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1. Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA−Protein Complexes

   https://doi.org/10.1021/acs.jctc.3c00833  

   Chakraborty, Debayan; Mondal, Balaka; Thirumalai, D (February 2024, Journal of Chemical Theory and Computation)

   DNA−protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA− protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence−specific DNA−protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA−protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA−protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA−protein complexes at the molecular length-scale. 

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2. Work in Progress: Formation of an engineering identity in first-year students through an intervention centered on senior design projects

   Richards, Abigail M; Anderson, Ryan; Myers, Carrie B (July 2020, ASEE annual conference exposition)

   Abstract This “work in progress” paper describes a multiyear project to study the development of engineering identity in a chemical and biological engineering program at Montana State University. The project focuses on how engineering identity may be impacted by a series of interventions utilizing subject material in a senior-level capstone design course and has the senior capstone design students serve as peer-mentors to first- and second-year students. A more rapid development of an engineering identity by first- and second-year students is suspected to increase retention and persistence in this engineering program. Through a series of timed interventions scheduled to take place in the first and second year, which includes cohorts that will serve as negative controls (no intervention), we hope to ascertain the following: (1) the extent to which, relative to a control group, exposure to a peer mentor increases a students’ engineering identity development over time compared to those who do not receive peer mentoring and (2) if the quantity and/or timing of the peer interactions impact engineering identity development. While the project includes interventions for both first- and second-year students, this work in progress paper focuses on the experiences of first year freshman as a result of the interventions and their development of an engineering identity over the course of the semester. Early in the fall semester, freshman chemical engineering students enrolled in an introductory chemical engineering course and senior students in a capstone design course were administered a survey which contained a validated instrument to assess engineering identity. The first-year course has 107 students and the senior-level course has 92 students and approximately 50% of the students in both cohorts completed the survey. Mid-semester, after the first-year students were introduced to the concepts of process flow diagrams and material balances in their course, senior design student teams gave presentations about their capstone design projects in the introductory course. The presentations focused on the project goals, design process and highlighted the process flow diagrams. After the presentations, freshman and senior students attended small group dinners as part of a homework assignment wherein the senior students were directed to communicate information about their design projects as well as share their experiences in the chemical engineering program. Dinners occurred overall several days, with up to ten freshman and five seniors attending each event. Freshman students were encouraged to use this time to discover more about the major, inquire about future course work, and learn about ways to enrich their educational experience through extracurricular and co-curricular activities. Several weeks after the dinner experience, senior students returned to give additional presentations to the freshman students to focus on the environmental and societal impacts of their design projects. We report baseline engineering identity in this paper. 

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3. Gamification of Chemical Engineering Pathways: Evidence from Introductory Courses

   https://doi.org/10.18260/1-2--37217  

   Brown, Michael; Lamm, Monica; Nadolny, Larysa (July 2021, ASEE Conferences)

   The retention of students pursuing chemical engineering degrees is essential to the future science, technology, engineering, and mathematics (STEM) workforce, but failure in introductory chemistry coursework is a barrier to degree persistence and completion. Despite the positive research on impact of gamification on engagement and academic achievement, only a small number of gamification studies focus on large enrollment STEM courses like those taken by chemical engineers early in their major program, and few incorporate robust measures to rigorously and systematically assess students’ behavioral, cognitive, and affective changes. The goal of this study is to establish effective strategies for the application of gamification in courses that appear early in the chemical engineering curriculum, supporting the retention of students in the major and the graduation of chemical engineers. This was achieved through the development of a chemistry and chemical engineering focused dashboard that is integrated within an online learning management system that includes gamification tools (i.e., leaderboard, badges, and rewards). We report the results of a design-based research study of the dashboard in the introductory chemistry sequence for chemical engineers at a large research university. Students were provided access to the dashboard as part of the learning management system. The dashboard was designed to align to course content. As part of ABET accreditation, chemical engineering majors complete a progress assessment in their second year before progressing in the major. The badges provided to students in the system were based on concepts from the course that would appear on a progress assessment, and provide students an indication of their proficiency on the topic based on their performance in the course. Students were also provided a visualization of tasks to complete within each week, a ‘health’ monitor that provides them their average score on recent assignments by type (homework, exam, lab quizzes), and interactive rewards that surprised students based on their performance and engagement. Our analysis involves complementary methods of quantitative evaluation and qualitative description of how dashboard use impacted chemical engineering students’ motivation and performance in introductory chemistry coursework. We conduct a multi-variate linear regression model to predict students’ academic performance given their use of the student facing dashboard (n=548/578). We control for initial motivational beliefs as measured by Perez’s adaptation of Eccles’ expectancy value scale for STEM courses, students’ emerging engineering identity as measured by XXX instrument, and demographic differences. Our findings suggest that students benefit from using the dashboard as part of their engagement with course resources, such that as students’ engagement with the dashboard (as measured in accumulated page views) increases, their end of term grade increases (B=5.8 points on final grade out of 100, p=0.000). We did not observe significant differences by initial motivational beliefs, engineering identity scales, demographics, or students’ estimates on the amount of time spent preparing for class. Additionally, we conducted thematic analyses of students’ qualitative feedback on the dashboard features. Students identified the utility of the visualization for helping them plan their time for the week, and appreciated the feedback from the health monitor. 

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4. The Role of Pairing Sustainability with Innovation Driven Learning: Observation on the Application of the Engineering-for-One-Planet Framework Guided by the Renaissance Foundry Model

   Wagale, D; Arce-Trigatti, A; Arce, P E; Sanders, J R (March 2024, American Society for Engineering Education Southeastern Annual Meeting)

   This work in progress investigates how the role of an educational intervention that coupled sustainability principles with an innovation-driven learning platform guides students through the development of a protype of innovative technology. Specifically, the intervention includes the purposeful pairing of the Engineering for One Planet (EOP) framework1 with the Renaissance Foundry model (i.e., the Foundry)2 in an undergraduate chemical engineering course that requires student teams to address societal challenges as learning outcomes. We argue that pairing the EOP framework with the Foundry results in an increase in students' sustainability efforts in the design of their prototype of innovative technology that addresses identified societal challenges. A preliminary analysis is presented comparing outcomes from two semesters of the CHE 3550, Transfer Science II (Fluids), course, which is a three-credit hour course with an additional one credit of laboratory work (CHE 3551). Preliminary implications related to holistic engineering education efforts and socially relevant learning will be presented and discussed. 

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5. General Chemistry for Engineers in the 21st Century: A Materials Science Approach

   https://doi.org/10.1557/adv.2017.40  

   Sinex, Scott A.; Halpern, Joshua B.; Johnson, Scott D. (January 2017, MRS Advances)

   ABSTRACT In the case of General Chemistry, many engineering students only take a one semester class with important topics such as kinetics and equilibrium being given limited coverage. Considerable time is spent covering materials already covered in other courses such as General Physics and Introduction to Engineering. Moreover, most GChem courses are oriented toward health science majors and lack a materials focus relevant to engineering. Taking an atoms first approach, we developed and now run a one-semester course in general chemistry for engineers emphasizing relevant materials topics. Laboratory exercises integrate practical examples of materials science enriching the course for engineering students. First-semester calculus and a calculus-based introduction to engineering course are prerequisites, which enables teaching almost all the topics from a traditional two semester GChem course in this new course with advance topics as well. To support this course, an open access textbook in LibreText, formerly ChemWiki was developed entitled General Chemistry for Engineering . Many of the topics were supported using Chemical Excelets and Materials Science Excelets, which are interactive Excel/Calc spreadsheets. The laboratory includes data analysis and interpretation, calibration, error analysis, reactions, kinetics, electrochemistry, and spectrophotometry. To acquaint the students with online collaboration typical of today’s technical workplace Google Drive was used for data analysis and report preparation in the laboratory. 

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