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- Creators: Arizona State University
- Creators: Haydn, Joseph, 1732-1809
ContributorsHaydn, Joseph, 1732-1809 (Composer)
ContributorsHaydn, Joseph, 1732-1809 (Composer)
ContributorsHaydn, Joseph, 1732-1809 (Composer)
Description
Computational biophysics is a powerful tool for observing and understanding the microscopic machinery that underpins the biological world. Molecular modeling and simulations can help scientists understand a cell’s behavior and the mechanisms that drive it. Empirical evidence can provide information on the structure and organization of biomolecular machines, which serve as the backbone of biomolecular modeling. Experimental data from probing the cell’s inner workings can provide modelers with an initial structure from which they can hypothesize and independently verify function, complex formation, and response. Additionally, molecular data can be used to drive simulations toward less probable but equally interesting states. With the advent of machine learning, researchers now have an unprecedented opportunity to take advantage of the wealth of data collected in a biomolecular experiment. This dissertation presents a comprehensive review of atomistic modeling with cryo-electron microscopy and the development of new simulation strategies to maximize insights gained from experiments. The review covers the integration of cryo-EM and molecular dynamics, highlighting the evolution of their relationship and the recent history of MD innovations in cryo-EM modeling. It also covers the discoveries made possible by the integration of molecular modeling with cryo-EM. Next, this work presents a method for fitting small molecules into cryo-electron microscopy maps, which uses neural network potentials to parameterize a diverse set of ligands. The method obtained fitted structures commensurate with, if not better than, the structures submitted to the Protein Data Bank. Additionally, the work describes the data-guided Multi- Map methodology for ensemble refinement of molecular movies. The method shows that cryo-electron microscopy maps can be used to bias simulations along a specially constructed reaction coordinate and capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. Finally, the study analyzes the SARS-CoV-2 spike protein and the conformational heterogeneity of its receptor binding domain. The simulation was guided along an experimentally determined free energy landscape. The resulting motions from following a pathway of low-energy states show a degree of openness not observed in the static models. This sheds light on the mechanism by which the spike protein is utilized for host infection and provides a rational explanation for the effectiveness of certain therapeutics. This work contributes to the understanding of biomolecular modeling and the development of new strategies to provide valuable insights into the workings of cellular machinery.
ContributorsVant, John Wyatt (Author) / Singharoy, Abhishek (Thesis advisor) / Heyden, Matthias (Committee member) / Presse, Steve (Committee member) / Arizona State University (Publisher)
Created2024
Description
The focus of this study is on enhancing cultural competency and increasing an ethnorelative worldview perspective among instructional designers through an innovative approach that integrates global professionals and reciprocal learning. The study is grounded in the context of Arizona State University’s mission to create inclusive learning experiences, particularly in online education, confronting the challenge of effectively providing instructional design that supports a global learner. The dissertation builds upon the existing literature on instructional design, highlighting the need for cultural competency in a globalized educational context. It underscores the growing necessity for instructional designers to adapt their skills and approaches to meet the diverse needs of global learners. The research aims to achieve professional development experiences through a reciprocal learning framework involving international instructional professionals. The research questions explore the role of reciprocal learning in fostering ethnorelative worldviews and the perceived value of this learning for the professional development of instructional designers. The study addresses critical skills such as cultural empathy, active listening, self-awareness of biases, and a commitment to continual learning. The research highlights the gaps in current instructional design training, particularly in the context of global education and cultural competency, contributing to the field of instructional design by proposing a model that integrates global perspectives into the professional development of instructional designers.
ContributorsPate, Amy Loree (Author) / Basile, Carole (Thesis advisor) / Maynard, Andrew (Committee member) / Silova, Iveta (Committee member) / Arizona State University (Publisher)
Created2024
Description
This mixed methods action research study was conducted in a Title I, K-12 public charter school with the purpose of exploring teachers’ capacities to implement student-centered learning after participating in effective professional development (PD). Participants attended a PD cycle where the staff chose the topic, learning was sustained over a three-month period, and teachers received monthly feedback on classroom observations through personalized coaching. The guiding framework for this study was sociocultural theory because the PD design mirrored student-centered learning where the teacher is seen as a guide alongside the student. In this theory, meaning making is a social experience where perspectives of both the teacher and the student contribute to creating new knowledge. Quantitative data collected included a pre-/post-study survey and classroom observations scored on a rubric, and qualitative data consisted of exit interviews. All data was collected and analyzed concurrently, and a researcher’s journal assisted in real-time by providing a space for reflection that was used to determine PD needs, coaching conversations, and interview questions. Quantitative data revealed that the teachers perceived the intervention as slightly boosting their capacity to implement student-centered learning; however, the classroom observations indicated that teachers did not reach levels of proficiency. Through thematic analysis of the qualitative data, six themes emerged, which support the idea that PD can be a transformative experience when it is centered around praxis: 1) collaboration with colleagues, 2) PD gives teachers new ideas, 3) classroom feedback is valuable, 4) teacher reflection, 5) thought partnership, and 6) student choice. The discussion includes limitations and implications for future practice.
ContributorsLoveall, Jill Nicole (Author) / Richardson, Carmen (Thesis advisor) / Frias, Elizabeth (Committee member) / Haddy, Lana (Committee member) / Arizona State University (Publisher)
Created2024
Description
Science, engineering, technology, and mathematics (STEM) classes are required for families in the United States. Due to this requirement, there have been more STEM focused schools present in the educational landscape. Traditionally a high school offering, middle schools are now developing more focused STEM curricula, opening STEM campuses, and creating opportunities for students to expand their STEM knowledge. Parental involvement at the middle school level can be lacking, which is also observed in STEM specific campuses. This action research study examines communication and connection with parents on a STEM middle school campus. The purpose of this study was to create a program where parents can meet once a month with each other and staff on campus to start building a thriving partnership. Ten parent participants were chosen to take part in this three-month study. Each month, participants would meet for an hour to discuss agenda items created by participants at previous meetings. The researcher employed a mixed methods design to understand connection and communication with parents on a STEM middle school campus. To analyze data, descriptive statistics were used for quantitative data, and themes were developed via grounded theory for qualitative data. Results determined that participants' views rose overall from pre to post-innovation in communication and connection. In addition to the gains seen quantitatively and qualitative data, the researcher developed three themes: connection, communication, and parent voice. Overall, the monthly parent meetings were a success overall and enhanced communication and connectivity in the STEM magnet campus. Several limitations, including a lack of diversity in the study population and researcher error, hindered this study. Suggestions for future research include replicating the study while removing the limitations seen in this study and conducting subsequent cycles of AR. Finally, suggestions for future practice indicate the vital need to involve parents in attending programs and in the design, delivery, and application of programs.
ContributorsWelch, Brian (Author) / Ross, Lydia (Thesis advisor) / Coudret, Dude (Committee member) / Marquez, Javier (Committee member) / Arizona State University (Publisher)
Created2024
Description
Late first row transitional metals have attracted attention for the development of sustainable catalysts due to their low cost and natural abundance. This dissertation discusses the utilization of redox-active ligands to overcome one electron redox processes exhibited by these base metals. Previous advances in carbonyl and carboxylate hydrosilylation using redox active ligand-supported complexes such as (Ph2PPrPDI)Mn and (Ph2PPrDI)Ni have been reviewed in this thesis to set the stage for the experimental work described herein.The synthesis and electronic structure of late first row transition metal complexes featuring the Ph2PPrPDI chelate was pursued. Utilizing these complexes as catalysts for a variety of reactions gave a recurring trend in catalytic activity. DFT calculations suggest that the trend in activity observed for these complexes is associated with the ease of phosphine arm dissociation.
Furthermore, the synthesis and characterization of a phosphine-substituted aryl diimine ligand, Ph2PPrADI-H was explored. Addition of Ph2PPrADI-H to CoCl2 resulted in C-H activation of the ligand backbone and formation of [(Ph2PPrADI)CoCl][Co2Cl6]0.5. Reduction of [(Ph2PPrADI)CoCl][Co2Cl6]0.5 afforded the precatalyst, (Ph2PPrADI)Co, that was found to effectively catalyze carbonyl hydrosilylation. At low catalyst loading, TOFs of up to 330 s-1 could be achieved, the highest ever reported for metal-catalyzed carbonyl hydrosilylation.
This dissertation also reports the first cobalt catalyzed pathway for dehydrocoupling diamines or polyamines with polymethylhydrosiloxanes to form crosslinked copolymers. At low catalyst loading, (Ph2PPrADI)Co was found to catalyze the dehydrocoupling of 1,3-diaminopropane and TMS-terminated PMHS with TOFs of up to 157 s-1, the highest TOF ever reported for a Si-N dehydrocoupling reaction. Dehydrocoupling of diamines with hydride-terminated polydimethylsiloxane yielded linear diamine siloxane copolymers as oils.
Finally, dehydrocoupling between diamines and organosilanes catalyzed by a manganese dimer complex, [(2,6-iPr2PhBDI)Mn(μ-H)]2, has allowed for the preparation of silane diamine copolymers. Exceptional solvent absorption capacity was demonstrated by the solid networks, which were found to absorb up to 7 times their own weight. Furthermore, degradation of these networks revealed that their Si-N backbones are easily hydrolysable when exposed to air. The use of lightly crosslinked copolymers as coatings was also studied using SEM analysis.
ContributorsSharma, Anuja (Author) / Trovitch, Ryan J. (Thesis advisor) / Seo, Dong-Kyun (Committee member) / Moore, Gary F. (Committee member) / Arizona State University (Publisher)
Created2024
Description
An efficient thermal solver is available in the CMC that allows modeling self-heating in the electrical simulations, which treats phonons as flux and solves the energy balance equation to quantify thermal effects. Using this solver, thermal simulations were performed on GaN-HEMTs in order to test effect of gate architectures on the DC and RF performance of the device. A Π- gate geometry is found to suppress 19.75% more hot electrons corresponding to a DC power of 2.493 W/mm for Vgs = -0.6V (max transconductance) with respect to the initial T-gate. For the DC performance, the output current, Ids is nearly same for each device configuration over the entire bias range. For the RF performance, the current gain was evaluated over a frequency range 20 GHz to 120 GHz in each device for both thermal (including self-heating) and isothermal (without self-heating). The evaluated cutoff frequency is around 7% lower for the thermal case than the isothermal case. The simulated cutoff frequency closely follows the experimental cutoff frequency. The work was extended to the study of ultra-wide bandgap material (Diamond), where isotope effect causes major deterioration in thermal conductivity. In this case, bulk phonons are modeled as semiclassical particles solving the nonlinear Peierls - Boltzmann transport equation with a stochastic approach. Simulations were performed for 0.001% (ultra-pure), 0.1% and 1.07% isotope concentration (13C) of diamond, showing good agreement with the experimental values. Further investigation was performed on the effect of isotope on the dynamics of individual phonon branches, thermal conductivity and the mean free path, to identify the dominant phonon branch. Acoustic phonons are found to be the principal contributors to thermal conductivity across all isotope concentrations with transverse acoustic (TA2) branch is the dominant branch with a contribution of 40% at room temperature and 37% at 500K. Mean free path computations show the lower bound of device dimensions in order to obtain maximum thermal conductivity. At 300K, the lowest mean free path (which is attributed to Longitudinal Optical phonon) reduces from 24nm to 8 nm for isotope concentration of 0.001% and 1.07% respectively. Similarly, the maximum mean free path (which is attributed to Longitudinal Acoustic phonon) reduces from 4 µm to 3.1 µm, respectively, for the same isotope concentrations. Furthermore, PETSc (Portable, Extensible Toolkit for Scientific Computation) developed by Argonne National Lab, was included in the existing Cellular Monte Carlo device simulator as a Poisson solver to further extend the capability of the simulator. The validity of the solver was tested performing 2D and 3D simulations and the results were compared with the well-established multigrid Poisson solver.
ContributorsAcharjee, Joy (Author) / Saraniti, Marco (Thesis advisor) / Goodnick, Stephen (Committee member) / Thornton, Trevor (Committee member) / Wang, Robert (Committee member) / Arizona State University (Publisher)
Created2024
Description
The Pennsylvania Department of Education recently adopted the new academic standards for Science, Technology & Engineering, and Environmental Literacy and Sustainability (STEELS). Scaling STEELS across the commonwealth is a challenging endeavor that depends upon local school districts' implementation of STEELS-based instruction. Therefore, it behooves local school districts to develop strategies supporting local STEELS adoption. The current action research study examined the influence of an intervention built around a Professional Learning Community (PLC) to support a local school district’s implementation of STEELS guided by the Concerns Based Adoption Model (CBAM; Hall & Hord, 2020). Four secondary science teachers from the Bellwood-Antis School District participated in a PLC. The implementation process of the PLC group was measured via the three diagnostic dimensions of CBAM: Innovation Configurations (IC), Stages of Concern (SoC), and Levels of Use (LoU). A concurrent mixed-methods action research design was employed to collect and analyze CBAM measures. The SoC dimension was measured quantitatively via the Stages of Concern Questionnaire. Individual scores were converted to a whole-group PLC SoC Profile for analysis. SoC, LoU, and IC dimensions were assessed qualitatively via semi-structured interviews. Meta-inferences were developed from combined data analysis of quantitative and qualitative data. A CBAM diagnosis for the PLC group was the primary outcome of this action research cycle, which indicated that the PLC members moved into the early phases of implementation during the intervention. Findings from the current cycle of action research informed an updated intervention game plan to be used in the next phase of implementation.
ContributorsMartin, Travis (Author) / Boutot, Amanda (Thesis advisor) / Coudret, Dude (Committee member) / Wagner, Don (Committee member) / Arizona State University (Publisher)
Created2024