Photochemical dynamics of laser-irradiated semiconductor nanostructures

Thesis (Ph.D.)--University of Washington, 2016-08

Age-Specific Fertility Dynamics: Sub-Saharan African Fertility in a Global Context

Thesis (Ph.D.)--University of Washington, 2016-08

Elliptical dust growth in astrophysical plasmas

Elongated dust grains exist in astrophysical plasmas. Anisotropic growth of elliptical dust grains, via plasma deposition, occurs if the deposited ions are non-inertial. In reality the extent of such growth depends upon the initial kinetic energy of the ions and the magnitude of the electric field in the sheath. Simulations of the dynamics of the ions in the sheath are reported, showing how elliptical growth is related to the initial eccentricity and size of the seed relative to the sheath length. Consequences for the eventual fate of elliptical dust are then discussed.

Big bang bifurcations in von Bertalanffy’s dynamics with strong and weak Allee effects

The main purpose of this work was to study population dynamic discrete models in which the growth of the population is described by generalized von Bertalanffy's functions, with an adjustment or correction factor of polynomial type. The consideration of this correction factor is made with the aim to introduce the Allee effect. To the class of generalized von Bertalanffy's functions is identified and characterized subclasses of strong and weak Allee's functions and functions with no Allee effect. This classification is founded on the concepts of strong and weak Allee's effects to population growth rates associated. A complete description of the dynamic behavior is given, where we provide necessary conditions for the occurrence of unconditional and essential extinction types. The bifurcation structures of the parameter plane are analyzed regarding the evolution of the Allee limit with the aim to understand how the transition from strong Allee effect to no Allee effect, passing through the weak Allee effect, is realized. To generalized von Bertalanffy's functions with strong and weak Allee effects is identified an Allee's effect region, to which is associated the concepts of chaotic semistability curve and Allee's bifurcation point. We verified that under some sufficient conditions, generalized von Bertalanffy's functions have a particular bifurcation structure: the big bang bifurcations of the so-called box-within-a-box type. To this family of maps, the Allee bifurcation points and the big bang bifurcation points are characterized by the symmetric of Allee's limit and by a null intrinsic growth rate. The present paper is also a significant contribution in the framework of the big bang bifurcation analysis for continuous 1D maps and unveil their relationship with the explosion birth and the extinction phenomena.

Effect of soil structure on temporal and spatial dynamics of bacteria

Soil is a complex heterogeneous system comprising of highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of resident microbiota. A question addressed in this research is how soil structure affects the temporal dynamics and spatial distribution of bacteria. Using repacked microcosms, the effect of bulk-density, aggregate sizes and water content on growth and distribution of introduced Pseudomonas fluorescens and Bacillus subtilis bacteria was determined. Soil bulk-density and aggregate sizes were altered to manipulate the characteristics of the pore volume where bacteria reside and through which distribution of solutes and nutrients is controlled. X-ray CT was used to characterise the pore geometry of repacked soil microcosms. Soil porosity, connectivity and soil-pore interface area declined with increasing bulk-density. In samples that differ in pore geometry, its effect on growth and extent of spread of introduced bacteria was investigated. The growth rate of bacteria reduced with increasing bulk-density, consistent with a significant difference in pore geometry. To measure the ability of bacteria to spread thorough soil, placement experiments were developed. Bacteria were capable of spreading several cm’s through soil. The extent of spread of bacteria was faster and further in soil with larger and better connected pore volumes. To study the spatial distribution in detail, a methodology was developed where a combination of X-ray microtopography, to characterize the soil structure, and fluorescence microscopy, to visualize and quantify bacteria in soil sections was used. The influence of pore characteristics on distribution of bacteria was analysed at macro- and microscales. Soil porosity, connectivity and soil-pore interface influenced bacterial distribution only at the macroscale. The method developed was applied to investigate the effect of soil pore characteristics on the extent of spread of bacteria introduced locally towards a C source in soil. Soil-pore interface influenced spread of bacteria and colonization, therefore higher bacterial densities were found in soil with higher pore volumes. Therefore the results in this showed that pore geometry affects the growth and spread of bacteria in soil. The method developed showed showed how thin sectioning technique can be combined with 3D X-ray CT to visualize bacterial colonization of a 3D pore volume. This novel combination of methods is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.

Multipartite entanglement in harmonic oscillators subjected to dissipative quantum dynamics

Una detallada descripción de la dinámica de bajas energías del entrelazamiento multipartito es proporcionada para sistemas armónicos en una gran variedad de escenarios disipativos. Sin hacer ninguna aproximación central, esta descripción yace principalmente sobre un conjunto razonable de hipótesis acerca del entorno e interacción entorno-sistema, ambas consistente con un análisis lineal de la dinámica disipativa. En la primera parte se deriva un criterio de inseparabilidad capaz de detectar el entrelazamiento k-partito de una extensa clase de estados gausianos y no-gausianos en sistemas de variable continua. Este criterio se emplea para monitorizar la dinámica transitiva del entrelazamiento, mostrando que los estados no-gausianos pueden ser tan robustos frente a los efectos disipativos como los gausianos. Especial atención se dedicada a la dinámica estacionaria del entrelazamiento entre tres osciladores interaccionando con el mismo entorno o diferentes entornos a distintas temperaturas. Este estudio contribuye a dilucidar el papel de las correlaciones cuánticas en el comportamiento de la corrientes energéticas.

Dynamics of a large submersed plant bed in upper Chesapeake Bay

A large SAV bed in upper Chesapeake Bay has experienced several abrupt shifts over the past half-century, beginning with near-complete loss after a record-breaking flood in 1972, followed by an unexpected, rapid resurgence in the early 2000’s, then partial decline in 2011 following another major flood event. Together, these trends and events provide a unique opportunity to study a recovering SAV ecosystem from several different perspectives. First, I analyzed and synthesized existing time series datasets to make inferences about what factors prompted the recovery. Next, I analyzed existing datasets, together with field samples and a simple hydrodynamic model to investigate mechanisms of SAV bed loss and resilience to storm events. Finally, I conducted field deployments and experiments to explore how the bed affects internal physical and biogeochemical processes and what implications those effects have for the dynamics of the system. I found that modest reductions in nutrient loading, coupled with several consecutive dry years likely facilitated the SAV resurgence. Furthermore, positive feedback processes may have played a role in the sudden nature of the recovery because they could have reinforced the state of the bed before and after the abrupt shift. I also found that scour and poor water clarity associated with sediment deposition during the 2011 flood event were mechanisms of plant loss. However, interactions between the bed, water flow, and waves served as mechanisms of resilience because these processes created favorable growing conditions (i.e., clear water, low flow velocities) in the inner core of the bed. Finally, I found that that interactions between physical and biogeochemical processes led to low nutrient concentrations inside the bed relative to outside the bed, which created conditions that precluded algal growth and reinforced vascular plant dominance. This work demonstrates that positive feedbacks play a central role in SAV resilience to both chronic eutrophication as well as acute storm events. Furthermore, I show that analysis of long-term ecological monitoring data, together with field measurements and experiments, can be an effective approach for understanding the mechanisms underlying ecosystem dynamics.

Microbial nitrogen dynamics in organic and mineral soil horizons along a latitudinal transect in western Siberia

Soil N availability is constrained by the breakdown of N-containing polymers such as proteins to oligopeptides and amino acids that can be taken up by plants and microorganisms. Excess N is released from microbial cells as ammonium (N mineralization), which in turn can serve as substrate for nitrification. According to stoichiometric theory, N mineralization and nitrification are expected to increase in relation to protein depolymerization with decreasing N limitation, and thus from higher to lower latitudes and from topsoils to subsoils. To test these hypotheses, we compared gross rates of protein depolymerization, N mineralization and nitrification (determined using N-15 pool dilution assays) in organic topsoil, mineral topsoil, and mineral subsoil of seven ecosystems along a latitudinal transect in western Siberia, from tundra (67 degrees N) to steppe (54 degrees N). The investigated ecosystems differed strongly in N transformation rates, with highest protein depolymerization and N mineralization rates in middle and southern taiga. All N transformation rates decreased with soil depth following the decrease in organic matter content. Related to protein depolymerization, N mineralization and nitrification were significantly higher in mineral than in organic horizons, supporting a decrease in microbial N limitation with depth. In contrast, we did not find indications for a decrease in microbial N limitation from arctic to temperate ecosystems along the transect. Our findings thus challenge the perception of ubiquitous N limitation at high latitudes, but suggest a transition from N to C limitation of microorganisms with soil depth, even in high-latitude systems such as tundra and boreal forest.

Essays on cultural and institutional dynamics in economic development using spatial analysis

This thesis seeks to research patterns of economic growth and development from a number of perspectives often resonated in the growth literature. By addressing themes about history, geography, institutions and culture the thesis is able to bring to bear a wide range of inter-related literatures and methodologies within a single content. Additionally, by targeting different administrative levels in its research design and approach, this thesis is also able to provide a comprehensive treatment of the economic growth dilemma from both cross-national and sub-national perspectives. The three chapters herein discuss economic development from two broad dimensions. The first of these chapters takes on the economic growth inquiry by attempting to incorporate cultural geography within a cross-country formal spatial econometric growth framework. By introducing the global cultural dynamics of languages and ethnic groups as spatial network mechanisms, this chapter is able to distinguish economic growth effects accruing from own-country productive efforts from those accruing from interconnections within a global productive network chain. From this, discussions and deductions about the implications for both developed and developing countries are made as regards potentials for gains and losses from such types and levels of productive integration. The second and third chapters take a different spin to the economic development inquiry. They both focus on economic activity in Africa, tackling the relevant issues from a geo-intersected dimension involving historic regional tribal homelands and modern national and subnational administrative territories. The second chapter specifically focuses on attempting to adopt historical channels to investigate the connection between national institutional quality and economic development in demarcated tribal homelands at the fringes of national African borders. The third chapter on the other hand focuses on looking closer at the effects of demarcations on economic activity. It particularly probes how different kinds of demarcation warranted by two different but very relevant classes of politico-economic players have affected economic activity quite distinguishably within the resulting subnational regions in Africa.

Fueling growth when oil peaks: directed technological change and the limits to efficiency

While fossil energy dependency has declined and energy supply has grown in the postwar world economy, future resource scarcity could cast its shadow on world economic growth soon if energy markets are forward looking. We develop an endogenous growth model that reconciles the current aggregate trends in energy use and productivity growth with the intertemporal dynamics of forward looking resource markets. Combining scarcity-rent driven energy supply (in the spirit of Hotelling) with profit-driven Directed Technical Change (in the spirit of Romer/Acemoglu), we generate transitional dynamics that can be qualitatively calibrated to current trends. The long-run properties of the model are studied to examine whether current trends are sustainable. We highlight the role of extraction costs in mining.

Is the meander growth in the Brazil Current system off Southeast Brazil due to baroclinic instability?

Temporally-growing frontal meandering and occasional eddy-shedding is observed in the Brazil Current (BC) as it flows adjacent to the Brazilian Coast. No study of the dynamics of this phenomenon has been conducted to date in the region between 22 degrees S and 25 degrees S. Within this latitude range, the flow over the intermediate continental slope is marked by a current inversion at a depth that is associated with the Intermediate Western Boundary Current (IWBC). A time series analysis of 10-current-meter mooring data was used to describe a mean vertical profile for the BC-IWBC jet and a typical meander vertical structure. The latter was obtained by an empirical orthogonal function (EOF) analysis that showed a single mode explaining 82% of the total variance. This mode structure decayed sharply with depth, revealing that the meandering is much more vigorous within the BC domain than it is in the IWBC region. As the spectral analysis of the mode amplitude time series revealed no significant periods, we searched for dominant wavelengths. This search was done via a spatial EOF analysis on 51 thermal front patterns derived from digitized AVHRR images. Four modes were statistically significant at the 95% confidence level. Modes 3 and 4, which together explained 18% of the total variance, are associated with 266 and 338-km vorticity waves, respectively. With this new information derived from the data, the [Johns, W.E., 1988. One-dimensional baroclinically unstable waves on the Gulf Stream potential vorticity gradient near Cape Hatteras. Dyn. Atmos. Oceans 11, 323-350] one-dimensional quasi-geostrophic model was applied to the interpolated mean BC-IWBC jet. The results indicated that the BC system is indeed baroclinically unstable and that the wavelengths depicted in the thermal front analysis are associated with the most unstable waves produced by the model. Growth rates were about 0.06 (0.05) days(-1) for the 266-km (338-km) wave. Moreover, phase speeds for these waves were low compared to the surface BC velocity and may account for remarks in the literature about growing standing or stationary meanders off southeast Brazil. The theoretical vertical structure modes associated with these waves resembled very closely to the one obtained for the current-meter mooring EOF analysis. We interpret this agreement as a confirmation that baroclinic instability is an important mechanism in meander growth in the BC system. (C) 2008 Elsevier B.V. All rights reserved.

A multi-sectoral version of the Post-Keynesian growth model

Neste artigo, pretende-se desenvolver uma versão desagregada da abordagem pós-Keynesiana para o crescimento econômico, mostrando que de fato esse modelo pode ser tratado como um caso particular do modelo Pasinettiano de mudança estrutural e crescimento econômico. Utilizando-se o conceito de integração vertical, torna-se possível conduzir a análise iniciada por Kaldor (1956) e Robinson (1956, 1962), e seguido por Dutt (1984), Rowthorn (1982) e, posteriormente, Bhaduri e Marglin (1990) em um modelo multi-sectorial em que há aumentos da demanda e produtividade em ritmos diferentes em cada setor. Ao adotar essa abordagem, é possível mostrar que a dinâmica de mudança estrutural está condicionada não apenas aos padrões de demanda de evolução das preferências e da difusão do progresso tecnológico, mas também com as características distributivas da economia, que podem dar origem a diferentes regimes setoriais de crescimento econômico. Além disso, é possível determinar a taxa natural de lucro que faz com que a taxa de mark-up seja constante ao longo do tempo. _________________________________________________________________________________ ABSTRACT

Metastability and dynamics of stem cells: from direct observations to inference at the single cell level

Organismal development, homeostasis, and pathology are rooted in inherently probabilistic events. From gene expression to cellular differentiation, rates and likelihoods shape the form and function of biology. Processes ranging from growth to cancer homeostasis to reprogramming of stem cells all require transitions between distinct phenotypic states, and these occur at defined rates. Therefore, measuring the fidelity and dynamics with which such transitions occur is central to understanding natural biological phenomena and is critical for therapeutic interventions.

While these processes may produce robust population-level behaviors, decisions are made by individual cells. In certain circumstances, these minuscule computing units effectively roll dice to determine their fate. And while the 'omics' era has provided vast amounts of data on what these populations are doing en masse, the behaviors of the underlying units of these processes get washed out in averages.

Therefore, in order to understand the behavior of a sample of cells, it is critical to reveal how its underlying components, or mixture of cells in distinct states, each contribute to the overall phenotype. As such, we must first define what states exist in the population, determine what controls the stability of these states, and measure in high dimensionality the dynamics with which these cells transition between states.

To address a specific example of this general problem, we investigate the heterogeneity and dynamics of mouse embryonic stem cells (mESCs). While a number of reports have identified particular genes in ES cells that switch between 'high' and 'low' metastable expression states in culture, it remains unclear how levels of many of these regulators combine to form states in transcriptional space. Using a method called single molecule mRNA fluorescent in situ hybridization (smFISH), we quantitatively measure and fit distributions of core pluripotency regulators in single cells, identifying a wide range of variabilities between genes, but each explained by a simple model of bursty transcription. From this data, we also observed that strongly bimodal genes appear to be co-expressed, effectively limiting the occupancy of transcriptional space to two primary states across genes studied here. However, these states also appear punctuated by the conditional expression of the most highly variable genes, potentially defining smaller substates of pluripotency.

Having defined the transcriptional states, we next asked what might control their stability or persistence. Surprisingly, we found that DNA methylation, a mark normally associated with irreversible developmental progression, was itself differentially regulated between these two primary states. Furthermore, both acute or chronic inhibition of DNA methyltransferase activity led to reduced heterogeneity among the population, suggesting that metastability can be modulated by this strong epigenetic mark.

Finally, because understanding the dynamics of state transitions is fundamental to a variety of biological problems, we sought to develop a high-throughput method for the identification of cellular trajectories without the need for cell-line engineering. We achieved this by combining cell-lineage information gathered from time-lapse microscopy with endpoint smFISH for measurements of final expression states. Applying a simple mathematical framework to these lineage-tree associated expression states enables the inference of dynamic transitions. We apply our novel approach in order to infer temporal sequences of events, quantitative switching rates, and network topology among a set of ESC states.

Taken together, we identify distinct expression states in ES cells, gain fundamental insight into how a strong epigenetic modifier enforces the stability of these states, and develop and apply a new method for the identification of cellular trajectories using scalable in situ readouts of cellular state.

SYSTEM DYNAMICS MODELING AS A QUANTITATIVE-QUALITATIVE FRAMEWORK FOR SUSTAINABLE WATER RESOURCES MANAGEMENT: INSIGHTS FOR WATER QUALITY POLICY IN THE GREAT LAKES REGION

Early water resources modeling efforts were aimed mostly at representing hydrologic processes, but the need for interdisciplinary studies has led to increasing complexity and integration of environmental, social, and economic functions. The gradual shift from merely employing engineering-based simulation models to applying more holistic frameworks is an indicator of promising changes in the traditional paradigm for the application of water resources models, supporting more sustainable management decisions. This dissertation contributes to application of a quantitative-qualitative framework for sustainable water resources management using system dynamics simulation, as well as environmental systems analysis techniques to provide insights for water quality management in the Great Lakes basin. The traditional linear thinking paradigm lacks the mental and organizational framework for sustainable development trajectories, and may lead to quick-fix solutions that fail to address key drivers of water resources problems. To facilitate holistic analysis of water resources systems, systems thinking seeks to understand interactions among the subsystems. System dynamics provides a suitable framework for operationalizing systems thinking and its application to water resources problems by offering useful qualitative tools such as causal loop diagrams (CLD), stock-and-flow diagrams (SFD), and system archetypes. The approach provides a high-level quantitative-qualitative modeling framework for "big-picture" understanding of water resources systems, stakeholder participation, policy analysis, and strategic decision making. While quantitative modeling using extensive computer simulations and optimization is still very important and needed for policy screening, qualitative system dynamics models can improve understanding of general trends and the root causes of problems, and thus promote sustainable water resources decision making. Within the system dynamics framework, a growth and underinvestment (G&U) system archetype governing Lake Allegan's eutrophication problem was hypothesized to explain the system's problematic behavior and identify policy leverage points for mitigation. A system dynamics simulation model was developed to characterize the lake's recovery from its hypereutrophic state and assess a number of proposed total maximum daily load (TMDL) reduction policies, including phosphorus load reductions from point sources (PS) and non-point sources (NPS). It was shown that, for a TMDL plan to be effective, it should be considered a component of a continuous sustainability process, which considers the functionality of dynamic feedback relationships between socio-economic growth, land use change, and environmental conditions. Furthermore, a high-level simulation-optimization framework was developed to guide watershed scale BMP implementation in the Kalamazoo watershed. Agricultural BMPs should be given priority in the watershed in order to facilitate cost-efficient attainment of the Lake Allegan's TP concentration target. However, without adequate support policies, agricultural BMP implementation may adversely affect the agricultural producers. Results from a case study of the Maumee River basin show that coordinated BMP implementation across upstream and downstream watersheds can significantly improve cost efficiency of TP load abatement.

FACTORS AFFECTING DIPOREIA GROWTH RATES IN LAKE SUPERIOR

An ability to predict population dynamics of the amphipod Diporeia is important in understanding how energy pathways in the Lake Superior food web might be altered by disturbances to the ecosystem. Estimating growth rates for this prominent prey item for fish requires information on the physiological effects of changes to its environment. These effects have been investigated for Diporeia in other Great Lakes, but little is known about Lake Superior populations. The primary objective of this study is to obtain quantitative data for rates of Diporeia respiration and consumption that can be incorporated into a bioenergetics model for Lake Superior. Benthic communities in Lake Superior were sampled bimonthly from April through September during 2011 and 2012 to investigate spatial and temporal trends of Diporeia abundances as well as size class structures of the population. Additional samples of Diporeia were collected and kept alive in natural sediment for laboratory experiments. Respiration rates for Diporeia were measured by monitoring dissolved oxygen concentrations in microcosoms using microelectrodes. Additionally, a series of experiments to estimate consumption rates based on food availability were conducted using 14C-labeled algae (Selenastrum capricornutum). Amphipod population densities are highest between 30-110 m (slope) compared to 0-30 m (shelf) or >110 m (profundal) regions in Lake Superior. This heterogeneous distribution of Diporeia in Lake Superior is an important component to quantifying lake-wide biomass. Rates of oxygen consumption by Diporeia range from 32.0 to 44.7 mgO2*gDW-1*d-1, and do not vary significantly with body size per individual. The predicted consumption rate corresponding to average Lake Superior algal carbon fluxes was 0.08 ± SE mgC*gDW-1*d-1. Data on Lake Superior Diporeia biomass and bioenergetics found in this study can be incorporated in a model used to estimate the viability of this population under potential future environmental stressors.