline. Lastly, a perception-driven rendering technique is developed to provide high-fidelity visual content in virtual reality displays while retaining computational efficiency.Jüngste Fortschritte im Bereich Echtzeit-Raytracing und Deep Learning haben den Realismus computergenerierter Bilder erheblich verbessert. Konventionelle 3DComputergrafik (CG) kann jedoch nach wie vor zeit- und ressourcenintensiv sein, insbesondere bei der Erstellung fotorealistischer Simulationen von komplexen oder animierten Szenen. Das bildbasierte Rendering (IBR) hat sich als alternativer Ansatz herauskristallisiert, bei dem vorab aufgenommene Bilder aus der realen Welt verwendet werden, um realistische Bilder in Echtzeit zu erzeugen, so dass keine umfangreiche Modellierung erforderlich ist. Obwohl IBR seine Vorteile hat, ist es eine Herausforderung, das gleiche Maß an Kontrolle über Szenenattribute zu bieten wie traditionelle CG-Pipelines und komplexe Szenen und Objekte mit unterschiedlichen Materialien, wie z.B. transparente Objekte, akkurat wiederzugeben. In dieser Arbeit wird versucht, diese Probleme zu lösen, indem die Möglichkeiten des Deep Learning genutzt und die grundlegenden Prinzipien der Grafik und des physikalisch basierten Renderings einbezogen werden. Sie bietet eine effiziente Lösung, die eine interaktive Manipulation von dynamischen Szenen aus der realen Welt ermöglicht, die aus spärlichen Ansichten, Beleuchtungspositionen und Zeiten erfasst wurden, sowie einen physikalisch basierten Ansatz, der eine genaue Reproduktion des Effekts der Sichtabhängigkeit ermöglicht, der sich aus der Interaktion zwischen transparenten Objekten und ihrer Umgebung ergibt. Darüber hinaus wird in dieser Arbeit eine Sichtbarkeitsmetrik entwickelt, mit der Artefakte in den rekonstruierten IBR-Bildern identifiziert werden können, ohne das Referenzbild zu betrachten, und die somit zur Entwicklung einer effektiven IBR-Erfassungspipeline beiträgt. Schließlich wird ein wahrnehmungsgesteuertes Rendering-Verfahren entwickelt, um visuelle Inhalte in Virtual-Reality-Displays mit hoherWiedergabetreue zu liefern und gleichzeitig die Rechenleistung zu erhalten

Computational Studies on Cellulose : Pyrolysis, Nanostructure and Hydrodynamic Behaviour

Cellulose, the major component of plant matter, has a complex hierarchical structure that extends from the scale of cells down to the molecular level. Knowledge of the structural fundamentals of cellulose is relevant, not only for an understanding of plant life, but also for numerous technologies that use it as a raw material. The methods of computational physics are increasingly used to support experimental efforts in cellulose research. This thesis reports molecular and fluid dynamics simulations that address questions related to the pyrolytic degradation of cellulose and the aggregation and deaggregation of cellulose microfibrils. Cellulose pyrolysis involves hundreds of chemical reactions and volatile products, the description of which remains a formidable challenge. Here, we demonstrate the use of reactive force field methods for predicting mechanisms and kinetics of cellulose pyrolysis. We show that reactive molecular dynamics simulations can reproduce essential features of the degradation process, most notably its onset via glycosidic bond cleavage, and thus offer a means to complement quantum chemistry methods and experimental analytics. The aggregation of microfibrils is fundamental to the structural hierarchy of native cellulose and has direct implications for its processing into nanostructured forms. Here, we use atomistic simulations to elaborate on the effects of chemical modification on microfibril interactions. Our simulations reveal the sensitivity of the interaction to non-uniform substitution patterns, a feature that is not captured by continuous theoretical models. Our findings suggest a connection between uneven charge distribution and heterogeneity observed in disintegration experiments. We also investigate the structure of microfibril bundles, and their relationship to the bound water of the cell wall, using molecular dynamics simulations. The simulations predict the spontaneous formation of a twisted ribbon-like bundle with a twist rate compatible with recent experimental evidence. This also leads to a reasonable prediction for the amount of bound water, which consists of molecular water layers surrounding the fibrils, along with several other experimental indicators. Microfibril interactions also manifest themselves in the rheology of aqueous cellulose nanofibril suspensions. Here, we demonstrate the coordinated use of rheometry, printing experiments and computational fluid dynamics simulations in the development of cellulose-based hydrogels for wound dressing applications. One of our key findings is the inadequacy of rotational rheometry as a basis for models of printer head flow, and the consequent need for an alternative model building strategy.Selluloosa on kasvien soluseinän keskeinen rakennusaine. Se on ketjumainen makromolekyyli, jota esiintyy osittain kiteisissä, kuitumaisissa mikrofibrilleissä ja niiden kimpuissa. Tämä rakenteellinen hierarkia vaikuttaa niin kasvikunnan biologisiin prosesseihin kuin selluloosaa raaka-aineena hyödyntäviin teknologioihin. Laskennallisen fysiikan menetelmiä käytetään yhä enemmän kokeellisen työn apuvälineenä selluloosatutkimuksessa. Tässä väitöskirjassa sovelletaan atomistisia simulointimenetelmiä ja laskennallista virtausmekaniikkaa selluloosan nanorakenteen ja pyrolyysireaktioiden kuvaamiseen. Selluloosan pyrolyyttinen hajoaminen on monimutkainen kemiallinen prosessi, johon liittyy satoja tutkimuksellisesti avoimia reaktiopolkuja. Olemme tutkineet reaktiivisten voimakenttämenetelmien soveltuvuutta selluloosan pyrolyysireaktioiden ja niiden kinetiikan ennustamiseen. Tulostemme mukaan hajoamisprosessin keskeisiä piirteitä voidaan toistaa reaktiivisten molekyylidynaamisten simulointien avulla. Tämä pätee erityisesti selluloosan glukoosiyksiköiden välisen glykosidisidoksen hajoamiseen ja kyseisen reaktionopeuden lämpötilariippuvuuteen. Selluloosapohjaisten nanomateriaalien valmistus perustuu mikrofibrillien muodostamien kimppujen hajottamiseen, mihin voidaan vaikuttaa selluloosan kemiallisella muokkauksella. Atomistiset simulointimme tarkentavat aiempien teoreettisten mallien antamaa kuvaa mikrofibrillien välisistä vuorovaikutuksista. Mikrofibrillien väliset voimat ovat erityisen herkkiä niiden pinnoilla oleville varausjakaumille. Tämä selittää nanofibrillien valmistuksessa havaitun kokovaihtelun silloin, kun kemiallinen muokkaus on vain osittainen. Lisäksi olemme tutkineet mikrofibrillikimppujen rakenteen yhteyttä sitoutuneen veden määrään soluseinässä tai siitä prosessoidussa kuidussa. Molekyylidynaamiset simuloinnit ennustavat kimpulle kierteisen nauhamaisen rakenteen, jonka kiertymisjakso vastaa hyvin viimeaikaisia kokeellisia tuloksia. Samalla saadaan lähellä koetuloksia olevia ennusteita sitoutuneen veden määrästä ja useista muista suureista, kuten mikrofibrillien ominaispinta-alasta. Mikrofibrillien väliset vuorovaikutukset vaikuttavat myös nanoselluloosasuspensioiden virtauskäyttäytymiseen. 3D-tulostuksessa käytettäviä selluloosapohjaisia hydrogeeleja voidaan kehittää kuvaamalla niiden virtauskäyttäytymistä laskennallisella virtausmekaniikalla. Tällaisilla malleilla voidaan esimerkiksi etsiä riippuvuuksia hydrogeelin reologisten ominaisuuksien, tulostusprosessin parametrien ja tulostusjäljen välillä. Väitöstyössä tätä on tutkittu 3D-tulostettujen haavatyynyjen valmistuksessa

Drivers of change in East Antarctic ice shelves

Antarctica holds enough landlocked ice to raise the global sea level by nearly 60 m in the event of wholesale ice sheet collapse. In East Antarctica, the Aurora Subglacial Basin is drained by Totten Glacier and is one of the world’s largest and most rapidly-changing ice catchment systems. In recent decades, Totten Glacier has exhibited variability in its flow rate, mass balance, and ice thickness, each led by changes at the ice sheet margin. Totten Glacier dynamics are linked to processes in the Totten Ice Shelf, which buttresses the flow of grounded ice while being subjected to variable ocean forcing from below. Understanding the stability of the Aurora Subglacial Basin in a changing climate requires an understanding of how Totten Ice Shelf responds to changes in its environment. This dissertation investigates ice shelf processes on spatial scales of 1 km to 100 km, that act on sub-annual to decadal time scales. The independent roles of channelized basal melt and large-scale basal melt resulting from a variable supply of oceanic heat content are examined using surface elevation changes measured by airborne laser altimetry, satellite laser altimetry, and a new method of photometry applied to satellite images. A new method of satellite image template matching is also developed to understand ice shelf velocity response to several environmental forcing mechanisms. On the interannual time scale, Totten Ice Shelf is seen accelerating in response to nearby upwelling of warm circumpolar deep water that enhances basal melt rates. On the subannual time scale, Totten Ice Shelf exhibits winter slowdown as buttressing from seasonal landfast sea ice at the ice shelf front slows the flow of the glacier. These findings show that the Totten Glacier catchment is sensitive to changes in its environment, and may be susceptible to changes in the coastal wind stress projected for the 21st century.Geological Science

Visual-auditory visualisation of dynamic multi-scale heterogeneous objects.

The multi-scale phenomena analysis is an area of active research that is connecting simulations with experiments to get a correct insight into the compound dynamic structure. Visualisation is a challenging task due to a large amount of data and a wide range of complex data representations. The analysis of dynamic multi-scale phenomena requires a combination of geometric modelling and rendering techniques for the analysis of the changes in the internal structure in the case of data coming from different sources of various nature. Moreover, the area often addresses the limitations of solely visual data representation and considers the introduction of other sensory stimuli as a well-known tool to enhance visual analysis. However, there is a lack of software tools allowing perform an advanced real-time analysis of heterogeneous phenomena properties. The hardware-accelerated volume rendering allows getting insight into the internal structure of complex multi-scale phenomena. The technique is convenient for detailed visual analysis and highlights the features of interest in complex structures and is an area of active research. However, the conventional volume visualisation is limited to the use of transfer functions that operate on homogeneous material and, as a result, does not provide flexibility in geometry and material distribution modelling that is crucial for the analysis of heterogeneous objects. Moreover, the extension to visual-auditory analysis emphasises the necessity to review the entire conventional volume visualisation pipeline. The multi-sensory feedback highly depends on the use of modern hardware and software advances for real-time modelling and evaluation. In this work, we explore the aspects of the design of visual-auditory pipelines for the analysis of dynamic multi-scale properties of heterogeneous objects that can allow overcoming well-known problems of complex representations solely visual analysis. We consider the similarities between light and sound propagation as a solution to the problem. The approach benefits from a combination of GPU accelerated ray-casting, geometry, optical and auditory properties modelling. We discuss how the modern GPU techniques application in those areas allows introducing a unified approach to the visual-auditory analysis of dynamic multi-scale heterogeneous objects. Similarly to the conventional volume rendering technique based on light propagation, we model auditory feedback as a result of initial impulse propagation through 3D space and its digital representation as a sampled sound wave obtained with the ray-casting procedure. The auditory stimuli can complement visual ones in the analysis of the dynamic multi-scale heterogeneous object. We propose a framework that facilitates the design of dynamic multi-scale heterogeneous objects visual-auditory pipeline and discuss the framework application for two case studies. The first is a molecular phenomena study that is a result of molecular dynamics simulation and quantum simulation. The second explores microstructures in digital fabrication with an arbitrary irregular lattice structure. For considered case studies, the visual-auditory techniques facilitate the interactive analysis of both spatial structure and internal multi-scale properties of volume nature in complex heterogeneous objects. A GPU-accelerated framework for visual-auditory analysis of heterogeneous objects can be applied and extend beyond this research. Thus, to specify the main direction of such extension from the point of view of the potential users, strengthen the value of this research as well as to evaluate the vision of the application of the techniques described above, we carry out a preliminary evaluation. The user study aims to compare our expectations on the visual-auditory approach with the views of the potential users of this system if it is implemented as a software product. A preliminary evaluation study was carried out with limitations imposed by 2020/2021 restrictions. However, it confirms that the main direction for the visual-auditory analysis of heterogeneous objects has been identified correctly and visual and auditory stimuli can complement each other in the analysis of both volume and spatial distribution properties of heterogeneous phenomena. The user reviews also highlight the necessary enhancements that should be introduced to the approach in terms of the design of more complex user interfaces and consideration of additional application cases. To provide a more detailed picture on evaluation results and recommendations introduced, we also identify the key factors that define the user vision of the approach further enhancement and its possible application areas, such as users experience in the area of complex physical phenomena analysis or multi-sensory area. The discussed in this work aspects of heterogeneous objects analysis task, theoretical and practical solutions allow considering the application, further development and enhancement of the results in multidisciplinary areas of GPU accelerated High-performance visualisation pipelines design and multi-sensory analysis

The possible implication of selected Fusarium Mycotoxins in the aetiology of brain cancer.

Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2004.The central nervous system is a potential site of action for the Fusarium mycotoxin Fumonisin B1 (FB1), and is exemplified in horses by the disease equine leukoencephalomalacia. Structurally resembling sphingoid bases, FB1 inhibits ceramide synthase, an enzyme involved in sphingolipid metabolism, leading to accumulation of free sphinganine (Sa) and sphingosine (So). This investigation focused on FB1, Sa, So and the Fusarium mycotoxins fusaric acid (FA), moniliformin (MaN), zearalenone (ZEA), deoxynivalenol (DON), and T-2 toxin (T2). Effects of the Fusarium mycotoxins and sphingoid bases on the N2a neuroblastoma cell line were assessed using the methylthiazol tetrazolium (MIT) and ApoGlow™ assays. The MIT assay revealed significant differences between the viability of N28 control cells and the cytotoxic effects of FB1 (p=0.001), So (p=1.1 x10-6 ), Sa (p=1.9x10-6 ), MON (p=0.002), DON (p=0.04) and ZEA (p=0.003) on N28 cells between 5-250µM. The cytotoxic effects of FA did not differ significantly from controls (p=0.1). The ApoGlow™ assay revealed that in N28 cells, FB1 at 8µg.ml-1, FA at 128µg.ml-1, and (FBI+FA) combined induced growth arrest at 2 and 4µg·ml-1. Assessment of the effects of FBI and FA on the Jurkat leukaemic suspension cell line revealed that FB1 induced apoptosis at 1.56,12.5 and 50µ.ml-1, growth arrest at 100, 200 and 800µg.ml-1 and proliferation at 400µg.mg-1. Fusaric acid induced proliferation at 1. 56µg.ml-1, apoptosis at 3.15µg.mrl, growth arrest at 100 and 200µg.mrl, and necrosis at 800µg.ml-1. Combined, (FB1+FA) induced apoptosis at 1.56, 3.15,12.5 and 800µg.ml-1. Flow cytometry and fluorescence microscopy revealed that mycotoxins, Sa and So induced varying levels of apoptosis and necrosis in N28 cells. Acridine orange and ethidium bromide staining facilitated discrimination between viable, apoptotic and necrotic cells. Transition of the mitochondrial transmembrane potential was measured using Rhodamine 123 with propidium iodide, and the dual emission potential sensitive stain JC-1. Changes in mitochondrial membrane potential and plasma membrane integrity were expressed as increases or decreases in fluorescence intensity. An increase in mycotoxin concentration from 50 to 200µM was usually paralleled by a decrease in J-aggregate formation, suggesting a decrease in the ?¦¥m. Staining with Rh 123/PI indicated at specific concentrations whether N28 cells were either late apoptotic or necrotic reflected by the levels of PI uptake. No dose dependant mechanism of cell death was established using either method, as fluctuations were evident. Immunolocalisation of T2, ZEA and FB1 within cellular organelles that exhibited ultrastructural pathology provided correlation between mycotoxin exposure and effects. Multinucleate giant cells and retraction of cellular processes were observed. At the electron microscope (EM) level, FB1 was immunolocalised within microsegregated and peripherally condensed nucleoli, the nucleoplasm, distorted mitochondria and dilated endoplasmic reticulum (ER). The capacity of cells to incorporate mycotoxins and effect cytological changes represents a major factor in the potential for initiation of malignant transformation. Exposure of N2a cells to FB1 for 72 hours increased intracellular free Sa and depleted complex sphingolipids. Using High Performance Liquid chromatography (HPLC), acid hydrolysis revealed reduction in Sa from a level of O.6±0.12µM in control cells, to 02±0.lµM in cells exposed to 50µM and lOOµM FB1. Base hydrolyses revealed increase in free Sa: So ratios from 0.52±0.2 in control cells, to 1.14±0.2 and 1.4±0.3 in cells exposed to 50 and l00µM FB1 respectively. The Sa: So ratio in the complete culture media (CCM) increased from 1. 7±0. 3 for control cells to 2.0±0.2 and 2.50±0.4 for cells exposed to 50 and lOOµM FB1 respectively. Correlation coefficients between Sa: So ratios to FB1 exposure in CCM (R=0.75) and within cells (R=0.85), imply that the free Sa: So ratio within cells appears to be a better biomarker for FB1-induced disruption of sphingolipid metabolism in vitro, than the Sa: So ratio in CCM. Optimisation of HPLC analytical procedures improved recovery of FB I from spiked human sera to 95.8% (n=15) and detection limits to -5ng.ml-1 at a signal to noise ratio of 5:1. Optimisation of methods for recovery of Sa and So from spiked sera, led to recoveries of 77.9% and 85.0%, for So and Sa respectively at levels of spiking with lOng per 500µl of serum. Matched sera Sa:So ratios and FB1 levels in brain cancer and non-cancer subjects in KwaZulu-Natal were determined using these optimised methods. Fumonisin B1 was detected in sera of non-cancer (76.7±62.2nM) and brain cancer subjects (l07.38±116nM). Mean serum Sa:So ratios of 21 non-cancer subjects was 1.7±0.7. There was no correlation (R=0.26) between these variables in non-cancer subjects. The mean serum FB1 level in brain cancer subjects was 107.4±116nM (range 10.5-298nM) (n=50) and the mean Sa:So ratio (n=50) was 1.9±1.7 (range 0.40-8.16). No correlation was found between these variables in the brain cancer subjects either (R = -0.23). Fumonisin B1 was irnmunolocalised in 49 of 76 brain tumour tissue samples analysed using immunohistochemistry (IHC). Thirty-eight of the 76 specimens had matched serum FBI levels and Sa: So ratios, and 23 of these were positive for FB1 presence. Although not significantly different (p=0.ll), the FBI sera levels in the cancer group with FBI within the tumour tissue had higher levels of FB1 in sera than the IHC FB1 negative group. Fumonisin B1 was localised within irregular profiles of nuclei, elongated and swollen mitochondria and ER. Immunolocalisation of FB1 within organelles in the brain showing ultrastructural cellular pathology suggests FBI may be implicated in the aetiology of human brain carcinogenesis