Dans ce travail, nous avons étudié en détails l'interaction de l'histone H1 avec l'ADN nucléosomal afin de comprendre comment cette interaction conduit à l'organisation en fibre nucléosomale. Nous avons pu résoudre ce problème ancien par l'utilisation de : (i) l'incorporation de H1 par une chaperonne d'histone physiologique, NAP-1, (ii) la reconstitution de nucléosomes parfaitement homogènes sur une matrice d'ADN contenant la séquence 601 fortement positionnante, (iii) une combinaison de cryo-microscopie électronique (EC-M) et de technique d'empreinte aux radicaux OH°, (iv) une modélisation mécanique du polymère ADN de type « coarse-grain ». Notre « cartographie » par empreinte OH° de résolution d'un nucléotide montre que le domaine globulaire de H1 (GH1) interagit à travers le petit sillon avec des « patch » d'ADN de 10 pb de part et d'autre de la dyade du nucléosome. De plus, GH1 organise environ un tour d'hélice d'ADN de chaque ADN de liaison du nucléosome. En même temps, une suite de 7 acides aminés (120-127) de la partie COOH-terminale est requise pour la formation de la structure en tige de l'ADN de liaison.

REDEFINE is a reconfigurable SoC architecture that provides a unique platform for high performance and low power computing by exploiting the synergistic interaction between coarse grain dynamic dataflow model of computation (to expose abundant parallelism in the applications) and runtime composition of efficient compute structures (on the reconfigurable computation resources). Computer architectures based on the dynamic dataflow model of computation have to be an infinite resource implementation to be able to exploit all available parallelism in all applications. It is not feasible for any real architectural implementation. When limited resource implementations are considered, there is a possibility of loss of performance (inability to efficiently exploit available parallelism). In this thesis, we study the throttling of execution in the REDEFINE architecture to maximize the architecture efficiency. We have formulated it as a design space exploration problem at two levels i.e. architectural configurations and throttling schemes. Reduced feature/high level simulation or feature specific analytical approaches are very useful for the selective study/exploration of early in design phase architectures/systems. Our approach is similar to that of SEASAME Framework which is used for the study of MPSoC (Multiprocessor SoC) architectures. We have used abstraction (feature reduction) at the levels of architecture and model of computation to make the problem approachable and practically feasible. A feature specific fast hybrid (mixed level) simulation framework for the early in design phase study is developed and implemented for the huge design space exploration (1284 throttling schemes, 128 architectural configurations and 10 applications i.e. 1.6 million executions). We have done performance modeling in terms of selection of important performance criteria, ranking of the explored throttling schemes and investigation of the effectiveness of the design space exploration using statistical hypothesis testing. We found some interesting obvious/intuitive and some non-obvious/counterintuitive results. The two performance criteria namely Exec.T and Avg.TU were found sufficient to represent the performance and the resource usage characteristics of the architecture independent of the throttling schemes, the architectural configurations and the applications. The ranking of the throttling schemes based on the selected performance criteria is found to be statistically very significant. The intuitive throttling schemes span the range of performance from the best to the worst. We found absence of trade-off amongst all of the performance criteria. The best throttling schemes give appreciable overall performance (25%) and resource usage (37%) gains in the throttling unit simultaneously. The design space exploration of the throttling schemes is found to be fine and uniform.

The overall objective of this PhD thesis research is to understand and control phase separation in mixed perfluorinated fatty acid-phospholipid surfactant systems that have applications as pulmonary surfactant (PS) mixtures, with an ultimate view of controlling film composition, morphology and mechanical properties. In this context the interaction between perfluorooctadecanoic acid (C18F), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), the major component of native PS extract, and 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) has been explored in Langmuir monolayers and Langmuir–Blodgett (LB) films using a combination of atomic force microscopy (AFM), fluorescence microscopy (FM) and Brewster angle microscopy (BAM) measurements. Thermodynamic and morphological studies of binary and ternary mixed films made of C18F, DPPC and DPPG indicated that both the phospholipids and C18F were miscible over a wide range of compositions. The mixed phospholipid-C18F films contained multimolecular aggregates that were highly enriched in the phospholipids. Furthermore, it was found that the magnitude of the DPPC-C18F interaction could be modulated by altering the concentration of sodium ions in the underlying subphase. Using a highly simplified lung mimic fluid (pH 7.4, 150mM NaCl), DPPC and C18F became fully immiscible. Moreover, the performance characteristics of the mixed films demonstrated the usefulness of C18F as an additive for PS formulations. The effectiveness of a PS protein mimicking peptide was evaluated against DPPC to allow comparison with previous measurements of DPPC-C18F mixed system. The mixing thermodynamics of the peptide and DPPC in Langmuir monolayer implied a repulsive interaction between the film components. The hysteresis response of the mixed monolayer films indicated that the lipid-protein mixture improved the re-spreading of DPPC films. Moreover, molecular-level organization of the mixed films explored by both FM and BAM confirmed the formation of liquid-expanded DPPC domains in the presence of minute amount of the peptide. In order to obtain a thorough understanding of the effect of the deposition process and surfactant tail polarities on the interfacial behavior of perfluorocarbon-hydrocarbon mixed monolayer films, both BAM and AFM measurements of arachidic acid (C20) with perfluorotetradecanoic acid (C14F) and palmitic acid (C16) with C18F mixed monolayer were performed. These measurements revealed that film morphology was minimally perturbed upon its deposition onto solid substrates. Coarse grained molecular dynamics (MD) simulations of films comprised of DPPC molecules with tails of various polarities suggested that the phase separation between the monolayer components could be controlled by varying surfactant tail polarities.

Thickened tailings production and disposal continue to grow in importance in the mining industry. In particular, the transport of oil sands tailings is of interest in this study. These tailings must be in a homogeneous state (non-segregating) during pipeline flow and subsequent discharge. Tailings are often transported in an open channel or flume. Slurries containing both clay and coarse sand particles typically exhibit non-Newtonian rheological behaviour. The prediction of the flow behaviour of these slurries is complicated by the limited research activity in this area. As a result, the underlying mechanisms of solids transport in these slurries are not well understood. To address this deficiency, experimental studies were conducted with kaolin clay slurries containing coarse sand in an open circular channel.<p> A numerical model has been developed to predict the behaviour of coarse solid particles in laminar, open channel, non-Newtonian flows. The model involves the simultaneous solution of the Navier-Stokes equations and a scalar concentration equation describing the behaviour of coarse particles within the flow. The model uses the theory of shear-induced particle diffusion (Phillips et al., 1992) to provide a number of relationships to describe the diffusive flux of coarse particles within laminar flows. A sedimentation flux has been developed and incorporated into the Phillips et al. (1992) model to account for gravitational flux of particles within the flow. Previous researchers (Gillies et al., 1999) have shown that this is a significant mechanism of particle migration.<p> The momentum and concentration partial differential equations have been solved numerically by applying the finite volume method. The differential equations are non-linear, stiff and tightly coupled which requires a novel means of analysis. Specific no-flux, no-slip and no-shear boundary conditions have been applied to the channel walls and free surface to produce simulated velocity and concentration distributions. The results show that the model is capable of predicting coarse particle settling in laminar, non-Newtonian, open channel flows. The results of the numerical simulations have been compared to the experimental results obtained in this study, as well as the experimental results of previous studies in the literature.

Thickened tailings production and disposal continue to grow in importance in the mining industry. In particular, the transport of oil sands tailings is of interest in this study. These tailings must be in a homogeneous state (non-segregating) during pipeline flow and subsequent discharge. Tailings are often transported in an open channel or flume. Slurries containing both clay and coarse sand particles typically exhibit non-Newtonian rheological behaviour. The prediction of the flow behaviour of these slurries is complicated by the limited research activity in this area. As a result, the underlying mechanisms of solids transport in these slurries are not well understood. To address this deficiency, experimental studies were conducted with kaolin clay slurries containing coarse sand in an open circular channel.<p> A numerical model has been developed to predict the behaviour of coarse solid particles in laminar, open channel, non-Newtonian flows. The model involves the simultaneous solution of the Navier-Stokes equations and a scalar concentration equation describing the behaviour of coarse particles within the flow. The model uses the theory of shear-induced particle diffusion (Phillips et al., 1992) to provide a number of relationships to describe the diffusive flux of coarse particles within laminar flows. A sedimentation flux has been developed and incorporated into the Phillips et al. (1992) model to account for gravitational flux of particles within the flow. Previous researchers (Gillies et al., 1999) have shown that this is a significant mechanism of particle migration.<p> The momentum and concentration partial differential equations have been solved numerically by applying the finite volume method. The differential equations are non-linear, stiff and tightly coupled which requires a novel means of analysis. Specific no-flux, no-slip and no-shear boundary conditions have been applied to the channel walls and free surface to produce simulated velocity and concentration distributions. The results show that the model is capable of predicting coarse particle settling in laminar, non-Newtonian, open channel flows. The results of the numerical simulations have been compared to the experimental results obtained in this study, as well as the experimental results of previous studies in the literature.

<p>This study seeks to investigate the dynamics of dead plant carbon over fifty years of old-field forest development at the Calhoun Long Term Soil-Ecosystem Experiment (LTSE) in South Carolina, USA. Emphasis is on the transition phase of the forest, which is less well studied than the establishment and early thinning phase or the steady state phase. At the Calhoun LTSE, the biogeochemical and ecosystem changes associated with old field forest development have been documented through repeated tree measurements and deep soil sampling, and archiving of those soils, which now allow us to examine changes that have occurred over the course of forest development to date.</p><p> In this dissertation, I first quantify the accumulation of woody detritus on the surface of the soil as well as in the soil profile over fifty years, and estimate the mean residence times of that detrital carbon storage. Knowing that large accumulations of C-rich organic matter have piled onto the soil surface, the latter chapters of my dissertation investigate how that forest-derived organic carbon has been incorporated into mineral soils. I do this first by examining concentrations of dissolved organic carbon and other constituents in soil solutions throughout the ecosystem profile and then by quantifying changes in solid state soil carbon quantity and quality, both in bulk soils and in soil fractions that are thought to have different C sources, stabilities, and residence times. To conclude this dissertation, I present the 50-year C budget of the Calhoun LTSE, including live and dead plant carbon pools, to quantify the increasing importance of detrital C to the ecosystem over time.</p><p>This exceptional long term soil ecosystem study shows that 50 years of pine forest development on a former cotton field have not increased mineral soil carbon storage. Tree biomass accumulated rapidly from the time seedlings were planted through the establishment phase, followed by accumulations of leaf litter and woody detritus. Large quantities of dissolved organic carbon leached from the O-horizons into mineral soils. The response of mineral soil C stocks to this flood of C inputs varied by depth. The most surficial soil (0-7.5cm), saw a large, but lagged, increase in soil organic carbon (SOC) concentration over time, an accumulation almost entirely due to an increase of light fraction, particulate organic matter. Yet in the deepest soils sampled, soil carbon content declined over time, and in fact the loss of SOC in deep soils was sufficient to negate all of the C gains in shallower soils. This deep soil organic matter was apparently lost from a poorly understood, exchangeable pool of SOM. This loss of deep SOC, and lack of change in total SOC, flies in the face of the general understanding of field to forest conversions resulting in net increases in soil carbon. These long term observations provide evidence that the loss of soil carbon was due to priming of SOM decomposition by enhanced transpiration, C inputs, and N demand by the growing trees. These results suggest that large accumulations of carbon aboveground do not guarantee similar changes below.</p> / Dissertation

Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this void. To this end, parallel molecular dynamics simulations of self-diffusion on metal surfaces have been developed and employed to address microscopic details of the system. However these simulations are not without their limitations and prove to be computationally impractical for a variety of chemically relevant systems, particularly for diffusive events occurring in the low temperature regime. To circumvent this difficulty, a corresponding coarse-grained representation of the surface is also developed resulting in a reduction of the required computational effort by several orders of magnitude, and this description becomes all the more advantageous with increasing system size and complexity. This representation provides a convenient framework to address fundamental aspects of diffusion in nonequilibrium environments and an interesting mechanism for directing diffusive motion along the surface is explored. In the ensuing discussion, additional topics including transition state theory in noisy systems and the construction of a checking function for protein structure validation are outlined. For decades the former has served as a cornerstone for estimates of chemical reaction rates. However, in complex environments transition state theory most always provides only an upper bound for the true rate. An alternative approach is described that may alleviate some of the difficulties associated with this problem. Finally, one of the grand challenges facing the computational sciences is to develop methods capable of reconstructing protein structure based solely on readily-available sequence information. Herein a checking function is developed that may prove useful for addressing whether a particular proposed structure is a viable possibility.

In this thesis, we present a new continuously variable high frequency standing wave oscillator and demonstrate its use in generating the phase locked clock signal of a digital IC. The ring based standing wave resonant oscillator is implemented with a plurality of wires connected in a mobius configuration, with a cross coupled inverter pair connected across the wires. The oscillation frequency can be modulated by coarse and fine tuning. Coarse modification is achieved by altering the number of wires in the ring that participate in the oscillation, by driving a digital word to a set of passgates which are connected to each wire in the ring. Fine tuning of the oscillation frequency is achieved by varying the body bias voltage of both the PMOS transistors in the cross coupled inverter pair which sustains the oscillations in the resonant ring. We validated our PLL design in a 90nm process technology. 3D parasitic RLCs for our oscillator ring were extracted with skin effect accounted for. Our PLL provides a frequency locking range from 6 GHz to 9 GHz, with a center frequency of 7.5 GHz. The oscillator alone consumes about 25 mW of power, and the complete PLL consumes a power of 28.5 mW. The observed jitter of the PLL is 2.56 percent. These numbers are significant improvements over the prior art in standing wave based PLLs.

La prévision de l'évolution des déchets radioactifs lors d'un stockage en couche géologique argileuse profonde nécessite une bonne compréhension du transport de l'eau et des ions dans l'argile. Leur diffusion dans ce milieu poreux et chargé est décrite par des paramètres empiriques, comme le coefficient de distribution (Kd) qui rend compte des interactions avec les surfaces minérales. Notre travail a porté sur la pertinence de ce concept et sa définition à partir de processus microscopiques. <br /><br />Nous avons d'abord modélisé la contribution ionique aux propriétés diélectriques des argiles, et proposé une détermination de Kd par spectroscopie diélectrique. <br /><br />Nous avons ensuite calculé par simulations microscopiques (Monte-Carlo et dynamique moléculaire) les enthalpies libres et enthalpies d'échange ionique pour les ions alcalins, qui contrôlent Kd et ses variations avec la température T. Les résultats pour le césium sont en bon accord avec des mesures de microcalorimétrie et de Kd en fonction de T. <br /><br />Après avoir contribué au développement d'une nouvelle méthode de simulation sur réseau (Lattice Fokker-Planck), nous l'avons utilisée pour établir un lien explicite entre la dynamique microscopique des ions et le modèle de diffusion-réaction qui sous-tend la notion de Kd. <br /><br />Enfin, nous avons étudié par simulation de dynamique moléculaire la cinétique d'échange d'eau et d'ions entre les particules d'argile (porosité interfoliaire) et la porosité extra-particulaire. Les résultats confirment les hypothèses généralement admises selon lesquelles l'eau et les cations peuvent explorer toute la porosité, tandis que les anions sont exclus des espaces interfoliaires.

This work is a multi-scale effort to confront the rapidly evolving threat of biological weapons attacks through improved bioaerosol surveillance, detection, and response capabilities. The effects of bioaerosol release characteristics, transport in the atmospheric surface layer, and implications for bioaerosol sampler design and real-time detection were studied to develop risk assessment and modeling tools to enhance our ability to respond to biological weapons attacks. A simple convection-diffusion-sedimentation model was formulated and used to simulate atmospheric bioaerosol dispersion. Model predictions suggest particles smaller than 60 micrometers in aerodynamic diameter (AD) are likely to be transported several kilometers from the source. A five fold increase in effective mass collection rate, a significant bioaerosol detection advantage, is projected for samplers designed to collect particles larger than the traditional limit of 10 micrometers AD when such particles are present in the source distribution. A family of dynamically scaled wetted-wall bioaerosol sampling cyclones (WWC) was studied to provide bioaerosol sampling capability under various threat scenarios. The effects of sampling environment, i.e. air conditions, and air flow rate on liquid recovery rate and response time were systematically studied. The discovery of a critical liquid input rate parameter enabled the description of all data with self-similar relationships. Empirical correlations were then integrated into system control algorithms to maintain microfluidic liquid output rates ideally suited for advanced biological detection technologies. Autonomous ambient air sampling with an output rate of 25 microliters per minute was achieved with open-loop control. This liquid output rate corresponds to a concentration rate on the order of 2,000,000, a substantial increase with respect to other commercially available bioaerosol samplers. Modeling of the WWC was performed to investigate the underlying physics of liquid recovery. The set of conservative equations governing multiphase heat and mass transfer within the WWC were formulated and solved numerically. Approximate solutions were derived for the special cases of adiabatic and isothermal conditions. The heat and mass transfer models were then used to supplement empirical correlations. The resulting semi-empirical models offer enhanced control over liquid concentration factor and further enable the WWC to be deployed as an autonomous bioaerosol sampler. / text