Browsing by Subject "Physical Chemistry"

Now showing 1 - 3 of 3
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    Integrated Fluorescence Spectroscopy for FRET Analysis of Novel Ionic Strength Sensors in the Presence of a Hofmeister Series of Salts
    (2019-07) Miller, Robert
    Living eukaryotic cells are complex, crowded, and dynamic organisms that continually respond to environmental and intracellular stimuli. In addition, these cells have heterogeneous ionic strength with compartmentalized variation of both intracellular concentrations and types of ions. The underlying mechanisms associated with ionic strength variations that trigger different biological functions and response to environmental cues remain largely unknown. Therefore, there is a need to develop a quantitative method for mapping the compartmentalized ionic strength and their temporal fluctuations within living cells. In this work, we investigate a class of novel ionic- strength sensors that consists of tethered mCerulean3 (a cyan fluorescent protein) and mCitrine (a yellow fluorescent protein) via a linker of varied amino acids. In these protein constructs, mCerulean3 and mCitrine act as a donor-acceptor pair undergoing fluorescence resonance energy transfer (FRET) based on both the linker amino acids and the environmental ionic strength. The energy transfer efficiency and the donor-acceptor distance of these sensors can be quantified noninvasively using integrated fluorescence methods in response to intracellular ionic strength in living eukaryotic cells. We employed time-resolved fluorescence methods to monitor the excited-state dynamics of the donor in the presence and absence of the acceptor as a function of the environmental ionic strength using potassium chloride (KCl, 0–500 mM). Towards mapping out the response to of these sensors towards biologically relevant salts, we carried out time- resolved fluorescence for FRET analysis of these sensors as a function of the Hofmeister series of salts (KCl, LiCl, NaCl, NaBr, NaI, Na2SO4). We also used these results towards technique development for FRET analysis based on time-resolved fluorescence polarization anisotropy. Our results show that the energy transfer efficiency of these sensors is sensitive to both the linker amino acid sequence and the environmental ionic strength. These studies in a controlled environment complement previous steady-state spectroscopy analysis of these sensors in a cuvette with the advantage of the compatibility of our approach with fluorescence lifetime imaging microscopy on living cells.
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    Perceptions of Undergraduate Physical Chemistry Instructors: Lessons from a Nationwide Survey, Assessment Analysis, and Reflections on Teaching and Learning
    (2016-05) Fox, Laura
    There are minimal policies in place that direct undergraduate education, and consequently there are scarce criteria that guide the pedagogical and curricular decisions of instructors. Thus, given their great degree of autonomy, instructors play a critical role in undergraduate education. In this dissertation, the perceptions of undergraduate physical chemistry instructors were investigated in three distinct, yet related studies, in order to understand how instructors’ beliefs and attitudes impact their role as educators. First, a nationwide survey of the undergraduate physical chemistry course was conducted to investigate the depth and breadth of course content, as well as how content is delivered and assessed. The results of the survey showed that a core group of thermodynamics and quantum mechanics topics were covered by almost all instructors, however there was a larger group of topics with a wide variability of coverage. Also, the majority of instructors created an instructor–centered environment, despite their degree of teacher preparation experience, and gave more mathematical assessment questions, which contradicted their conceptual leaning goals. Ultimately, the goal of the first study was to provide an awareness of the current state of physical chemistry education across the United States. Second, an analysis of physical chemistry assessments was conducted to investigate characteristics of assessment questions including format, type of knowledge, and type of cognitive processes. The assessment analysis found that instructors used a subjective format more often than an objective format, there was an approximate equal distribution among questions that elicited factual, conceptual, and procedural knowledge, and the majority of questions utilized simple cognitive processes. Ultimately, the goal of the second study was to examine assessment practices of physical chemistry instructors across the United States. Third, instructor reflections were utilized to investigate instructors’ pedagogical content knowledge. Reflection questions were designed to elicit various components of pedagogical content knowledge, as well as how components of pedagogical content knowledge are associated with successful teaching moments, challenging teaching moments, and proposed changes. The analysis of reflections showed that instructors had a strong orientation towards teaching, a varied knowledge of curriculum, a weak knowledge of students’ understanding, and a constantly evolving knowledge of instructional strategies. Ultimately, the goal of the third study was to use instructor reflections to provide a rich description of their pedagogical content knowledge. Together, the three studies of this dissertation helped broaden the landscape of physical chemistry education research. The diverse levels of scale, ranging from nationwide perspectives to individual viewpoints, as well as varied methodologies, including both quantitative and qualitative approaches, helped expand and transform physical chemistry education research.
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    Two-Dimensional Infrared Spectroscopy of Heterogeneous Systems: On the Path to Measuring Charge Transfer in Solution Processed Organic Electronic Thin Films
    (2020-12) Spector, Ivan
    Entering graduate studies, I had a clear vision: renewable, tunable, biodegradable organic electronics. Renewable technologies and luxuries enjoyed by society might prevent catastrophe due to energy shortage as demand increases. With this vision in mind, my focus was to work towards applications of organic electronics. Specifically, work towards the goal of biodegradable, tunable, renewable organic electronics was focused on heterogeneous systems. Scientists and engineers most often work with composites, mixtures, and amorphous materials and Nature has produced optimized structures that are heterogeneous. Recognizing this and knowing that energy is the world’s primary concern motivated the study of electronic processes in heterogeneous systems. Being a physical chemist with a background in automotive repair meant having an interest in both fundamental science and its applications. I believed that the farthest reaches of computation could meet the farthest reaches of experiment on challenging but applicable systems. Applicable implies commercially and industrially viable systems. This also implies ease of processing which is often associated with an increase in heterogeneity. Ideally, measuring charge transfer in heterogeneous organic electronics on a mechanical level would enable their rational design. Mechanical here refers to ultrafast time scales or molecular scales. For example, the measurement of the rate of individual charges hopping would be the mechanical level as opposed to a thermodynamic bulk level measurement like charge mobility or conductivity. Researching the connection between mechanical properties like ultrafast vibrational dynamics or molecular charge hopping and then correlating thermodynamic bulk properties of heat capacity, charge mobility, or conductivity is still an enticing challenge. Bulk properties that have been historically observed are catalysis reaction rates, charge mobility, large-scale morphological changes like glass transition or annealing, coefficient of thermal expansion, etc. Their mechanical corollaries would be molecules reaching transition states, charge hopping between molecular sites or distinct subensembles as opposed to bulk mobility, or ultrafast changes in vibrational correlation as these processes occur. Catalysis is an example of why this might be of interest. For a rate of catalysis with a given concentration, one could have 100% of the catalytic species facilitating 10 times the uncatalyzed reaction rate. Alternatively, one could have 1% of the catalytic species facilitating 1000 times the uncatalyzed reaction rate. Both scenarios would appear the same on the thermodynamic level but would differ on the mechanical level. Rational design of chemical systems begins at the mechanical level, but the effects of interest are often observed on the bulk scale. This connection between the quantum mechanical and the thermodynamic is an open area of research both theoretically and experimentally. These connections are almost completely obfuscated for disordered systems and in many respects are only approachable with phenomenological analysis. Affirming or negating hypotheses that specific vibrational dynamics unique to each molecular configuration give rise to protein function, catalytic mechanisms, or are the source of the apparent charge mobility ceiling in organic electronics (OEs) would change the direction of a tremendous amount of research effort. To illustrate with another example, if it were known that charge mobility were limited byvi charge hopping rates, and charge hopping was limited by molecular motions modulating wavefunction overlap, then the applications of OEs would be limited. If this were known, it would prevent wasted effort on applications that were practiallly beyond reach. Similarly, if a catalytic species had only a small population of extremely active conformers it would be necessary to know this in order to improve their function in an efficient rational way. Given the challenges in applying theory to heterogeneous systems, comparative experiments are one way to connect 2D-IR data to physical processes on both the thermodynamic and mechanical level. This approach involves changing one variable within the molecule or system, observing changes in spectra, and then connecting these to system properties to enable rational design of systems or their moieties. The ultrafast time scales of 2D-IR and its multidimensional nature allow one to decompose ensembles within heterogeneous systems experimentally. Then the efficient application of theory to a subset of a system is approachable. This is opposed to the currently intractable task of modeling an entire heterogeneous system and all its properties at once. Ultrafast 2D-IR is a technique capable of decomposing ensemble measurements and monitoring their dynamics on femtosecond time scales. The capabilities of this technique are manifest in the results below: measurement of temperature dependent intramolecular proton exchange rates, gas adsorption and exchange within heterogeneous systems, solvent effects on complex formation, and morphological changes in the surfaces of nanoparticles