Large Eddy Simulation of Complex Turbulent Flows: Physical Aspects and Research Trends

In the current paper, we have primarily addressed one powerful simulation tool developed during the last decades-Large Eddy Simulation (LES), which is most suitable for unsteady three-dimensional complex turbulent flows in industry and natural environment. The main point in LES is that the large-scale motion is resolved while the small-scale motion is modeled or, in geophysical terminology, parameterized. With a view to devising a subgrid-scale(SGS) model of high quality, we have highlighted analyzing physical aspects in scale interaction and-energy transfer such as dissipation, backscatter, local and non-local interaction, anisotropy and resolution requirement. They are the factors responsible for where the advantages and disadvantages in existing SGS models come from. A case study on LES of turbulence in vegetative canopy is presented to illustrate that LES model is more based on physical arguments. Then, varieties of challenging complex turbulent flows in both industry and geophysical fields in the near future-are presented. In conclusion; we may say with confidence that new century shall see the flourish in the research of turbulence with the aid of LES combined with other approaches.

Activation of violaxanthin cycle in darkness is a common response to different abiotic stresses : a case study in Pelvetia canaliculata

Background: In the violaxanthin (V) cycle, V is de-epoxidized to zeaxanthin (Z) when strong light or light combined with other stressors lead to an overexcitation of photosystems. However, plants can also suffer stress in darkness and recent reports have shown that dehydration triggers V-de-epoxidation in the absence of light. In this study, we used the highly stress-tolerant brown alga Pelvetia canaliculata as a model organism, due to its lack of lutein and its non-photochemical quenching independent of the transthylakoidal-ΔpH, to study the triggering of the V-cycle in darkness induced by abiotic stressors. Results: We have shown that besides desiccation, other factors such as immersion, anoxia and high temperature also induced V-de-epoxidation in darkness. This process was reversible once the treatments had ceased (with the exception of heat, which caused lethal damage). Irrespective of the stressor applied, the resulting de-epoxidised xanthophylls correlated with a decrease in Fv/Fm, suggesting a common function in the down-regulation of photosynthetical efficiency. The implication of the redox-state of the plastoquinone-pool and of the differential activity of V-cycle enzymes on V-de-epoxidation in darkness was also examined. Current results suggest that both violaxanthin de-epoxidase (VDE) and zeaxanthin-epoxidase (ZE) have a basal constitutive activity even in darkness, being ZE inhibited under stress. This inhibition leads to Z accumulation. Conclusion: This study demonstrates that V-cycle activity is triggered by several abiotic stressors even when they occur in an absolute absence of light, leading to a decrease in Fv/Fm. This finding provides new insights into an understanding of the regulation mechanism of the V-cycle and of its ecophysiological roles.

Water quality impacts of mechanical shredding of aquatic macrophytes

We examined the impacts of mechanical shredding (i.e.. shredding plants and leaving biomass in the system) of the water chestnut (Trapa natans) on water quality and nutrient mobilization in a control and experimental site in Lake Champlain (Vermont-New York). A 1-ha plot was mechanically shredded within 1 h on 26 July, 1999. Broken plant material was initially concentrated on the lake surface of the experimental station after shredding, and was noticeable on the lake surface for 19 d. Over a two week period after shredding. concentrations of total nitrogen (N) and phosphorus (P), and soluble reactive P increased in the lower water column of the experimental station, coinciding with decomposition of water chestnut. Sediments in the control and experimental stations exhibited vet-v low rates of N and P release and could not account for increases in nutrient concentrations in the water column after mechanical shredding. Shredded plant material deployed in mesh bags at the experimental station lost similar to 70% of their total mass, and 42%, N and 70% P within 14 d. indicating Substantial nutrient mobilization via autolysis and decomposition. Chlorophyll a concentrations increased to 35 g/L at the experimental station on day 7 after shredding, compared to a concentration of 4 g/L at the control station. suggesting uptake of mobilized nutrients by phytoplankton. Disruption Of the Surface canopy of water chestnut by shredding was associated with marked increases in turbidity and dissolved oxygen, suggesting increased mixing at the experimental site.

Distribution and Density of Vegetative Hydrilla Propagules in the Sediments of Two New Zealand Lakes

The distribution and density of hydrilla (Hydrilla verticillata (L.f.)Royle) turions and tubers in two New Zealand lakes were assessed by sampling cores of sediment from Lakes Tutira and Waikapiro each year from 1994 to 1997. Turion and tuber density differed with water depth, with maximum numbers of tubers and turions found in the 1-2 m and 1.5-4m water depth ranges respectively. A high turion to tuber ratio was observed, with turions accounting for over 80% of propagules. The relatively low numbers of turions and tubers compared with other reports, and the distribution of most tubers within the shallow water is likely to be associated with black swan grazing (Cygnus atratus Latham), with maintains a canopy of hydrilla consistently 1 m below the water surface.

Some relationships of meteorological, hydrographic, and biological variables in the Gulf of Panama

ENGLISH: An average of 78 m. of water was vertically displaced by wind-driven upwelling during the dry season (January-April) in Panama Bay at the head of the Gulf of Panama. The standing crop of phytoplankton and its productivity were significantly greater during the months of upwelling than during the rainy season. Equivalent results were found by three different methods used to calculate photosynthesis: direct measurement with radiocarbon; increase of dissolved oxygen in the water column; and decrease of phosphate-phosphorus in the water column. About 90 g. of carbon per square meter of sea surface were fixed by the phytoplankton during each upwelling season (January-April) and about 90 g. of carbon were fixed during each rainy season (May-December) resulting in an annual production of about 180 g. of carbon per square meter of sea surface SPANISH: Un promedio de 78 m. de agua fué desplazado verticalmente por la fuerza de los vientos que ocasionan el fenómeno conocido por afloramiento durante la estación seca (enero a abril) en la Bahía de Panamá, a la cabeza del Golfo de Panamá. La cosecha estable de fitoplancton y su productividad fueron significativamente mayores durante los meses de afloramiento, que durante la estación lluviosa. Se obtuvieron resultados equivalentes por medio de tres diferentes métodos usados para calcular la fotosíntesis: medición directa con radiocarbono, aumento del oxígeno disuelto en la columna de agua, y disminución del fosfato-fósforo en la columna de agua. Por medio del fitoplancton durante cada estación de afloramiento (enero-abril), se fijaron alrededor de 90 g. de carbono por metro cuadrado de la superficie del mar, y durante cada estación lluviosa (mayo-diciembre) se fijaron 90 g. de carbono lo que resulta en una producción anual de aproximadamente 180 g. de carbono por metro cuadrado de la superficie del mar.

Some aspects of the temperature, oxygen and nutrient distributions in Monterey Bay, California. Annual Report, Part 1, 1973

Seasonal variations in temperature, dissolved oxygen, and nutrients in the nearshore areas and in the canyon area of Monterey Bay, California during 1971-1972 were similar~ During upwelling periods, however, water in the nearshore areas was higher in temperature and oxygen and lower in nutrients than water in the canyon area~ This was caused by upwelled water moving north and south of the canyon into counterclockwise and clockwise flow in the northern and southern ends of the bay respectively. The water was heated by insolation and depleted of its nutrients by photosynthesis during this movement. The residence time of water in the nearshore northern and southern bay during upwelling is estimated to be 3 to 8 days, and this fits well into the above circulation pattern and average measured current velocities of 10 to 15 cm/sec~ There is sorne evidence that this circulation pattern and the estimated residence time may be also valid for on-upwelling periods. Upwelling apparently occurred in Monterey Submarine Canyon at rates of 0.4 to 2.9 m/day and was stronger in 1971 than 1972. (PDF contains 107 pages)

Long-lived oscillatory incoherent electron dynamics in molecules: trans-polyacetylene oligomers

We identify an intriguing feature of the electron-vibrational dynamics of molecular systems via a computational examination of trans-polyacetylene oligomers. Here, via the vibronic interactions, the decay of an electron in the conduction band resonantly excites an electron in the valence band, and vice versa, leading to oscillatory exchange of electronic population between two distinct electronic states that lives for up to tens of picoseconds. The oscillatory structure is reminiscent of beating patterns between quantum states and is strongly suggestive of the presence of long-lived molecular electronic coherence. Significantly, however, a detailed analysis of the electronic coherence properties shows that the oscillatory structure arises from a purely incoherent process. These results were obtained by propagating the coupled dynamics of electronic and vibrational degrees of freedom in a mixed quantum-classical study of the Su-Schrieffer-Heeger Hamiltonian for polyacetylene. The incoherent process is shown to occur between degenerate electronic states with distinct electronic configurations that are indirectly coupled via a third auxiliary state by vibronic interactions. A discussion of how to construct electronic superposition states in molecules that are truly robust to decoherence is also presented

An evaluation of the pelagic primary productivity and potential fish yield of Kainji Lake, Nigeria

The environmental conditions of Kainji Lake from 1971/72 to date appear to have stabilized to a large extent, judging from the similarity of physico-chemical parameters investigated in this study over the period. Solar radiation (as reflected in variation in temperature) and pH have remained largely constant over the years, while conductivity (index of nutrient enrichment), though significantly higher in 1995/96, could be described as sporadic and needs further monitoring to ascertain its trend in the lake. While water transparency and dissolved oxygen were higher in 1971/72 compared to the other years, these increases cannot be said to be overwhelming. The lower transparency in 1995/96 was due to the exceptional flood of that year and may have also accounted for the poorer dissolved oxygen concentration compared to the other years due to its impact on photosynthesis. There is no evidence from this study to indicate that primary productivity has increased over the years. Consequently, the observed increase in fish yield by the KLFPP from CAS, which is corroborated by estimates from the MEI, cannot be supported on the basis of improved photosynthetic production. The phenomenal high levels of conductivity recorded during certain periods in 1995 (600 mu mhos cm super(-1)) are hitherto unknown in the lake and may indicate a trend towards nutrient enrichment. However, it is premature at this stage to conclude on its long-term impact on primary production and consequently, on fish yield. Secondly, the notion of overfishing in the 80s (Ita, 1993), may need to be further examined as low or dwindling catches could be due to a number of factors among which are the level of fishing effort, the type and efficiency of gears and the intensity of sampling. It would appear that with the intervention of KLFPP, the better management of the lake's fisheries would increase the current level of catch. It also needs to be examined how much of the clupeid fisheries, which is now known to account for a substantial proportion of the total fish yield in Kainji Lake, was included in the sampling of the 80s. (PDF contains 43 pages)

Dinâmica populacional de Halodule wrightii Ascherson e sua fauna e flora associada em Cabo Frio RJ

Fanerógamas marinhas (gramas marinhas) são plantas com flores adaptadas ao ambiente marinho costeiro da maioria dos continentes do mundo. As gramas marinhas formam extensos bancos e proveem valiosos recursos em águas costeiras rasas em todo o mundo, servindo de alimento e berçário para espécies importantes de pescados comerciais e recreacionais. Nesse estudo foi realizada uma revisão sobre o estado de conhecimento das fanerógamas marinhas no Brasil até o presente momento; avaliou-se a importância do monitoramento em longo prazo e a influência de fatores ambientais, como o número de manchas solares; pesquisou-se também a distribuição espacial da grama marinha, bem como a fauna e flora associada; e o crescimento de Halodule wrightii em duas condições ambientais extremas (exposta no ciclo de maré baixa e permanentemente submersa). A revisão bibliográfica sobre as gramas marinhas foi abrangente e verificou a existência de algumas lacunas no conhecimento. Através do monitoramento a longo prazo pôde ser observado que o número de manchas solares tem forte relação negativa sobre a altura do dossel das gramas marinhas de região entre marés. A variação de marés na região de mediolitoral está relacionada diretamente com a distribuição espacial de Halodule wrightii e, consequentemente na distribuição da fauna e flora associada. A diferença de crescimento nos eixos de Halodule wrightii em condições ambientais diferentes é compensada pelas variações nas características de distribuição da planta no ambiente, tais como a altura do dossel, a densidade e biomassa de eixos. O monitoramento a longo prazo pode permitir a tomada de ações que auxiliem no manejo e na recuperação desses importantes habitats costeiros.

Development and collapse of an Oscillatoria bloom in Loch Leven during July 1994

During 1994, weekly spot-sampling of open water sites on Loch Leven took place from 16th March onwards. Very little difference between spot-sampling sites was observed from 16th March to 5th July. Throughout April and May there was a slow increase in levels of chlorophyll-a, followed by a rapid increase through June, reaching a maximum of 230 micrograms per litre. On 8th July there was a very rapid rise in water temperature, with a corresponding increase in dissolved oxygen and pH. At 0915 hours on 9th July there was a drop in all three variables. These changes were coincident with a marked reduction in chlorophyll-a values falling to 70 micrograms per litre on 12th July. On 16th July evidence of a resurgence of photosynthesis was observed.

Comunidades de anfíbios anuros em duas fitofisionomias do Parque Estadual da Serra do Tabuleiro, estado de Santa Catarina

O estado de Santa Catarina possuía sua área inteiramente coberta por Mata Atlântica, um dos biomas mais ameaçados mundialmente. Mesmo com o crescente aumento de informações sobre os anfíbios no estado, ainda existe muitas lacunas de informações para este grupo e o desconhecimento é alto mesmo no interior das Unidades de Conservação. O Parque Estadual da Serra do Tabuleiro é a maior unidade de conservação de proteção integral de Santa Catarina e ainda assim possui inúmeras ameaças e pressões antrópicas. Os objetivos deste estudo foram estudar os anfíbios anuros em duas fitofisionomias, restinga e floresta ombrófila densa submontana, do Parque Estadual da Serra do Tabuleiro, verificar as diferenças dos parâmetros da comunidade entre três mesohábitats na restinga, compreender em que extensão algumas variáveis estruturais do hábitat afetam a riqueza e abundância dos anuros na restinga e na floresta ombrófila densa submontana, conhecer os anuros de folhiço na área de floresta e, adicionalmente, verificar o atual conhecimento sobre os anuros de folhiço no mundo. Os anuros no parque foram amostrados por meio dos métodos de procura ativa em transecções, armadilhas de queda com cerca guia e parcelas no chão da floresta durante três anos consecutivos com amostragens trimestrais, de julho de 2007 a abril de 2010. As variáves estruturais foram medidas nos locais amostrados enquanto que os dados climáticos foram obtidos da estação meteorológica mais próxima da área de estudo. A revisão sobre os anuros de folhiço no mundo foi realizada por uma busca na base de dados ISI Web if Science entre os anos de 1945 e 2008. Foram registradas 39 espécies de anuros no Parque, sendo 15 espécies para a restinga, 31 espécies na floresta. No folhiço do chão da floresta, a comunidade foi composta por 13 espécies de anuros. No total, 66% dos anuros registrados aqui, foram endêmicos da Mata Atlântica, 17% possuíram distribuição restrita à Santa Catarina e quatro espécies foram consideradas como vulneráveis na lista de espécies ameaçadas de extinção de Santa Catarina. Na restinga, a área aberta e a mata de restinga foram as mais dissimilares com relação à composição e abundância de anuros e também para as variáveis estruturais do hábitat. Na floresta ombrófila densa, a cobertura de dossel e o número de corpos dágua foram as variáveis mais importantes para a riqueza e abundância das espécies de anuros. Também para os anuros de folhiço do parque, a cobertura de dossel foi importante, conjuntamente com a umidade do ar e a profundidade de folhiço. O atual conhecimento sobre os anuros de folhiço no mundo se concentra nas regiões tropicais, sendo que o Brasil possui o maior número de estudos. Algumas tendências para as comunidades de anuros de folhiço puderam ser identificadas, mas estudos adicionais são necessários para que mais inferências possam ser feitas. O presente estudo contribuiu para preencher parte das lacunas de conhecimento existentes para a biodiversidade dos anuros do estado de Santa Catarina e em especial para o Parque Estadual da Serra do Tabuleiro.

Models of the Oxygen-Evolving Complex of Photosystem II

<p>In the five chapters that follow, I delineate my efforts over the last five years to synthesize structurally and chemically relevant models of the Oxygen Evolving Complex (OEC) of Photosystem II. The OEC is nature’s only water oxidation catalyst, in that it forms the dioxygen in our atmosphere necessary for oxygenic life. Therefore understanding its structure and function is of deep fundamental interest and could provide design elements for artificial photosynthesis and manmade water oxidation catalysts. Synthetic endeavors towards OEC mimics have been an active area of research since the mid 1970s and have mutually evolved alongside biochemical and spectroscopic studies, affording ever-refined proposals for the structure of the OEC and the mechanism of water oxidation. This research has culminated in the most recent proposal: a low symmetry Mn₄CaO₅ cluster with a distorted Mn₃CaO₄ cubane bridged to a fourth, dangling Mn. To give context for how my graduate work fits into this rich history of OEC research, Chapter 1 provides a historical timeline of proposals for OEC structure, emphasizing the role that synthetic Mn and MnCa clusters have played, and ending with our Mn₃CaO₄ heterometallic cubane complexes.</p> <p>In Chapter 2, the triarylbenzene ligand framework used throughout my work is introduced, and trinuclear clusters of Mn, Co, and Ni are discussed. The ligand scaffold consistently coordinates three metals in close proximity while leaving coordination sites open for further modification through ancillary ligand binding. The ligands coordinated could be varied, with a range of carboxylates and some less coordinating anions studied. These complexes’ structures, magnetic behavior, and redox properties are discussed.</p> <p>Chapter 3 explores the redox chemistry of the trimanganese system more thoroughly in the presence of a fourth Mn equivalent, finding a range of oxidation states and oxide incorporation dependent on oxidant, solvent, and Mn salt. Oxidation states from Mn^II₄ to Mn^IIIMn^IV₃ were observed, with 1-4 O^2– ligands incorporated, modeling the photoactivation of the OEC. These complexes were studied by X-ray diffraction, EPR, XAS, magnetometry, and CV.</p> <p>As Ca²⁺ is a necessary component of the OEC, Chapter 4 discusses synthetic strategies for making highly structurally accurate models of the OEC containing both Mn and Ca in the Mn₃CaO₄ cubane + dangling Mn geometry. Structural and electrochemical characterization of the first Mn₃CaO₄ heterometallic cubane complex— and comparison to an all-Mn Mn₄O₄ analog—suggests a role for Ca²⁺ in the OEC. Modification of the Mn₃CaO₄ system by ligand substitution affords low symmetry Mn₃CaO₄ complexes that are the most accurate models of the OEC to date.</p> <p>Finally, in Chapter 5 the reactivity of the Mn₃CaO₄ cubane complexes toward O- atom transfer is discussed. The metal M strongly affects the reactivity. The mechanisms of O-atom transfer and water incorporation from and into Mn₄O₄ and Mn₄O₃ clusters, respectively, are studied through computation and ¹⁸O-labeling studies. The μ3-oxos of the Mn₄O₄ system prove fluxional, lending support for proposals of O^2– fluxionality within the OEC.</p>

Constraining the interpretation of 2-methylhopanoids through genetic and phylogenetic methods

Hopanoids are a class of sterol-like lipids produced by select bacteria. Their preservation in the rock record for billions of years as fossilized hopanes lends them geological significance. Much of the structural diversity present in this class of molecules, which likely underpins important biological functions, is lost during fossilization. Yet, one type of modification that persists during preservation is methylation at C-2. The resulting 2-methylhopanoids are prominent molecular fossils and have an intriguing pattern over time, exhibiting increases in abundance associated with Ocean Anoxic Events during the Phanerozoic. This thesis uses diverse methods to address what the presence of 2-methylhopanes tells us about the microbial life and environmental conditions of their ancient depositional settings. Through an environmental survey of hpnP, the gene encoding the C-2 hopanoid methylase, we found that many different taxa are capable of producing 2-methylhopanoids in more diverse modern environments than expected. This study also revealed that hpnP is significantly overrepresented in organisms that are plant symbionts, in environments associated with plants, and with metabolisms that support plant-microbe interactions; collectively, these correlations provide a clue about the biological importance of 2-methylhopanoids. Phylogenetic reconstruction of the evolutionary history of hpnP revealed that 2-methylhopanoid production arose in the Alphaproteobacteria, indicating that the origin of these molecules is younger than originally thought. Additionally, we took genetic approach to understand the role of 2-methylhopanoids in Cyanobacteria using the filamentous symbiotic Nostoc punctiforme. We found that hopanoids likely aid in rigidifying the cell membrane but do not appear to provide resistance to osmotic or outer membrane stressors, as has been shown in other organisms. The work presented in this thesis supports previous findings that 2-methylhopanoids are not biomarkers for oxygenic photosynthesis and provides new insights by defining their distribution in modern environments, identifying their evolutionary origin, and investigating their role in Cyanobacteria. These efforts in modern settings aid the formation of a robust interpretation of 2-methylhopanes in the rock record.

Toxicidade e bioacumulação de cobre em micro-organismos fotoautotróficos

Microalgas e cianobactérias têm sido amplamente recomendadas para biomonitoração de metais pesados e outros poluentes, sendo considerados indicadores sensíveis às alterações ambientais e utilizados como organismos testes na regulamentação dos níveis de metal. Estes micro-organismos fotossintetizantes são produtores primários da base da cadeia alimentar aquática e são os primeiros a serem afetados pela poluição por metais pesados. O cobre é um metal normalmente considerado como nutriente essencial para a vida aquática mas pode ser tóxico para algumas espécies. Portanto, neste estudo foram avaliados o efeito tóxico e a bioacumulação de cobre (II) em quatro espécies de micro-organismos fotoautotróficos componentes do fitoplâncton dulcícola, duas cianobactérias filamentosas (Anabaena sp. e Oscillatoria sp) e duas microalgas da classe das clorofíceas (Monorraphidium sp. e Scenedesmus sp.). O meio de cultivo utilizado nos ensaios foi o ASM-1 com e sem a presença de cobre (0,6 mg/L a 12 mg Cu2+/L) onde, o efeito tóxico do metal foi monitorado por contagem celular para as microalgas e por peso seco para as cianobactérias. A bioacumulação do metal foi avaliada da mesma forma para todos os micro-organismos, através de coletas de amostras no decorrer do experimento e determinação da concentração de cobre em solução por espectrometria de absorção atômica com chama. Os resultados obtidos mostram que o efeito tóxico do metal é diretamente proporcional à concentração inicial para os micro-organismos estudados, mas que o cobre (II) foi mais tóxico para as cianobactérias que para as microalgas verdes. A bioacumulação teve uma relação direta com o efeito tóxico do metal sobre os micro-organismos. Os resultados obtidos permitem sugerir que cobre (II) tem efeito negativo no fitoplâncton, inibindo o crescimento e alterando parâmetros metabólicos como a fotossíntese. A bioacumulação do metal pode comprometer os níveis tróficos da cadeia alimentar, afetando seu transporte para seres superiores

Ceratium hirundinella - ecology of a complex, mobile, and successful plant

Recent work carried out in the English Lake District (Esthwaite Water and Blelham Tarn) is reported. The seasonal growth cycle, diel growth cycle, photosynthesis, vertical distribution and migrations, horizontal distribution, and the interaction of environmental factors, were investigated.