In this thesis, we report on our studies of water dynamics and structure in various biological environments which include: the surfaces of proteins and various oligosaccharides, the intervening space between proteins; and in the vicinity of cryoprotectant disaccharides in the liquid and ice phases. From a theoretical perspective, we propose methodology to compute diffusivity and residence times on the surface of biomolecules. In particular our proposed algorithm to compute residence times appears to be better in dealing with poor statistics associated with the number of water molecules that remain on a surfaces for extended times. The type of linkage between monomers and the anomeric configuration all play a major role in determining the structure and dynamics of water on the surface of carbohydrates.

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The thesis, which contains nine chapters, reports extensive large scale atomistic molecular dynamics (MD) simulation studies of water structure and dynamics at the surface of an anionic micelle, hydration layer of two proteins, and in the grooves of a 38-base pairs long DNA. Understanding the structure and dynamics of water molecules at the surfaces of self-organized assemblies and complex biological macromolecules has become a subject of intense research in recent times. Chapter 1 contains a brief overview of the biomolecular hydration dynamics. Relevant experimental, computational, and theoretical studies of biomolecular hydration and the time scales associated with the water dynamics are discussed. In Chapters 2 and 3, the structure, environment, energetics, and dynamics of constrained water molecules in the aqueous anionic micelle of cesium perfluorooctanoate (CsPFO) have been studied using large scale atomistic molecular dynamics simulations. Based on the number of hydrogen bond (HB) that interfacial water molecule makes with the polar head group (PHG) oxygen of the micelle, we find the existence of three kinds of water at the interface. We introduce a nomenclature to identify the species as IBW2 (form two HBs with two different PHG), IBW1 (form one HB with PHG), and IFW (no HB with PHG). Despite of possessing two strong w-PHG bonds, the concentration of the IBW2 species is rather low due to entropic effect. The ion solvation dynamics study at the interface shows the presence of a slow component, with a relaxation time 1-2 order of magnitude slower than that in the corresponding bulk solvent in agreement with the experimental results. Both the translational and orientational dynamics of the water molecules near the micellar surface is found to be much slower than those in the bulk. The HB between the PHG of the micelle and the water molecule has almost 13 times longer life time than that in the bulk between two tagged water molecules. In Chapter 4, we present results of extensive atomistic MD simulation studies of the structure and dynamics of aqueous protein solution of the toxic domain of Enterotoxin (1ETN) and the chicken villin headpiece sub-domain containing 36 amino acid residues (HP-36). Reduced water structure and the faster water dynamics around the active site of these proteins have been observed which may have biological significance. Chapter 5 presents an extensive atomistic molecular dynamics simulations study of water dynamics in the hydration layer of a 38 base long hydrated DNA duplex. The computed rotational time correlation function (TCF) of the minor groove water dipoles is found to be markedly non-exponential with a slow component at long time. The constrained water molecule is also found to exhibit anisotropic diffusion in both the major and minor grooves. At short-to-intermediate times, translational motion of water molecules in minor groove is sub-diffusive. Chapter 6 presents the study of water entropy in both the grooves DNA. The average values of the entropy of water at 300K in both the grooves of DNA are found to be significantly lower than that in bulk water. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or micro viscosity) of water molecules in a given domain. In Chapter 7, we study the specific DNA base-water hydrogen bond lifetime (HBLT) dynamics at the major and the minor grooves of a hydrated duplex. The base-water HBLT correlation functions are in general multi-exponential and the average lifetime depends significantly on the specificity of the DNA sequence. The average HBLT is longer in the minor groove than that in the major groove by almost a factor of 2. Chapter 8 presents the solvation dynamics of constituent bases of aqueous DNA duplex. The solvation TCFs of the four individual bases display highly non-exponential decay with time. An interesting negative cross-correlation between water and counterions is observed which makes an important contribution to relaxation at intermediate to longer times. In the concluding note, Chapter 9 presents a brief summary of the outcome of the thesis and suggests several relevant problems that may prove w orthwhile to be addressed in future

O entendimento dos processos hídricos do solo, tais como infiltração, drenagem, e disponibilidade de água para as plantas, necessita do conhecimento da relação entre o conteúdo de água no solo e o potencial matricial, representado pela curva de retenção de água no solo (CRA). No entanto, a determinação da CRA demanda tempo e possui um custo relativo alto. Uma alternativa é sua determinação através de modelos que estimam a CRA a partir de alguns atributos de fácil determinação, chamados funções de pedotransferência (FPT). A finalidade desse trabalho foi quantificar os efeitos da mudança do uso do solo sobre os atributos físicos e hídricos no Sudeste do Estado do Pará. Utilizou-se o banco de dados do Projeto Serviços ecossistêmicos e sustentabilidade das paisagens agrosilvipastoris da Amazônia Oriental, para obter dados de textura (areia, silte e argila), densidade do solo (Ds), carbono orgânico (CO), pH, capacidade de troca de cátions (CTC) e, as vezes, as CRA. Primeiramente, foram avaliadas 16 FPT existentes na literatura; 8 FPT paramétricas, que estimam os parâmetros empíricos do modelo de van Genuchten e 8 FPT pontuais, que estimam a umidade em potenciais específicos de água no solo. Posteriormente, buscando maior capacidade preditiva das FPT, através da técnica de regressão múltipla, desenvolveu-se uma FPT utilizando os atributos do solo mensurados no projeto. As melhores FPT foram utilizadas para estimar os parâmetros do modelo de van Genuchten nos sítios onde não havia CRA medida. Através desta extrapolação, avaliou-se o efeito da mudança de uso do solo sobre a distribuição dos tamanhos de poros, utilizando-se análise de componentes principais (ACP). Dentre as FPT testadas, as que apresentaram melhor resultado foram as FPT propostas por Tomasella et al. (2000), no entanto, a avaliação de desempenho realizada mostrou resultados não satisfatórios. Por outro lado, os resultados apresentados pela FPT desenvolvida neste trabalho alcançaram boa capacidade preditiva dos parâmetros empíricos do modelo de van Genuchten (1980). A ACP possibilitou identificar uma grande variabilidade entre os atributos medidos e estimados dos solos. Devido a esta variabilidade, não foram detectadas diferenças marcantes nos atributos dos solos em função do uso. Para isso, faz-se necessário estudos complementares, aumentando a escala e/ou classes de solo. / The understanding of soil water attributes, such as infiltration, drainage, solute movement and water availability for plants, needs the knowledge of the relationship between water content and soil matric potential, represented by the soil water retention curve (SWRC). However, the determination of the SWRC demands considerable time and has a relatively high cost. An alternative is to model its determination using pedotransfer functions (PTF) that calculate the SWRC parameters using easily obtainable soil attributes. The aim of this study was to use PTF to quantify the effects of changing land use on soil hydro-physical attributes at three locations in southern Pará. The database obtained in the project \"Ecosystem services and sustainable agroforestry landscapes in Eastern Amazonia\" was used in order to obtain soil texture data (sand, silt and clay), bulk density (Bd), organic carbon (OC), pH, cation exchange capacity (CEC) and the SWRC. First, 16 PTF found in the literature were evaluated (8 estimating the empirical parameters of the van Genuchten (1980) model and 8 to estimate soil moisture at specific matric potentials). Later, aiming at a greater predictive ability, a PTF was developed using the technique of multiple regression and the soil attributes determined in the project. The best PTF were used to estimate the model parameters of van Genuchten (1980) at the locations where there was no SWRC data. These results were used to determine the changes in pore distribution due to land use using principal component analysis (PCA). These changes were also associated with changes in content of OC and Bd using multivariate analysis. Of the FPT found in the literature the one that showed the best performance was the FPT developed by Tomasella et al. (2000), however, the evaluation performed showed poor results when the data was extrapolated to the locations where no SWRC were determined. The results presented by the FPT developed in this work showed a better efficiency in determining the SWRC in the locations that did not have this information. The PCA analysis performed on this data identified a large variability among the measured and estimated soil attributes. Because of this variability, there were no marked differences in soil attributes depending on land use. For this, more detailed studies are necessary at a increasing scale and/or at the soil class level.

O entendimento dos processos hídricos do solo, tais como infiltração, drenagem, e disponibilidade de água para as plantas, necessita do conhecimento da relação entre o conteúdo de água no solo e o potencial matricial, representado pela curva de retenção de água no solo (CRA). No entanto, a determinação da CRA demanda tempo e possui um custo relativo alto. Uma alternativa é sua determinação através de modelos que estimam a CRA a partir de alguns atributos de fácil determinação, chamados funções de pedotransferência (FPT). A finalidade desse trabalho foi quantificar os efeitos da mudança do uso do solo sobre os atributos físicos e hídricos no Sudeste do Estado do Pará. Utilizou-se o banco de dados do Projeto Serviços ecossistêmicos e sustentabilidade das paisagens agrosilvipastoris da Amazônia Oriental, para obter dados de textura (areia, silte e argila), densidade do solo (Ds), carbono orgânico (CO), pH, capacidade de troca de cátions (CTC) e, as vezes, as CRA. Primeiramente, foram avaliadas 16 FPT existentes na literatura; 8 FPT paramétricas, que estimam os parâmetros empíricos do modelo de van Genuchten e 8 FPT pontuais, que estimam a umidade em potenciais específicos de água no solo. Posteriormente, buscando maior capacidade preditiva das FPT, através da técnica de regressão múltipla, desenvolveu-se uma FPT utilizando os atributos do solo mensurados no projeto. As melhores FPT foram utilizadas para estimar os parâmetros do modelo de van Genuchten nos sítios onde não havia CRA medida. Através desta extrapolação, avaliou-se o efeito da mudança de uso do solo sobre a distribuição dos tamanhos de poros, utilizando-se análise de componentes principais (ACP). Dentre as FPT testadas, as que apresentaram melhor resultado foram as FPT propostas por Tomasella et al. (2000), no entanto, a avaliação de desempenho realizada mostrou resultados não satisfatórios. Por outro lado, os resultados apresentados pela FPT desenvolvida neste trabalho alcançaram boa capacidade preditiva dos parâmetros empíricos do modelo de van Genuchten (1980). A ACP possibilitou identificar uma grande variabilidade entre os atributos medidos e estimados dos solos. Devido a esta variabilidade, não foram detectadas diferenças marcantes nos atributos dos solos em função do uso. Para isso, faz-se necessário estudos complementares, aumentando a escala e/ou classes de solo. / The understanding of soil water attributes, such as infiltration, drainage, solute movement and water availability for plants, needs the knowledge of the relationship between water content and soil matric potential, represented by the soil water retention curve (SWRC). However, the determination of the SWRC demands considerable time and has a relatively high cost. An alternative is to model its determination using pedotransfer functions (PTF) that calculate the SWRC parameters using easily obtainable soil attributes. The aim of this study was to use PTF to quantify the effects of changing land use on soil hydro-physical attributes at three locations in southern Pará. The database obtained in the project \"Ecosystem services and sustainable agroforestry landscapes in Eastern Amazonia\" was used in order to obtain soil texture data (sand, silt and clay), bulk density (Bd), organic carbon (OC), pH, cation exchange capacity (CEC) and the SWRC. First, 16 PTF found in the literature were evaluated (8 estimating the empirical parameters of the van Genuchten (1980) model and 8 to estimate soil moisture at specific matric potentials). Later, aiming at a greater predictive ability, a PTF was developed using the technique of multiple regression and the soil attributes determined in the project. The best PTF were used to estimate the model parameters of van Genuchten (1980) at the locations where there was no SWRC data. These results were used to determine the changes in pore distribution due to land use using principal component analysis (PCA). These changes were also associated with changes in content of OC and Bd using multivariate analysis. Of the FPT found in the literature the one that showed the best performance was the FPT developed by Tomasella et al. (2000), however, the evaluation performed showed poor results when the data was extrapolated to the locations where no SWRC were determined. The results presented by the FPT developed in this work showed a better efficiency in determining the SWRC in the locations that did not have this information. The PCA analysis performed on this data identified a large variability among the measured and estimated soil attributes. Because of this variability, there were no marked differences in soil attributes depending on land use. For this, more detailed studies are necessary at a increasing scale and/or at the soil class level.

Efficient use of irrigation and nutrients are becoming increasingly important in commercial orchards in the Hawkesbury area. Proper irrigation scheduling practices can help in the better use of irrigation water and reduce environmental impacts. Field experiments were conducted during February 1999 to June 2000 to understand soil-water use, and to evaluate farmer’s irrigation practice under an alley cropping system consisting of turf and stone fruits. The study was carried out at Atlas Farm, 3.5 km from the University of Western Sydney, Hawkesbury campus. The experimental site is a floodplain of the Hawkesbury River. The river flows within 1 km of the farm boundaries. The study was conducted under the farmer’s existing irrigation water and nutrient management practices. The main aims of the thesis were to study the movement and redistribution of soil-water and soil-moisture dynamics in the turf and stone fruit alley cropping system and to understand deep percolation losses and nitrogen leaching using the water balance approach. The study indicated that drainage occurred mainly after heavy rainfall and when there was rainfall for a few consecutive days. Thus irrigation application should be delayed if there is a likelihood of rain in a few consecutive days to prevent loss of water due to deep drainage. Furthermore, the study showed irrigation scheduling was essential to reduce nitrate leaching in the field; that irrigation depths should be varied according to the stage of crop growth, and the proper timing of irrigation application could help reduce deep percolation and runoff losses. / Master of Science (Hons) (Agriculture)

Baltic archipelago areas have high nature values despite being polluted from various antrophogenic activities within the Baltic Sea catchment area and from long-range transport of airborne substances. The discovery of environmental problems in the Baltic Sea in the 1960s led to countermeasures that gradually gave results in reducing the toxic pollution, e.g. from PCBs. Today, much of the environmental management is focused on reducing the effects of eutrophication. There is a demand from society on science to develop strategies that can direct remedial actions so that the cost-effectiveness is maximised. This work focuses on how mass-balance models can be used to understand how coastal ecosystems are controlled by abiotic processes and to predict the response to changes in loading of different substances. Advection, sedimentation and burial are examples of general transport processes that are regulated by morphometrical characteristics, e.g. size, form, effective fetch and topographical openness. This is why different coastal areas have different sensitivity to loading of pollutants. A comparison of six phosphorus and chlorophyll models of different complexity showed that the model performance was not improved with more state variables of total phosphorus (TP) than two water and two sediment compartments. Modelling chlorophyll as a separate state variable did not improve the results for individual values compared to a simple regression against total phosphorus in surface water. Field investigations of the phosphorus content in accumulation sediments along the coast of Svealand showed a distribution pattern that probably is related to differences in the redox status. The average content of mobile phosphorus was much higher than previously found in offshore Baltic sediments indicating that sediments may play an important role for the phosphorus turnover in Baltic archipelago areas. A one-year field study to measure the levels of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in water, sediments and fish during different seasons was carried out in Kallrigafjärden Bay. The collected data set was used to test a mass-balance model for PCCD/F-turnover. It was possible to reproduce the concentrations of different PCDD/F-congeners with high accuracy using a general model approach, including one water compartment and two sediment compartments, indicating that the applied model has the necessary qualifications for successful predictions of PCDD/F-turnover in Baltic coastal areas. / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 736

Nipah belongs to the family of paramyxoviruses that cause numerous fatal diseases in humans and farm animals. There are no FDA approved drugs for Nipah or any of the paramyxoviruses. Designing antiviral therapies that are more resistant to viral mutations require understanding of molecular details underlying infection. This dissertation focuses on obtaining molecular insights into the very first step of infection by Nipah. Such details, in fact, remain unknown for all paramyxoviruses. Infection begins with the allosteric stimulation of Nipah virus host binding protein by host cell receptors. Understanding molecular details of this stimulation process have been challenging mainly because, just as in many eukaryotic proteins, including GPCRs, PDZ domains and T-cell receptors, host receptors induce only minor structural changes (< 2 Å) and, consequently, thermal fluctuations or dynamics play a key role. This work utilizes a powerful molecular dynamics based approach, which yields information on both structure and dynamics, laying the foundation for its future applications to other paramyxoviruses. It proposes a new model for the initial phase of stimulation of Nipah’s host binding protein, and in general, highlights that (a) interfacial waters can play a crucial role in the inception and propagation of allosteric signals; (b) extensive inter-domain rearrangements can be triggered by minor changes in the structures of individual domains; and (c) mutations in dynamically stimulated proteins can induce non-local changes that spread across entire domains.

Ce travail s’inscrit dans le cadre de l’étude de liants aluminosilicatés que sont les géopolymères. La première partie de ce travail a consisté à caractériser la texture poreuse des géopolymères, par des techniques intrusives (porosimétrie à eau, adsorption-désorption d’azote, intrusion mercure) et non-intrusives (diffusion des rayons X et des neutrons aux petits angles). Le terme « texture poreuse » regroupe la forme et la taille des pores, le volume poreux, la surface spécifique et la connectivité des pores. En parallèle, l’évolution de la texture poreuse et des propriétés mécaniques a été suivie sur une période de deux ans, en évitant les échanges avec le milieu extérieur afin d’étudier l’évolution intrinsèque des géopolymères. La seconde étape a consisté à étudier les propriétés thermodynamiques, la structure et la dynamique de l’eau confinée dans la porosité, par calorimétrie différentielle à balayage basse température, par diffusion des neutrons et par des essais de migration. La structure poreuse des géopolymères est complexe, puisqu’il s’agit d’une porosité multi échelle, méso- et macroporeuse, essentiellement ouverte et connectée. Elle consiste en un réseau vermiculaire de mésopores et un réseau de macropores connecté via les mésopores. La taille caractéristique (comprise entre 4 et 10 nm environ) et le volume des mésopores dépendent de la formulation de la pâte de géopolymère, à savoir de la teneur en eau, du rapport molaire Si/Al et de la nature du cation compensateur de charge. Il a été montré que les géopolymères étudiés sont très poreux, la porosité représentant entre 40 et 50 % du volume total du matériau. Le volume mésoporeux représente entre 7 et 15 % du volume total, le reste étant attribué à un volume macroporeux. Au cours du temps, la porosité des géopolymères se ferme légèrement, ceci étant attribué à un mécanisme de dissolution-reprécipitation au niveau des murs de pores. Les propriétés mécaniques atteignent un maximum entre 7 et 10 jours, puis sont stables dans le temps lorsque les échantillons sont conservés à 20°C et à l’abri du séchage ou de la carbonatation de la solution porale. Par ailleurs, trois types d’eau ont été mises en évidence au sein des pores : (i) l’eau liée chimiquement et/physiquement à la surface des parois, (ii) l’eau libre confinée dans les mésopores, et (iii) l’eau libre dans les macropores. A l’échelle locale, les molécules d’eau possède une mobilité proche de celle de l’eau libre, tandis qu’à l’échelle macroscopique, une diminution d’un ordre de grandeur du coefficient de diffusion a été observé, avec un effet probable de la taille des mésopores. / In this study, we have investigated the porous network of geopolymers. The first step consisted in characterizing the structure of the porous network by the means of both intrusive experimental techniques (water porosimetry, gas sorption and mercury intrusion) and non-intrusive techniques (small-angle X-ray and neutron scattering). By the same time, the evolutions of the porous structure as well as the mechanical properties were followed over time. The second step was to determine the structure, the thermodynamics and the dynamics of water confined in the porosity by differential scanning calorimetry, quasi-elastic neutron scattering and migration tests.Geopolymer pore structure is a complex multi-scale porosity, a meso- and macroporous network, essentially open and connected. It consists in a vermicular mesoporous network which connects the macropores. The mesopore characteristic size depends on the formulation of the geopolymer paste and is ranged between about 4 and 10 nm. Geopolymer have a total pore volume comprised between 40 and 50 %, the mesoporous volume represents between 7 and 15 % of the material global volume. The majority of the pore volume is then attributed to macropores. A slight closure of porosity was observed with time and was attributed to a dissolution-precipitation mechanism occurring at pore wall interfaces. The mechanical properties reach a maximum within 10 days, and then are stable over time when the samples were kept from drying and carbonation and at the temperature of 20°C. Besides, three kinds of water were highlighted inside the porosity: (i) an interfacial water linked at the pore surfaces, (ii) free water inside the mésopores and (iii) free water inside macropores. At local time scale, the mobility of water was found close to the one of free water, and at the macroscopic scale, a decrease in diffusion coefficient of one order of magnitude was observed, together with an effect of mesopore size.

Differences in water dynamics between deciduous aspen (Populus tremuloides) and co-occurring evergreen conifer species in the Northern Rocky Mountains result from complex physical and biological interactions. A comprehensive evaluation of individual water transfer mechanisms was used to elucidate the relative importance of several components of the hydro logic cycles of aspen and conifer, and determine which water transfer mechanisms have potential to cause differences in net water yield. Adjacent aspen and conifer stands were monitored to determine snow accumulation and ablation (snow survey), soil moisture recharge (capacitance probes), snowpack sublimation (sublimation pan), transpiration period (thermal dissipation probes), and evapotranspiration (soil water content). Snow accumulation was 34 and 44% higher in aspen during springs of 2005 and 2006, respectively. Ablation rates in aspen (9.58 mm day-1 ) were nearly double that of conifer (4.9 mm day-1). When changes in soil moisture (due to over winter snowmelt) were combined with snow accumulation in 2006, aspen had greater potential (42-83%) for runoff and groundwater recharge. Snowpack sublimation during the ablation period was not different between open, aspen, and conifer sites and comprised -1). Summertime ET rate was higher in an aspen stand (3.6 mm day-1) than in an adjacent conifer stand (2.7 mm day-1) amounting to ~126 mm more water lost over the growing season, but largely reflected post-ablation differences in stored soil water. The net effects of these water transfer processes could result in more watershed water yield from aspen than conifer forests. However, the difference in water yield between these two forests will largely depend on the fate of snow lost from the conifer canopy. Snow intercepted by conifer branches can be removed by the processes of sublimation (reduces water yield) and redistribution (does not affect water yield). Future studies should focus on partitioning the ratio of sublimation to redistribution to predict hydro logic response of vegetation conversions for water yield augmentation in snow-dominated watersheds.