As variáveis biológicas de muitos seres vivos apresentam ritmos diários, em paralelo ao dia e à noite do ambiente. A maioria desses ritmos não é uma mera reação aos estímulos cíclicos do ambiente: eles são ritmos circadianos gerados endogenamente por um temporizador interno - o oscilador circadiano - que sustenta uma ritmicidade com período diferente de 24 horas na ausência de pistas ambientais, mas se sincroniza para um período de 24 horas quando exposto ao ambiente cíclico. Em mamíferos, o oscilador circadiano se localiza no cérebro e pode ser sincronizado pelo ciclo diário de claridade e escuridão (ciclo CE) do dia e da noite transmitido através das retinas. Animais subterrâneos passam boa parte do tempo abaixo da terra, onde as condições ambientais variam menos que na superfície. Em razão disso, questiona-se até que ponto estes animais mantêm ritmos circadianos e se seus osciladores circadianos se baseiam no ciclo CE para se sincronizar com o ambiente. Procuramos responder essas questões nos roedores subterrâneos da espécie Ctenomys cf. knighti (tuco-tucos). Em campo, realizamos observações visuais diretas para registrar o padrão temporal de exposição à luz. Em laboratório, construímos a Curva de Resposta de Fase (CRF), que consiste em medir indiretamente a resposta do oscilador circadiano a estímulos luminosos em diferentes momentos do dia. Por fim, recorremos a simulações computacionais de um modelo matemático de oscilador, para integrar os dados anteriores. Verificamos, em campo, que os tuco-tucos se expõem, diariamente, a pulsos de luz irregularmente distribuídos nas horas claras do dia levantando alguns questionamentos sobre sua capacidade como sincronizador dos ritmos em campo. Contudo, a CRF nos indicou que o sistema circadiano dos tuco-tucos responde a estímulos luminosos de forma semelhante aos animais não-subterrâneos. Nós verificamos 3 hipóteses: ou a informação da exposição à luz em campo é suficiente para sincronizar o oscilador circadiano, apesar da aparente irregularidade; ou a CRF do tuco-tuco possui alguma característica que facilita a sincronização pelo regime observado de exposição à luz; ou seu sistema circadiano se baseia em outra pista temporal do ambiente para se manter sincronizado. Nossas simulações computacionais indicaram que a primeira hipótese é a mais provável, visto que os padrões de exposição à luz simulados, como aqueles observados em campo, com o mínimo de informação temporal, ainda assim são suficientes para sincronizar os osciladores. Em conjunto, nossos dados indicam que o ciclo claro-escuro tem um papel importante na sincronização dos ritmos circadianos dos tuco-tucos na natureza. / Daily rhythms are found in the biological variables of many organisms, in parallel to the environmental day and night. Most of those rhythms are not mere reactions to the cyclic stimulus of the environment. They are actually circadian rhythms, endogenously generated by an internal timer, the circadian oscillator, which sustains a non-24-hour rhythm under constant conditions, but is synchronized to a 24-hour period when exposed do a cyclic environment. In mammals, this oscillator is located in the brain, and can be synchronized by the daily light-dark cycle (LD cycle) of day and night. Subterranean animals remain most of the time in an underground habitat, where environmental conditions vary less markedly than aboveground. Therefore, there are doubts whether these animals maintain circadian rhythms and whether their circadian oscillators rely on the LD cycle for environmental synchronization. We attempted to answer those questions in subterranean rodents of the species Ctenomys cf. knighti (tuco-tucos). In the field, we performed direct visual observations to assess their temporal pattern of light-exposure. In the lab, we build the Phase Response Curve (PRC), which consists in an indirect measurement of the circadian oscillator responses to light stimuli applied at different times of the day. Finally, computer simulations of an oscillator model were used to integrate these previous data. We verified that tuco-tucos expose themselves to light pulses that are irregularly distributed through day-light hours, raising some questions about its validity as an environmental synchronizer. However, the PRC results indicated that the tuco-tucos circadian system responds to light stimuli in a way similar to non-subterranean animals. We then verified three hypothesis: either the light-exposure temporal information was enough for the synchronization of the circadian system, despite its apparent irregularity; or the tuco-tuco\'s PRC present some feature that facilitates the synchronization by the observed light-exposure regimen; or the tuco-tuco\'s circadian system rely on another environmental temporal cue to maintain its synchronization. Our computer simulations support the first hypothesis, given that the simulated regimens, despite being little informative in the temporal sense, were still sufficient to synchronize the simulated oscillators. Together, our data indicate that the light-dark cycle plays an important role in the synchronization of the tuco-tucos\' circadian rhythms in nature.

A base evolucionaria da senescência é um problema biológico de longa data. Senescência, no sentido da deterioração progressiva de um organismo, distingue-se de envelhecimento, ou a mera passagem do tempo. Como, pelo menos em mamíferos, senescência e envelhecimento ocorrem simultaneamente, os termos são tomados erroneamente como sinônimos. A senescência parece explicada pelo desgaste do organismo, levando a um paradoxo frente aos mecanismos de seleção natural, pois, sendo a maquinaria biológica portadora de mecanismos de auto-reparo, esperáramos o aprimoramento destes, com gradual eliminação da deterioração associada ao envelhecimento. Historicamente, procurou-se resolver este paradoxo imaginando-se que a senescência conferisse uma vantagem adaptativa, mas este argumento, que requereria distinguir os indivíduos mais velhos, é circular. A partir de meados do século XX, três hipóteses prevaleceram. O acúmulo de mutações, proposto por Medawar (1951), considera que o decaimento gradual da força de seleção com a idade favorece o acúmulo de genes deletérios expressos em idades avançadas. O antagonismo pleiotrópico, proposto por Williams (1957), defende que genes ligados a características benéficas e deletérias poderiam ser, em certas condições, favoravelmente selecionados. Finalmente, a teoria da soma descartável, proposta por Kirkwood (1975), sugere que organismos são favoravelmente selecionados quando investem em Reprodução mesmo em detrimento da manutenção somática. A descrição dinâmica dos fenômenos envolvidos em cada hipótese e a contribuição relativa de cada uma é, ainda, objeto de debate. O presente trabalho visa ao desenvolvimento de modelos computacionais estocásticos que mimetizem as condição para cada uma delas. Iniciamos o desenvolvimento pela ordem histórica, testando o mecanismo proposto por Medawar, que é o objeto desta tese. A teoria do acúmulo de mutações encontrou críticos que sugerem que este mecanismo levaria os efeitos deletérios à sincronia em idades muito avançadas, tornando a senescência um fenômeno repentino e limitado a tais idades. Isto contrariaria a observação experimental, pois a senescência é um processo gradual e mesmo animais silvestres exibem fenômenos senescentes detectáveis precocemente. Para manter a modelagem compatível com o conhecimento atual sobre genética de populações, incluímos neste modelo os efeitos da seleção, da deriva genética e de diferentes taxas de mutação. Como previsto, em nossas simulações a moda das idades de manifestação dos genes deletérios se estabilizou apenas em idades muito avançadas, próximas ao término das distribuições etárias. Também como esperado, estas distribuições terminaram em idades mais precoces nos cenários de maior mortalidade extrínseca. No entanto, em todas as nossas simulações, houve distribuição mais ou menos larga das idades de manifestação em torno da moda. A distribuição alargou-se com o aumento da probabilidade de mutação, sugerindo que as idades de manifestação podem espalhar-se ao longo da vida, chegando, em alguns cenários, à manutenção de alelos com manifestação ao nascer. Isto é compatível com o modelo de alelos ineptos utilizado em genética populacional, em que diferentes variantes concorrem até atingirem um equilíbrio entre seleção, mutação e deriva genética. Considerando-se o critério demográfico para senescência, em que a mortalidade aumenta em função da idade, podemos dizer que as nossas simulações evoluíram populações senescentes. Embora nossos dados não contrariem as outras teorias da senescência, claramente mostram que a perda da força de seleção não é um mecanismo suficiente para a senescência. Especialmente com alelos de expressão tardia, as forças de deriva podem ser preponderantes e devem ser levadas em conta para explicar a evolução da senescência / The evolutionary basis of senescence is a long standing biological problem. Senescence, in the sense of progressive deterioration of an organism, is distinguished from aging, or the mere passage of time. Because, at least in mammals, aging and senescence occur simultaneously, the terms are wrongly taken as synonyms. Senescence seems explained by the wear of the organism, leading to a paradox facing the mechanisms of natural selection, because, being the biological machinery bearer of self-repair mechanisms, we would expect their improvement, with gradual elimination of the deterioration associated with aging. Historically, there were attempts to resolve this paradox by supposing that senescence confers an adaptive advantage, but this argument would require that older individuals were previously distinct from younger ones and is, therefore, circular. From mid-twentieth century, three hypotheses have prevailed. The mutation accumulation, proposed by Medawar (1951), proposes that the gradual decay of the force of selection with age favors the accumulation of deleterious genes expressed in advanced ages. The antagonistic pleiotropy, proposed by Williams (1957), argues that genes linked to benecial and deleterious traits could, under certain conditions, be favorably selected. Finally, the disposable soma theory, proposed by Kirkwood (1975), suggests that organisms are positively selected when they invest in reproduction even at the expense of somatic maintenance. The dynamic description of the phenomena involved in each mechanism and the relative contribution of each one is still debated. The present work aims to develop stochastic computer models that mimic the conditions for each. We started by historical order, testing the mechanism proposed by Medawar, which is the subject of this thesis. The theory of mutation accumulation found critics who suggest that this mechanism would cause deleterious eects to synchronize in very advanced ages, causing senescence to be a sudden phenomenon limited to these ages. This is a contradiction with the experimental observation, because senescence is a gradual process and even wild animals exhibit senescent phenomena detectable in young ages. To keep the model consistent with the current knowledge on population genetics, this model included the eects of selection, genetic drift and dierent mutation rates. As predicted, in our simulations the mode of the age of onset of deleterious genes stabilized only in very advanced ages, near the end of the age distribution. Also as expected, these distributions ended in earlier ages in scenarios of higher extrinsic mortality. However, in all our simulations, there was more or less wide distribution of ages of onset around the mode. The distribution is enlarged with increased probabilities of mutation, suggesting that the ages of onset may spread throughout life, including, in some scenarios, the maintenance of alleles with manifestation at birth. This is consistent with the innite alleles\' model used in population genetics, where dierent variants compete until achieving an equilibrium between selection, mutation and genetic drift. Considering the demographic criterion for senescence, in which mortality increases with age, we can say that our simulations evolved senescent populations. Although our data do not con ict with the other theories of senescence, they clearly show that the falling force of selection with age is not a sucient mechanism for senescence. Especially with alleles of late expression, the forces of genetic drift may be prominent and should be taken into account to explain the evolution of senescence

No region has felt the effects of global climate change more acutely than the cryosphere, which has changed at an unprecedented rate in the past two decades. The scientific consensus is that these changes are driven largely by increasing ocean heat content at high latitudes. In southeast Greenland, acceleration and retreat of the marine-terminating glaciers contributes significantly towards global sea level rise. Circulation in the fjords which accommodate these glaciers is thought to be driven both by freshwater input and by barrier wind-driven shelf exchange. Due to a scarcity of data, particularly from winter, the balance between these two mechanisms is not fully understood. In Svalbard, increasing water temperature has decimated sea ice cover in many of the fjords, and had substantial implications for the local ecosystem. While there is a relatively comprehensive literature on shelf exchange mechanisms in Svalbard fjords, questions remain over how the internal circulation interacts with exchange mechanisms. The region shares a similar underwater topography and oceanographic setting with southeast Greenland, with marine-terminating glaciers in close proximity to warm Atlantic waters, and results from Svalbard can hence be used to inform studies of high-latitude fjord-shelf exchange in a broader context. A realistic numerical model was constructed with the aim of better understanding the interaction between Kangerdlugssuaq Fjord and the adjacent continental shelf, and quantifying heat exchange during winter. The model was initially run in an idealised configuration with winter climatological forcing fields, incorporating a parameterisation for melting at the terminus, and used to test the impact of barrier wind events. The Earth's rotation played a crucial role in the nature of the circulation and exchange in the fjord, with inflow on the right (looking up-fjord) and outflow on the left. While the heat delivered into the fjord-mouth was smaller than that observed in summer, the background internal circulation was found to efficiently distribute waters through the fjord without external forcing, and the heat delivered to the glacier terminus was comparable to summer values. Barrier winds were found to excite coastally-trapped internal waves which propagated into the fjord along the right-hand side. The process was capable of doubling the heat delivery. The process also enhanced the background circulation, likely via Stokes' Drift. The model was then adapted to simulate winter 2007-08 under historical forcing conditions. Time series of glacial melt rate, as well as the heat flux through fjord cross-sections, were constructed and compared to the variability in wind forcing. Long periods of moderate wind stress were found to induce greatly enhanced heat flux towards the ice sheet, while short, strong gusts were found to have little influence, suggesting that the timescale over which the shelf wind field varies is a key parameter in dictating wintertime heat delivery from the ocean to the Greenland Ice Sheet. An underwater glider was deployed to Isfjorden, a large fjord system in Svalbard, to measure the temperature, salinity and depth-averaged currents over the course of November 2014. Like in Kangerdlugssuaq, the circulation in Isfjorden was found to be heavily influenced by the Earth's rotation and by wind activity both locally and on the shelf. The combination of hydrography and high-resolution velocity data provided new insights, suggesting that the approach will be useful for studying high-latitude fjords in the future.

Thesis (M.Sc. (Agriculture)) --University of Limpopo,2008 / Cellulose is regarded as the most abundant polymer in nature and the first on which X-ray investigations had been performed, a year after the discovery of diffraction of X-rays on crystalline materials in 1912. It is one of the most abundant and important polymers on the planet. It comprises of four allomorphs, cellulose Iβ, II, III and IV1 and IV2 of which Iβ and II are the most stable and industrially important. Cellulose I is the native form of cellulose. Molecular dynamics (MD) simulations have been carried out to study the structural and mechanical properties of cellulose, cellulose Iβ, II, III and IV1 and IV2 bulk systems. Simulations were carried out using Polymer Consistence Force Field (PCFF) and Compass force field in conjunction with the Discover simulation program at various temperatures. We used molecular dynamics simulation to obtain a better insight about temperature dependence of cellulose. Further investigations on mechanical properties of this material at various temperatures were carried out. Using pair correlation functions g(r) or radial distribution functions (rdf’s) we were able to investigate phase transitions wherein as the temperature was increased we observed peak broadening. These enabled us to study the similarities between the structures investigated. Also studied was water uptake in celluloses by way of introducing water at different concentrations. Analysis of lattice parameters compared reasonably well with the experimental. Lattice parameters were calculated using PCFF and they compared well with results found using Compass force field. Calculation of temperature and pressure dependence on bulk systems has been done and it was noted that as the pressure increases the lattice parameters decrease. / National Research Foundation and CSIR

Thesis (Ph.D (Physics)) --University of Limpopo, 2005 / We have derived a potential model for °uorapatite Ca10(PO4)6F2, ¯tted to structure, elastic constants and vibrational frequencies of the phosphate groups, which is compatible with existing calcite and °uorite potential mod- els. We then modelled the structure and stabilities of the dry and hydrated f0 0 0 1g, f1 0 1 0g, f1 0 1 1g, f1 1 2 0g, f1 0 1 3g and f1 1 2 1g surfaces, which calculations con¯rmed the experimental dominance of the f0 0 0 1g surface, which is prominently expressed in the calculated thermodynamic morphologies. The dehydrated morphology further shows the experimental f1 1 2 1g twinning plane, while the f1 0 1 0g cleavage plane is expressed in the hydrated morphology. Molecular adsorption of water has a stabilising e®ect on all six surfaces, where the surfaces generally show Langmuir be- haviour and the calculated hydration energies indicate physisorption (73 - 88 kJ mol¡1). The chains of °uoride ions surrounded by hexagonal calcium channels can become distorted in two major ways during relaxation: either by a shortening/lengthening of the FF distances, when the channel is perpendicular to the surface, or by distortion of the CaF bonds when the channel is parallel to the surface. Both distortions occur when the channel runs at an angle to the surface. Other relaxations include compression of the calcium sub-lattice and rotation of surface phosphate groups. We have modelled adsorption of a range of organic molecules onto dif- ferent °uorapatite surfaces, due to the importance of organic/ inorganic in- teractions in biological situations. We have selected organic molecules that represent a model for the carboxylic acids, alkyl hydroxamates and those 3 that contain both the aldehyde and hydroxyl functional groups. Adhesion of these organic molecules on the surfaces has shown strong interaction between the surface's Ca ions and the molecule's oxygens, more especially the car- bonyl oxygens than any other interactions. It was found that the number of interactions between the ions of adsorbate molecule and the mineral surfaces thus contribute signi¯cantly to the exothemicity of adsorption. Further more, simulations of apatite thin ¯lms at a range of ®-quartz surfaces have shown how the strength of adhesion between thin ¯lms of ap- atite material and ceramic silica surfaces is crucially dependent upon both the orientation of the ¯lm relative to the substrate and the nature of the silica surfaces, a ¯nding that is important in a wide number of applications, from basic geological research on intergrowth of phosphate and silicate rock minerals to the search for more e®ective surgical implant materials. It was shown that although the unrelaxed quartz surface is more reactive toward the apatite ¯lm, the more regular thin ¯lm structures grown at the pre-relaxed quartz surfaces lead to more stable interfaces. Film growth at the unrelaxed quartz surface is energetically increasingly unfavorable, whereas growth at the pre-relaxed surface is calculated to continue beyond the ¯rst layer, where the adhesion energy is convergent with the layer growth of the thin ¯lm. Ad- hesion of apatite thin ¯lm on hydroxylated surfaces of ®-quartz has shown to be energetically less favourable than at dry surfaces. This was because the thin ¯lm interact mainly with the hydroxyl ions on the surface of quartz. However, the adhesion energy is still convergent with layer growth of the thin ¯lm on the hydroxylated surfaces. / National Research Foundation of South Africa (NRF), Council for Scientific and Industrial research (CSIR), and the University of the North

Skyline analysis is important for multi-criteria decision making applications. The data in some of these applications are inherently uncertain due to various factors. Although a considerable amount of research has been dedicated separately to efficient skyline computation, as well as modeling uncertain data and answering some types of queries on uncertain data, how to conduct skyline analysis on uncertain data remains an open problem at large. In this thesis, we tackle the problem of skyline analysis on uncertain data. We propose a novel probabilistic skyline model where an uncertain object may take a probability to be in the skyline, and a p-skyline contains all the objects whose skyline probabilities are at least p. Computing probabilistic skylines on large uncertain data sets is challenging. An uncertain object is conceptually described by a probability density function (PDF) in the continuous case, or in the discrete case a set of instances (points) such that each instance has a probability to appear. We develop two efficient algorithms, the bottom-up and top-down algorithms, of computing p-skyline of a set of uncertain objects in the discrete case. We also discuss that our techniques can be applied to the continuous case as well. The bottom-up algorithm computes the skyline probabilities of some selected instances of uncertain objects, and uses those instances to prune other instances and uncertain objects effectively. The top-down algorithm recursively partitions the instances of uncertain objects into subsets, and prunes subsets and objects aggressively. Our experimental results on both the real NBA player data set and the benchmark synthetic data sets show that probabilistic skylines are interesting and useful, and our two algorithms are efficient on large data sets, and complementary to each other in performance.

Skyline analysis is important for multi-criteria decision making applications. The data in some of these applications are inherently uncertain due to various factors. Although a considerable amount of research has been dedicated separately to efficient skyline computation, as well as modeling uncertain data and answering some types of queries on uncertain data, how to conduct skyline analysis on uncertain data remains an open problem at large. In this thesis, we tackle the problem of skyline analysis on uncertain data. We propose a novel probabilistic skyline model where an uncertain object may take a probability to be in the skyline, and a p-skyline contains all the objects whose skyline probabilities are at least p. Computing probabilistic skylines on large uncertain data sets is challenging. An uncertain object is conceptually described by a probability density function (PDF) in the continuous case, or in the discrete case a set of instances (points) such that each instance has a probability to appear. We develop two efficient algorithms, the bottom-up and top-down algorithms, of computing p-skyline of a set of uncertain objects in the discrete case. We also discuss that our techniques can be applied to the continuous case as well. The bottom-up algorithm computes the skyline probabilities of some selected instances of uncertain objects, and uses those instances to prune other instances and uncertain objects effectively. The top-down algorithm recursively partitions the instances of uncertain objects into subsets, and prunes subsets and objects aggressively. Our experimental results on both the real NBA player data set and the benchmark synthetic data sets show that probabilistic skylines are interesting and useful, and our two algorithms are efficient on large data sets, and complementary to each other in performance.

This paper presents the computer simulation results on the delivery of Etanidazole (radiosensitiser) to the brain tumor and examines several factors affecting the delivery. The simulation consists of a 3D model of tumor with poly (lactide-co-glycolide) (PLGA) wafers of 1% Etanidzole loading implanted in the resected cavity. A zero-order release device will produce a concentration profile in the tumor which increases with time until the drug in the carrier is depleted. This causes toxicity complications during the later stages of drug treatment. However, for wafers of similar loading, such release results in a higher drug penetration depth and therapeutic index as compared to the double drug burst profile. The numerical accuracy of the model was verified by the similar results obtained in the two-dimensional and three-dimensional models. / Singapore-MIT Alliance (SMA)

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Nanocrystalline materials have been under extensive study in the past two decades. The reduction in grain size induces many abnormal behaviors in the properties of nanocrystalline materials, that have been investigated systematically and quantitatively. As one of the most fundamental relations in materials science, the structure-property relation should still apply on materials of nano-scale grain sizes. The characterization of grain boundaries (GBs) and related entities remains a big obstacle to understanding the structure-property relation in nanocrystalline materials. It is challenging experimentally to determine the topological properties of polycrystalline materials due to the complex and disordered grain boundary network presented in the nanocrystalline materials. The constantly improving computing power enables us to study the structure-property relation in nanocrystalline materials via Monte Carlo and molecular dynamic simulations. In this study, we will first propose a geometrical construction method based on inverse Monte Carlo simulation to generate digital microstructures with desired topological properties such as grain size, interface area, triple junction length as well as their statistical distributions. The influences on the grain shapes by different topological properties are studied. Two empirical geometrical laws are examined including the Lewis rule and Aboav-Weaire law. Secondly, defect free nanocrystalline Copper (nc-Cu) samples are generated by filling atoms into the Voronoi structure and then relaxed by molecular dynamics simulations. Atoms in the relaxed nc-Cu samples are then characterized into grain atoms, GB interface atoms, GB triple junction atoms and vertex atoms using a newly proposed method. Atoms in each GB entity can also be identified. Next, the topological properties of nc-Cu samples before and after relaxation are calculated and compared, indicating that there exists a physical limit in the number of atoms to form a stable grain boundary interface and triple junction in nanocrystalline materials. In addition, we are able to obtain the statistical averages of geometrical and thermal properties of atoms across each GB interfaces, the so-called GB profiles, and study the grain size, misorientation and temperature effects on the microstructures in nanocrystalline materials. Finally, nc-Cu samples with different topological properties are deformed under simple shear using MD simulation in an attempt to study the structure-property relation in nanocrystalline materials.