<p>The primary focus of the research presented here is the characterization of diffusion using Fluorescence Correlation Spectroscopy (FCS). To understand the nature of the anomalous diffusion observed in living systems, we characterized diffusion in complex in vitro systems including the diffusion of proteins. random-coil polymers. or dyes in crowded random-coil polymer solutions and the diffusion of polymer beads in agarose gels. Anomalous diffusion is defined where the mean-square-displacement follows a power law in time,</p> / Doctor of Philosophy (PhD)

<p>Here we present direct numerical simulations of a shearing box which models the MHD turbulence in astrophysical systems with cylindrical geometries. The purpose of these simulations is to detect the source of the electromotive force - the driver of large scale magnetic field evolution. This electromotive force is responsible for the large scale dynamo action which builds and maintains the magnetic field against dissipation in plasmas. We compare the estimates of the electromotive force from the kinematic approximation of mean field theory - the most prevalent theory for astrophysical dynamos - with a modified version of mean field theory which restricts the electromotive force by the consideration of magnetic helicity conservation. We will show that in general the kinematic approximation overestimates the observed electromotive force for the majority of the simulation, while the term derived from the helicity conservation estimates the electromotive force very well. We will also illustrate the importance of the shear in the fluid to the growth and strength of the resulting large scale magnetic field. Too strong and the small scale dynamo does not grow enough to properly seed a strong large scale dynamo. Too weak, and no large scale magnetic field is observed after the small scale dynamo has saturated. Finally, we will find that in order to maintain the strength of the emerged large scale magnetic dynamo we require a magnetic Prandtl number ($Pr \equiv \nu/\eta$) that is at least an order of magnitude above unity.</p> / Master of Science (MSc)

Craters within Arabia Terra, Mars, contain hundreds of meters of layered strata showing systematic alternation between slope- and cliff-forming units, suggesting either rhythmic deposition of distinct lithologies or lithologies that experienced differential cementation. Hypothesized origins of these intercrater layered deposits include lacustrine, aeolian, volcanic airfall, and impact surge deposition. On Earth, rhythmically deposited strata can be examined in terms of stratal packaging, wherein the interplay of tectonics, sediment deposition, and change in base level results in predictable patterns with respect to changes in the amount of space available for sediment accumulation. Fundamental differences between tectonic regimes of Earth and Mars demand that packaging of layered strata primarily reflects changes in sediment influx and base level. Analysis of stratal packaging may therefore help us understand the relative roles of these parameters, and provide crucial constraint on martian depositional models. Rhythmic stratal patterns in Becquerel Crater (7°W 22°N) have been attributed to astronomical forcing of regional climate. A clear depositional model, however, has yet to be presented. Here, we reanalyze strata of Becquerel Crater and compare results with two additional crater successions. Results indicate that, by contrast with Becquerel Crater, strata within Danielson Crater (7°W 8°N) and an unnamed crater (Crater X; 1.2°W 9°N) do not record hierarchical packaging readily attributable to astronomical effects, and suggest that regional climate forcing may not be readily applied as a paradigm for all intracrater deposition. Similarities in depositional style in these three craters, however, may be linked by a model for sediment accumulation—with potential links to regional climate—wherein episodic melting of ground ice raised local base level, stabilized aeolian sedimentation, and resulted in differential cementation of accumulated strata.

Comets, remnants of the solar system's formation, exhibits partially unexplained outbursts that are closely tied to the physical structure of the nucleus. To investigate outbursts, we employed pore network modeling techniques, such as the Bower-Watson algorithm and Voronoi diagrams, to better represent the nucleus' complex porous structure and simulate gas transfer processes. We examined heat diffusion in the comet's subsurface and its influence on crystallization. The extra heat generated by crystallization can shift the crystalline front deeper into the nucleus, accelerating subsurface evaporation rates. This process results in the formation of a thicker ice mantle with reduced porosity on the surface, trapping evaporated gas in the underlying layers. As gas pressure accumulates over time, the mantle eventually succumbs to the buildup. By applying percolation theory, we identified the critical point at which trapped gas breaks through the surface, ultimately leading to a better understanding of comet outburst formation.

Charge-Conjugation (C) and Charge-Conjugation-Parity (CP) Violation is one of the three Sakharov conditions to explain via baryogenesis the observed baryon asymmetry of the universe (BAU). The Standard Model of particle physics (SM) contains sources of CP violation, but cannot explain the BAU. This motivates searches for new physics beyond the standard model (BSM) which address the Sakharov criteria, including high-precision searches for new sources of CPV in systems for which the SM contribution is small, but larger effects may be present in BSM theories. A promising example is the search for the electric dipole moment of the neutron (nEDM), which is a novel system to observe CPV due to the initial and final state being identical. A non-zero measurement necessarily requires violation of P and T discrete symmetries; invoking CPT invariance requires that CP is violated. There are BSM theories which predict a magnitude for the nEDM larger than SM predictions, so that such studies are beneficial at setting constraints on new physics. The current experimental limit of dn < 3.0 x 10-26 e cm at 90% CL as set by the Institut Laue-Langevin (ILL) [1] was largely limited by systematic effects related to the magnetic field. The research presented here supported technical progress toward a new measurement of the nEDM, with the goal of improving the result by an order of magnitude. A novel approach to the problem of limiting systematics is proposed, studied in Monte Carlo simulations, and an optimized prototype was constructed for use in a magnetic resonance experiment.

Radio-loud active galactic nuclei (AGN) are one class of objects associated with accretion activity onto supermassive black holes in centers of massive galaxies. They are believed to be in a radiatively-inefficient accretion mode with low accretion rate. To understand this accretion mode, it is important to measure its radiative output at high energies (> 13.6eV), which can be traced through optical emission lines. However, little is known about their true radiative output. This is because no correlation between optical emission-line and radio luminosity has been found for the majority of low-luminosity radio AGN, which are often classified as low-excitation radio galaxies, or Fanaroff-Riley Class I (FR-I) radio galaxies. We demonstrate that most of the line emission found in these galaxies is not powered by the central AGN, but likely powered by some old stellar population. Only when this component is subtracted or otherwise taken into account can we estimate the true line emission associated with the AGN. These emissions may show interesting correlations with the radio luminosities in some cases.

The Hindu-Kush Himalayan region possesses a large resource of snow and ice, which acts as a freshwater reservoir for irrigation, domestic water consumption or hydroelectric power for billions of people in South Asia. Monitoring hydrologic resources in this region is challenging because of the difficulty of installing and maintaining a climate and hydrologic monitoring network, limited transportation and communication infrastructure and difficult access to glaciers. As a result of the high, rugged topographic relief, ground observations in the region are extremely sparse. Reanalysis data offer the potential to compensate for the data scarcity, which is a barrier in hydrological modeling and analysis for improving water resources management. Reanalysis weather data products integrate observations with atmospheric model physics to produce a spatially and temporally complete weather record in the post-satellite era. This dissertation creates an integrated hydrologic modeling system that tests whether streamflow prediction can be improved by taking advantage of the National Aeronautics and Space Administration (NASA) remote sensing and reanalysis weather data products in physically based energy balance snow melt and hydrologic models. This study also enhances the energy balance snowmelt model by adding capability to quantify glacier melt. The novelty of this integrated modeling tool resides in allowing the user to isolate various components of surface water inputs (rainfall, snow and glacier ice melt) in a cost-free, open source graphical-user interface-based system that can be used for government and institutional decision-making. Direct, physically based validation of this system is challenging due to the data scarcity in this region, but, to the extent possible, the model was validated through comparison to observed streamflow and to point measurements at locations in the United States having available data

Doctor of Philosophy(PhD) / This thesis describes the exploration and the development of computational means to investigate the behaviour of design objects before they are available for investigation in the physical world. The motivation is to inform the design process about the design object’s performance in order to achieve better – more performance-oriented – design outcomes in the sense of energy efficiency and comfort performance than can be achieved by conventional design techniques. The research is structured into five successive parts. - Concept Development – A review of the objective domains comfort assessment and energy efficiency assessment is conducted and the design process, human design activity and the application of simulation in the architectural domain is discussed in order to identify requirements for the development of computational means for design analysis. Requirements regarding model content, model features and model integration are developed. The main requirements are that a highly integrated, three-dimensional and dynamic representation of physical processes is needed and that a universal and integrated representation is required. - Concept Formulation – Based on the identified requirements, the concept for a model is formulated. In order to achieve a universal and integrated representation of physical processes the concept uses the approach of a constructive language. Space is represented with autonomous spatial elements, called congeneric cells. Interaction between the cells is represented by near- and remote-conjunctions. Physical and geometric self-contained formulations of the model reduce the model input requirements, so that geometric information and simple property specification (material, activity) is sufficient to describe the design object in the model. - Model Development – The concept is formulated in mathematical physical terms based on well known physical laws and building physical models (first-principle approach). Heat and moisture conduction, diffusion of various components and a flow model is formulated as near-conjunction processes. Heat radiation, light and sound are modelled with a radiosity approach as remote-conjunctions. The simulation algorithm, which governs the interaction between the cells in order to represent the behaviour of space, is explained. - Computational Implementation – The concept and the model is tested by implementation of a prototype using C++ and OpenGL on a conventional Pentium 4 notebook. The prototype consists of three parts: user-interface, model translator and simulation engine. The user interface functions as model-input and result-output device. The implementation of the concept and of further model parts is described in detail. - Assessment and Testing – The developed concept and the model, as implemented in the prototype, are tested and assessed against the initially developed requirements. The physical model is assessed in regard to plausibility and accuracy of the representation of the physical phenomena. At the end of the thesis the project is summarized, the achievements of the project’s objectives are discussed critically and issues for future research are suggested. Possible applications of the developed model are listed, and the contributions to the application of computational simulation in the architectural domain, developed in this research, are named. At the current stage the required processing time and high memory requirements prevent implementation of a design assessment system, following the suggested concept, at a useful scale. Also the developed physical models require further refinement and testing. Although the general feasibility of the concept and the model was successfully demonstrated, its implementation in a fully applicable design assessment system based on the universal and integrated representation of physical processes was not achieved at this stage. While detailed description and analysis is given in the body of the thesis, detailed formulations of the work and the developed model are given in the appendix. The body and the appendix together provide a complete picture of the research presented.

Nyanza Gulf is a large, shallow and long river-influenced embayment located in northeastern Lake Victoria. The gulf opens to the main lake through the narrow and deep Rusinga Channel, the exchange zone between the two ecosystems with different physical chemical and biogeochemical conditions. The main goals of this study are to characterize physicochemical and nutrient gradients along the gulf-main-lake transect, characterize and quantify the water and nutrient fluxes between the gulf and the main lake, and assess the response of phytoplankton community and photosynthesis to the spatially varying physical and nutrient conditions along the study transect. Between March 2005 and March 2006, measurements of physicochemical profiles as well as nutrient and the phytoplankton community analysis were conductued monthly along the study transect. Additionally, analysis of different surficial sediment phosphorus fractions was done in order to asses the potential role of bottom sediment in contributing to phosphorus enrichment in the lake water column. A box mass balance model was used to calculate the exchange of water and nutrient fluxes between different zones along the study transect and to estimate ecosystem metabolism in the gulf and the channel. Spatial variability in physicochemical and biogeochemical conditions was observed along the study transect, especially between the shallow and river-influenced inner-gulf, the deep and physically active Rusinga Channel, and the main lake, mainly in response to river inputs and varying morphometry along the study transect. The gulf had significantly higher electrical conductivity (EC), turbidity, total nitrogen (TN), and dissolved reactive silica (DRSi) but the levels declined monotonically along the channel in response to mixing with the main lake water. The channel and the main lake had, respectively, significantly higher dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) compared to the gulf. Spatial variability in morphometry and exposure to varying wind forcing lead to differential mixing and differential heating and cooling along the transect, resulting in density driven fronts and horizontal exchange of water and nutrients between the gulf and the main lake. Upwelling and downwelling maintained mixing conditions in the channel which consequently influenced nutrient recycling, the light environment and hence affecting phytoplankton community composition and productivity. The net residual water flow from the gulf to the main lake was 36 m3/s but the mixing flux was approximately 20 times higher and both fluxes accounted for a gulf exchange time of 1981 days. The advective and mixing fluxes between the gulf and the main lake resulted in net export of dissolved inorganic phosphorus (DIP; 400 kg P/d) from the main lake into the gulf and net export of DRSi (10 t Si/d) from the gulf into the main lake. In the deep, narrow and physically active Rusinga Channel there was net production of dissolved nutrients whereas in the gulf there was net consumption of dissolved nutrients, which helped to maintain high net ecosystem production (NEP; 566 mg C/m2/d) in the gulf in contrast the channel which showed net heterotrophy. The high NEP in the gulf and the associated high nutrient demand coupled with possibly low SRP to DIN supply ratio lead to P limitation of algal growth in the gulf as indicated by all indicators of nutrient status. This has important implications for management since increased P input into the gulf will translate into increased algal blooms in the gulf and therefore compromise water quality. Spatial variability in physical conditions and nutrient status along the study transect influenced phytoplankton community composition and photosynthesis. The shallow and turbid gulf was dominated by cyanobacteria but diatoms dominated in the channel in response to reduced turbidity and increased physical mixing and nutrient availability (DRSi, SRP). In the main lake seasonal stratification and deep mixing depth favoured both cyanobacteria and diatoms. The phytoplankton community in channel had a higher photosynthetic capacity (Fv/Fm, PBm) compared to both the gulf and the main lake.

Nyanza Gulf is a large, shallow and long river-influenced embayment located in northeastern Lake Victoria. The gulf opens to the main lake through the narrow and deep Rusinga Channel, the exchange zone between the two ecosystems with different physical chemical and biogeochemical conditions. The main goals of this study are to characterize physicochemical and nutrient gradients along the gulf-main-lake transect, characterize and quantify the water and nutrient fluxes between the gulf and the main lake, and assess the response of phytoplankton community and photosynthesis to the spatially varying physical and nutrient conditions along the study transect. Between March 2005 and March 2006, measurements of physicochemical profiles as well as nutrient and the phytoplankton community analysis were conductued monthly along the study transect. Additionally, analysis of different surficial sediment phosphorus fractions was done in order to asses the potential role of bottom sediment in contributing to phosphorus enrichment in the lake water column. A box mass balance model was used to calculate the exchange of water and nutrient fluxes between different zones along the study transect and to estimate ecosystem metabolism in the gulf and the channel. Spatial variability in physicochemical and biogeochemical conditions was observed along the study transect, especially between the shallow and river-influenced inner-gulf, the deep and physically active Rusinga Channel, and the main lake, mainly in response to river inputs and varying morphometry along the study transect. The gulf had significantly higher electrical conductivity (EC), turbidity, total nitrogen (TN), and dissolved reactive silica (DRSi) but the levels declined monotonically along the channel in response to mixing with the main lake water. The channel and the main lake had, respectively, significantly higher dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) compared to the gulf. Spatial variability in morphometry and exposure to varying wind forcing lead to differential mixing and differential heating and cooling along the transect, resulting in density driven fronts and horizontal exchange of water and nutrients between the gulf and the main lake. Upwelling and downwelling maintained mixing conditions in the channel which consequently influenced nutrient recycling, the light environment and hence affecting phytoplankton community composition and productivity. The net residual water flow from the gulf to the main lake was 36 m3/s but the mixing flux was approximately 20 times higher and both fluxes accounted for a gulf exchange time of 1981 days. The advective and mixing fluxes between the gulf and the main lake resulted in net export of dissolved inorganic phosphorus (DIP; 400 kg P/d) from the main lake into the gulf and net export of DRSi (10 t Si/d) from the gulf into the main lake. In the deep, narrow and physically active Rusinga Channel there was net production of dissolved nutrients whereas in the gulf there was net consumption of dissolved nutrients, which helped to maintain high net ecosystem production (NEP; 566 mg C/m2/d) in the gulf in contrast the channel which showed net heterotrophy. The high NEP in the gulf and the associated high nutrient demand coupled with possibly low SRP to DIN supply ratio lead to P limitation of algal growth in the gulf as indicated by all indicators of nutrient status. This has important implications for management since increased P input into the gulf will translate into increased algal blooms in the gulf and therefore compromise water quality. Spatial variability in physical conditions and nutrient status along the study transect influenced phytoplankton community composition and photosynthesis. The shallow and turbid gulf was dominated by cyanobacteria but diatoms dominated in the channel in response to reduced turbidity and increased physical mixing and nutrient availability (DRSi, SRP). In the main lake seasonal stratification and deep mixing depth favoured both cyanobacteria and diatoms. The phytoplankton community in channel had a higher photosynthetic capacity (Fv/Fm, PBm) compared to both the gulf and the main lake.