The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

An Ethnographic Study: Becoming a Physics Expert in a Biophysics Research Group

Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the common practices of graduate students in their biophysics weekly research group meetings. I recorded notes on observations and conduct interviews with all participants of the biophysics research group for a period of eight months. I apply the theoretical framework of Communities of Practice to distinguish the cultural norms of the group that cultivate physics expert practices. Results indicate that physics expertise is specific to a topic or subfield and it is established through effectively publishing research in the larger biophysics research community. The participant biophysics research group follows a learning trajectory for its students to contribute to research and learn to communicate their research in the larger biophysics community. In this learning trajectory students develop expert member competencies to learn to communicate their research and to learn the standards and trends of research in the larger research community. Findings from this dissertation expand the model of physics expertise beyond the cognitive realm and add the social and cultural nature of physics expertise development. This research also addresses ways to increase physics graduate student success towards their PhD. and decrease the 48% attrition rate of physics graduate students. Cultivating effective research experiences that give graduate students agency and autonomy beyond their research groups gives students the motivation to finish graduate school and establish their physics expertise.

A comparative analysis of school satisfaction and dropout risk of middle school students attending programs for students with emotional handicaps, severe emotional disturbance and general education students attending center schools and satellite schools

This study evaluated school satisfaction as an indicator of dropout risk of students with Emotional Handicaps (EH) and students with Severe Emotional Disturbance (SED). The students attended two different kinds of middle schools in a largely urban school district in South Florida. One hundred eight students in grade 8 (ages 13-16) participated in this study. Participants were administered the National Dropout Prevention Assessment (NDPA). Forty participants with EH and SED attended a special center school. Thirty-one participants with EH and SED attended satellite programs in a regular middle school. Thirty-seven general education participants attended the same regular middle school. Overall school satisfaction scores were generated, as well as three primary factors (school, environment and personal) and 16 subscales (school atmosphere, future income, difficulty level of classwork, teacher relationships, peer relationships, intrinsic interest in classwork, school hours, classwork stress, general attitude towards school, family influence, perceived opportunity for career, future goals, travel distance, leisure time, self-appraisal of performance, and self-esteem).^ Comparison of students with EH and SED revealed that both groups of students were rated at "low risk" of becoming dropouts on the Environmental factor and the Difficulty of Schoolwork subscale. Students with EH were rated at "caution risk" risk on the Travel Distance subscale. Students with SED were rated at "high risk" on this subscale.^ There were no significant differences in school satisfaction and dropout risk between different program delivery models. There were also no significant differences for category of students (EH, SED) by school type (center school, satellite program). All students were rated at "low risk" of dropping out of school.^ There were significant differences between general education students and students with EH and SED attending satellite programs. Students with EH and SED were rated at "caution risk" for dropping out on the Travel Distance and the Leisure Time subscales. Discussion of results, implications for practice and recommendations for further research are included. ^

Dark matter in dwarf irregular galaxies, DDO 210 and DDO 169

It has been proposed that dwarf irregular galaxies can be separated into two classes based on their formation mechanism; that they are the result of the collapse of a primordial gas cloud or that they are the product of condensation of gas in the tidal tails of interacting galaxies. Simulations of galaxy interactions indicate that one can differentiate between these two scenarios by the dark matter content, with a low dark matter content indicating a fossil tidal dwarf. The purpose of this dissertation was to explore the dark matter distribution of two dwarf irregular galaxies using optical and neutral atomic hydrogen data. For DDO 210, the method of mass-modelling was used to determine its dark matter. About 64% of the galaxy mass was calculated to be in the form of dark matter and hence it is unlikely to be a fossil tidal dwarf. The method of mass-modelling could not be used for DDO 169 as the galaxy shows evidence of being tidally disrupted and hence, has a disturbed velocity field. Instead, the suggestion that dark matter might be responsible for a pressure anomaly in DDO 169 was tested to determine its dark matter content. According to this method, a pressure anomaly does exist but without a concrete value for the scale-height, it is unclear whether the anomaly is due to the presence of dark matter. Hence one cannot say how much dark matter might actually be present in DDO 169. A rotation curve would be required to do this. ^

The use of curriculum modifications and instructional accommodations to provide access for middle school students with autism to the general curriculum

The number of students identified as having autism increased by 500% in the past 10 years (United States Government Accountability Office, 2005). All students with disabilities are required to be placed in least restrictive environments and to be given access to the general curriculum in the major subjects of math, reading, writing, and science as mandated by federal legislation such as the Individuals with Disabilities Education Act (IDEA, 2004) and No Child Left Behind (NCLB, 2001). As a result of this legislation, an increasing number of students with autism are being educated in inclusive classrooms. Most studies on general education access and curriculum modifications and/or instructional accommodations center on students with intellectual disabilities (e.g. Soukup, Wehmeyer, Bashinski, & Boviard, 2007; Wehmeyer, Lattin, Lapp-Rincker, & Agran, 2003). Wehmeyer et al. (2003) and Soukup et al. (2007) found included students with intellectual disabilities had more access to the general curriculum than mostly self-contained students. This meant included students were more likely to be working on the general curriculum as mandated by NCLB than those in only self-contained classrooms. This study builds and expands the research of Wehmeyer et al., as well as Soukup et al., by examining how students with autism are given access to the general curriculum through curriculum modifications and instructional accommodations used by general education teachers in three schools. This investigation focused on nine inclusive classrooms for students with autism using a parallel mixed methods design (Newman, Newman, & Newman, 2011). Classroom observations using both an IEP related checklist and field notes, teacher interviews, an archival document review of the Individual Education Plan (IEP) for the selected students with autism were performed. Findings of this study were organized by interview questions and subsequent coding categories. Quantitative data were organized in a nominal scale. Participants asserted that their middle school students with autism functioned well in their classrooms, occasionally exhibiting behavioral differences. Most instructional accommodations on IEPs were being implemented by participants, and participants often provided additional instructional accommodations not mandated by the IEP. The majority of participants credited county workshops for their knowledge of instructional accommodations.

Study on Pore Distribution and Formation Rule of Sepiolite Mineral Nanomaterials

Theoretical research and specific surface area analysis of nitrogen adsorption indicated that a lot of structural micropores exist in sepiolite minerals fibers. However, the microporous size, existing form, and the distribution relationship between microporous structures were not proved yet. In this paper, the section TEM samples of nanofibers were prepared on the basis of the metal embedding and cutting technique, and the inner structure of sepiolite nanofibers was observed by TEM. The results showed that sepiolite fibers have multiplayer structure similar to concentric circles, and many micropores with the size of about 2–5 nm are normal and parallel to the -axis. The reason for the previously mentioned phenomenon was explained by using BET analysis and X-ray diffraction analysis results.

Synthesis and Thermoelectric Properties of Bi2Se3 Nanostructures

Bismuth selenide (Bi2Se3) nanostructures were synthesized via solvothermal method. The crystallinity of the as-synthesized sample has been analyzed by X-ray diffraction, which shows the formation of rhombohedral Bi2Se3. Electron microscopy examination indicates that the Bi2Se3 nanoparticles have hexagonal flake-like shape. The effect of the synthesis temperature on the morphology of the Bi2Se3 nanostructures has also been investigated. It is found that the particle size increases with the synthesis temperature. Thermoelectric properties of the Bi2Se3 nanostructures were also measured, and the maximum value of dimensionless figure of merit (ZT) of 0.096 was obtained at 523 K.

AFM and SPR studies of protein adsorption at solid/liquid interface

Membrane-like structure formed by surfactant molecules of didodecyldimethylammonium bromide (DDAB) on both HOPG and gold electrodes were studied with AFM and SPR techniques. The study shows that the thickness of the adsorbed layer of DDAB is strongly dependent on the concentration of the vesicle solution. We have also investigated the adsorption of redox protein, Cytochrome c, on graphite electrode with in situ tapping mode AFM. The protein adsorbs spontaneously onto the electrode covered with an adsorbed phosphate layer and forms a uniform monolayer. The adsorbed protein exhibits a reversible electron transfer at 0.17 V (Ag/AgCI) once the electrode potential has been increased to 0.75V. Using surface plasmon resonance spectroscopy we have measured subtle conformational change in protein, Cyt c, due to electron transfer of a single electron on MPA-coated gold electrode. The electron transfer induced change in the resonant angle is about 0.006 deg., which corresponds to ~ 0.2 A decreases in the thickness. This is consistent with that reduced state is more compact than the oxidized state.

Mechanical and Electrical Properties of Single-walled Carbon Nanotubes Synthesized by Chemical Vapor Deposition

Despite the tremendous application potentials of carbon nanotubes (CNTs) proposed by researchers in the last two decades, efficient experimental techniques and methods are still in need for controllable production of CNTs in large scale, and for conclusive characterizations of their properties in order to apply CNTs in high accuracy engineering. In this dissertation, horizontally well-aligned high quality single-walled carbon nanotubes (SWCNTs) have been successfully synthesized on St-cut quartz substrate by chemical vapor deposition (CVD). Effective radial moduli (Eradial) of these straight SWCNTs have been measured by using well-calibrated tapping mode and contact mode atomic force microscopy (AFM). It was found that the measured Eradial decreased from 57 to 9 GPa as the diameter of the SWCNTs increased from 0.92 to 1.91 nm. The experimental results were consistent with the recently reported theoretical simulation data. The method used in this mechanical property test can be easily applied to measure the mechanical properties of other low-dimension nanostructures, such as nanowires and nanodots. The characterized sample is also an ideal platform for electrochemical tests. The electrochemical activities of redox probes Fe(CN)63-/4-, Ru(NH3)63+, Ru(bpy)32+ and protein cytochrome c have been studied on these pristine thin films by using aligned SWCNTs as working electrodes. A simple and high performance electrochemical sensor was fabricated. Flow sensing capability of the device has been tested for detecting neurotransmitter dopamine at physiological conditions with the presence of Bovine serum albumin. Good sensitivity, fast response, high stability and anti-fouling capability were observed. Therefore, the fabricated sensor showed great potential for sensing applications in complicated solution.