Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Gait Regulation for Bipedal Locomotion

This work explores regulation of forward speed, step length, and slope walking for the passive-dynamic class of bipedal robots. Previously, an energy-shaping control for regulating forward speed has appeared in the literature; here we show that control to be a special case of a more general time-scaling control that allows for speed transitions in arbitrary time. As prior work has focused on potential energy shaping for fully actuated bipeds, we study in detail the shaping of kinetic energy for bipedal robots, giving special treatment to issues of underactuation. Drawing inspiration from features of human walking, an underactuated kinetic-shaping control is presented that provides efficient regulation of walking speed while adjusting step length. Previous results on energetic symmetries of bipedal walking are also extended, resulting in a control that allows regulation of speed and step length while walking on any slope. Finally we formalize the optimal gait regulation problem and propose a dynamic programming solution seeded with passive-dynamic limit cycles. Observations of the optimal solutions generated by this method reveal further similarities between passive dynamic walking and human locomotion and give insight into the structure of minimum-effort controls for walking.

Exact Solution of Bayes and Minimax Change-Detection Problems

The challenge of detecting a change in the distribution of data is a sequential decision problem that is relevant to many engineering solutions, including quality control and machine and process monitoring. This dissertation develops techniques for exact solution of change-detection problems with discrete time and discrete observations. Change-detection problems are classified as Bayes or minimax based on the availability of information on the change-time distribution. A Bayes optimal solution uses prior information about the distribution of the change time to minimize the expected cost, whereas a minimax optimal solution minimizes the cost under the worst-case change-time distribution. Both types of problems are addressed. The most important result of the dissertation is the development of a polynomial-time algorithm for the solution of important classes of Markov Bayes change-detection problems. Existing techniques for epsilon-exact solution of partially observable Markov decision processes have complexity exponential in the number of observation symbols. A new algorithm, called constellation induction, exploits the concavity and Lipschitz continuity of the value function, and has complexity polynomial in the number of observation symbols. It is shown that change-detection problems with a geometric change-time distribution and identically- and independently-distributed observations before and after the change are solvable in polynomial time. Also, change-detection problems on hidden Markov models with a fixed number of recurrent states are solvable in polynomial time. A detailed implementation and analysis of the constellation-induction algorithm are provided. Exact solution methods are also established for several types of minimax change-detection problems. Finite-horizon problems with arbitrary observation distributions are modeled as extensive-form games and solved using linear programs. Infinite-horizon problems with linear penalty for detection delay and identically- and independently-distributed observations can be solved in polynomial time via epsilon-optimal parameterization of a cumulative-sum procedure. Finally, the properties of policies for change-detection problems are described and analyzed. Simple classes of formal languages are shown to be sufficient for epsilon-exact solution of change-detection problems, and methods for finding minimally sized policy representations are described.

Ecological and evolutionary effects of dispersal on freshwater zooplankton

A recent focus on contemporary evolution and the connections between communities has sought to more closely integrate the fields of ecology and evolutionary biology. Studies of coevolutionary dynamics, life history evolution, and rapid local adaptation demonstrate that ecological circumstances can dictate evolutionary trajectories. Thus, variation in species identity, trait distributions, and genetic composition may be maintained among ecologically divergent habitats. New theories and hypotheses (e.g., metacommunity theory and the Monopolization hypothesis) have been developed to understand better the processes occurring in spatially structured environments and how the movement of individuals among habitats contributes to ecology and evolution at broader scales. As few empirical studies of these theories exist, this work seeks to further test these concepts. Spatial and temporal dispersal are the mechanisms that connect habitats to one another. Both processes allow organisms to leave conditions that are suboptimal or unfavorable, and enable colonization and invasion, species range expansion, and gene flow among populations. Freshwater zooplankton are aquatic crustaceans that typically develop resting stages as part of their life cycle. Their dormant propagules allow organisms to disperse both temporally and among habitats. Additionally, because a number of species are cyclically parthenogenetic, they make excellent model organisms for studying evolutionary questions in a controlled environment. Here, I use freshwater zooplankton communities as model systems to explore the mechanisms and consequences of dispersal and to test these nascent theories on the influence of spatial structure in natural systems. In Chapter one, I use field experiments and mathematical models to determine the range of adult zooplankton dispersal over land and what vectors are moving zooplankton. Chapter two focuses on prolonged dormancy of one aquatic zooplankter, Daphnia pulex. Using statistical models with field and mesocosm experiments, I show that variation in Daphnia dormant egg hatching is substantial among populations in nature, and some of that variation can be attributed to genetic differences among the populations. Chapters three and four explore the consequences of dispersal at multiple levels of biological organization. Chapter three seeks to understand the population level consequences of dispersal over evolutionary time on current patterns of population genetic differentiation. Nearby populations of D. pulex often exhibit high population genetic differentiation characteristic of very low dispersal. I explore two alternative hypotheses that seek to explain this pattern. Finally, chapter four is a case study of how dispersal has influenced patterns of variation at the community, trait and genetic levels of biodiversity in a lake metacommunity.

Seeing Turkish state formation processes: Mapping language and education census data

Language provides an interesting lens to look at state-building processes because of its cross-cutting nature. For example, in addition to its symbolic value and appeal, a national language has other roles in the process, including: (a) becoming the primary medium of communication which permits the nation to function efficiently in its political and economic life, (b) promoting social cohesion, allowing the nation to develop a common culture, and (c) forming a primordial basis for self-determination. Moreover, because of its cross-cutting nature, language interventions are rarely isolated activities. Languages are adopted by speakers, taking root in and spreading between communities because they are legitimated by legislation, and then reproduced through institutions like the education and military systems. Pádraig Ó’ Riagáin (1997) makes a case for this observing that “Language policy is formulated, implemented, and accomplishes its results within a complex interrelated set of economic, social, and political processes which include, inter alia, the operation of other non-language state policies” (p. 45). In the Turkish case, its foundational role in the formation of the Turkish nation-state but its linkages to human rights issues raises interesting issues about how socio-cultural practices become reproduced through institutional infrastructure formation. This dissertation is a country-level case study looking at Turkey’s nation-state building process through the lens of its language and education policy development processes with a focus on the early years of the Republic between 1927 and 1970. This project examines how different groups self-identified or were self-identified (as the case may be) in official Turkish statistical publications (e.g., the Turkish annual statistical yearbooks and the population censuses) during that time period when language and ethnicity data was made publicly available. The overarching questions this dissertation explores include: 1.What were the geo-political conditions surrounding the development and influencing the Turkish government’s language and education policies? 2.Are there any observable patterns in the geo-spatial distribution of language, literacy, and education participation rates over time? In what ways, are these traditionally linked variables (language, literacy, education participation) problematic? 3.What do changes in population identifiers, e.g., language and ethnicity, suggest about the government’s approach towards nation-state building through the construction of a civic Turkish identity and institution building? Archival secondary source data was digitized, aggregated by categories relevant to this project at national and provincial levels and over the course of time (primarily between 1927 and 2000). The data was then re-aggregated into values that could be longitudinally compared and then layered on aspatial administrative maps. This dissertation contributes to existing body of social policy literature by taking an interdisciplinary approach in looking at the larger socio-economic contexts in which language and education policies are produced.

An examination of factors that influence entrepreneurial intention of high school students in Kenya

Abstract Considerable research has been carried out on entrepreneurship in efforts to understand its incidence in order to influence and maximize its benefits. Essentially, researchers and policy makers have sought to understand the link between individuals and business creation: Why some people start businesses while others do not. The research indicates that personality traits, individual background factors and association of entrepreneurship with career choice and small business enterprises, cannot sufficiently explain entrepreneurship. It is recognized that entrepreneurship is an intentional process and based on Ajzen’s Theory of Planned Behavior, the most defining characteristic of entrepreneurship is the intention to start a business. The purpose of this study was, therefore, to examine factors that influence entrepreneurial intention in high school students in Kenya. Specifically, the study aimed at determining if there were relationships between the perceptions of desirability, and feasibility of entrepreneurship with entrepreneurial intention of the students, identifying any difference in these perceptions with students of different backgrounds, and developing a model to predict entrepreneurship in the students. The study, therefore, tested how well Ajzen’s Theory of Planned Behavior applied in the Kenyan situation. A questionnaire was developed and administered to 969 final year high school students at a critical important point in their career decision making. Participants were selected using a combined convenience and random sampling technique, considering gender, rural/urban location, cost, and accessibility. Survey was the major method of data collection. Data analysis methods included descriptive statistics, correlation, ANOVA, factor analysis, effect size, and regression analysis. iii The findings of this study corroborate results from past studies. Attitudes are found to influence intention, and the attitudes to be moderated by individual background factors. Perceived personal desirability of entrepreneurship was found to have the greatest influence on entrepreneurial intention and perceived feasibility the lowest. The study findings also showed that perceived social desirability and feasibility of entrepreneurship contributed to perception of personal desirability, and that the background factors, including gender and prior experience, influenced entrepreneurial intention both directly and indirectly. In addition, based on the literature reviewed, the study finds that entrepreneurship promotion requires reduction of the high small business mortality rate and creation of both entrepreneurs and entrepreneurial opportunities (Kruger, 2000; Shane & Venkataraman, 2000). These findings have theoretical and practical implications for researchers, policy makers, teachers, and other entrepreneurship practitioners in Kenya.

From the human rights-based approach to an ecological approach on how to achieve successful inclusion in international disability education

The barriers that people with disabilities face around the world are not only inherent to the limitations resulting from the disability itself, but, more importantly, these barriers rest with the societal technologies of exclusion. Using a mixed methodology approach, I conduct a quest to revealing several societal factors that limit full participation of people with disabilities in their communities, which will contribute to understanding and developing a more comprehensive framework for full inclusion of people with disabilities into the society. First, I conduct a multiple regression analysis to seek whether there is a statistical relationship between the national level of development, the level of democratization, and the level of education within a country’s population on one hand, and expressed concern for and preparedness to improve the quality of life for people of disabilities on another hand. The results from the quantitative methodology reveal that people without disabilities are more prepared to take care of people with disabilities when the level of development of the country is higher, when the people have more freedom of expression and hold the government accountable for its actions, and when the level of corruption is under control. However, a greater concern for the well-being of people with disabilities is correlated with a high level of country development, a decreased value of political stability and absence of violence, a decreased level of government effectiveness, and a greater level of law enforcement. None of the dependent variables are significantly correlated with the level of education from a given country. Then, I delve into an interpretive analysis to understand multiple factors that contribute to the construction of attitudes and practices towards people with disabilities. In doing this, I build upon the four main principles outlined by the United Nations as strongly recommended to be embedded in all international programmes: (1) identification of claims of human rights and the corresponding obligations of governments, hence, I assess and analyze disability rights in education, looking at United Nation, United States, and European Union Perspectives Educational Rights Provisions for People with Disabilities (Ch. 3); (2) estimated capacity of individuals to claim their rights and of governments to fulfill their obligations, hence, I look at the people with disabilities as rights-holders and duty-bearers and discuss the importance of investing in special capital in the context of global development (Ch. 4); (3) programmes monitor and evaluate the outcomes and the processes under the auspices of human rights standards, hence, I look at the importance of evaluating the UN World Programme of Action Concerning People with Disabilities from multiple perspectives, as an example of why and how to monitor and evaluate educational human rights outcomes and processes (Ch. 5); and (4) programming should reflect the recommendations of international human rights bodies and mechanisms, hence, I focus on programming that fosters development of the capacity of people with disabilities, that is, planning for an ecology of disabilities and ecoducation for people with disabilities (Ch. 6). Results from both methodologies converge to a certain point, and they further complement each other. One common result for the two methodologies employed is that disability is an evolving concept when viewed in a broader context, which integrates the four spaces that the ecological framework incorporates. Another common result is that factors such as economic, social, legal, political, and natural resources and contexts contribute to the health, education and employment opportunities, and to the overall well-being of people with disabilities. The ecological framework sees all these factors from a meta-systemic perspective, where bi-directional interactions are expected and desired, and also from a human rights point of view, where the inherent value of people is upheld at its highest standard.