An XSEDE-wide effort is underway to expand the community by recruiting and enabling a diverse group of students who have the skills - or are interested in acquiring the skills - to participate in the actual work of XSEDE. The name of this effort is XSEDE EMPOWER ( Expert Mentoring Producing Opportunities for Work, Education, and Research ).
Table of Contents
Participant Publications, Presentations, and Evidence of Impact
Manuscripts are being prepared that include the work of:
- Zachery Casey, Northeastern University, participant in Fall 2019 and Spring 2020
- Nicholas Grabill, Michigan State University, participant in Summer 2020
- Carlos Gutierrez, California State Polytechnic University, Pomona, participant in Spring 2019 through Spring 2020
- Umairullah Khan, Portland State University, participant in Spring, Summer, and Fall 2020
- Phan Phu, California State Polytechnic University, Pomona, participant in Spring and Summer 2018
- Kai Pinckard, Reed College, participant in Summer 2020
- Olivia Shaw, University of Delaware, participant in Spring and Summer 2020
From a participant in 2020:
"The EMPOWER program kept me in school. I was considering taking a gap year due to the COVID-19 Pandemic, but my interest in research was strong enough to make me want to stay in school." (written in October 2020)
From Alan Andonian, University of Massachusetts Dartmouth, participant in fall 2020:
"The Empower program has given me the opportunity to research and implement software for the conversion of tomographic images to 3D meshed volumes. The Goal being to take the 3D volume into Abaqus for FEA analysis. Participation in the EMPOWER program has helped me grow my capabilities with Finite Element Software and my ability to do computational research. The EMPOWER program has allowed me to learn about 3D visualization software and the process behind creating a CT to FEA workflow. For research projects I learned the important of creating a plan and documenting steps." (written October 2020)
From Umairullah Khan, Portland State University, participant in spring, summer, and fall 2020:
"My work in the Reichow Lab, supported by the EMPOWER program, is actually the primary driver of my intent to pursue a computational research career in the life sciences. I have been exposed to a discipline and a community of scientists that I hope to contribute to and be a productive member of throughout my career. Moreover, the connections I've made so far will be invaluable in driving my future plans, into graduate school and beyond. In particular, the EMPOWER program has supported my long-term participation in the lab, particularly over the summer months. Otherwise, I would be unable to dedicate extended and uninterrupted time towards the Reichow Lab's various research projects. Continued support from XSEDE is the reason I have co-authored recent publications." (written October 2020)
Yue, B., Haddad, B.G., Khan, U., Atalla, M., Reichow, S.L., & Bai, D. (2020, February). Functional Characterization of VJ-gating and Single Channel Conductance of Sheep Cx46 and Cx50 Gap Junctions. Poster presented at the 64th Annual Meeting of The Biophysical Society, San Diego, CA. https://doi.org/10.1016/j.bpj.2019.11.1573
Yue B., Haddad, B.G., Khan, U., Chen, H., Atalla, M., Zhang, Z., Zuckerman, D.M., Reichow, S.L., & Bai, D. (2020). Connexin 46 and connexin 50 gap junction channel open stability and unitary conductance are shaped by structural and dynamic features of their N-terminal domains. Unpublished manuscript. https://doi.org/10.1101/2020.07.01.182584
From Christopher Sherald, University of Kansas, participant in fall 2020:
"As an aspiring physicist, the XSEDE EMPOWER program has helped me in realizing my career goals in a number of ways. The program is currently helping to familiarize me with programming and supercomputing, to learn more about data analysis, and providing computation resources that will help in speeding up sizeable simulations. My research with XSEDE and my current mentor is being used to create a presentation at the National Society of Black Physicists (NSBP) conference." (written October 2020)
From Adith Srivatsa, Georgia Institute of Technology, participant in fall 2020:
"My participation with the EMPOWER program has given me a better understanding of ion channels, its mechanism, and its generalizability across all fields. Under the guidance of my mentor, I was able to critically analyze literature, develop novel protocols, and reach out to experts in the field for advice on my scripts. I believe that EMPOWER has allowed me to have a better vision for the direction of simulation research. I hope to continue getting hands-on experience in the future. Two abstracts for poster presentations were submitted to the Biophysical Society Annual Meeting as a result of the work performed under the EMPOWER program. I am the first author on the submission "Molecular dynamic simulations suggest novel PIP2 binding sites for SK2 channels regulation". I am second author on the submission "Utilizing umbrella MD sampling to assess contradictory PIP2 binding site in the membrane embedded SK2-CaM complex to help further understanding of sk2 activation"." (written October 2020)
From Billy Stone, University of Colorado Colorado Springs, participant in summer and fall 2020:
"I'm grateful for the program because it connected me to a professor that could teach me these techniques [in multiscale (quantum mechanical/ classical mechanical) chemical simulations]. I am presenting at the Biophysical Society annual meeting in Feb. 2021, and hopefully a publication will follow shortly after that." (written October 2020)
From Alexandra Ballow, Youngstown State University, participant in summer 2020:
Presentation at Scientific Computing with Python Virtual Conference (SciPy 2020): https://www.youtube.com/watch?v=Av5htgmVb3s
From Nicholas Grabill, Michigan State University, participant in summer 2020:
Grabill, N. (2020, August 4). Analysis of Scaling Techniques in SEE Image Segmentation Software Utilizing Evolutionary Algorithms. Poster presented at the 2020 MID-SURE Research Symposium, Michigan State University.
From Tori Zottarelli, University of Portland, participant in summer 2020:
Zottarelli, T. & Taylor, B. (2020, July 29). DFT Studies of the Transmetalation Mechanism in Stille Cross-Coupling Reactions. Poster presented at the virtual MU3CCC Conference, Iowa State University.
From Andrew Roberts, Southwestern Oklahoma State University, participant in spring 2020:
Roberts, A., & Evert, J. (2020, March). Using Supercomputers to Control Multiple Robots. Poster presented at Oklahoma Research Day, Weatherford, OK.
From Vatsal Shah, New Jersey Institute of Technology, participant in fall 2019 and spring 2020:
Tong, A., Pham, Q.L., Shah, V., Naik, A., Abatemarco, P., & Voronov, R. (2020). Automated Addressable Microfluidics Device for Minimally Disruptive Manipulation of Cells and Fluids within Living Cultures. ACS Biomater. Sci. Eng., 6(3), 1809-1820. https://doi.org/10.1021/acsbiomaterials.9b01969
From Manuel E Santiago Rodríguez, University of Puerto Rico-Mayaguez, participant in spring and fall 2019:
Santiago, M., Torres, G., & Araya, G. (2019). High order statistics in Favorable Pressure Gradient (FPG) flows. Unpublished manuscript.
"My participation in the XSEDE EMPOWER program had a positive impact on my academic and professional life. Participation helps me increase my knowledge and experience. Now I have a better knowledge of turbulent flow behavior and better programming skills. In my professional life, I would like to participate in future research like this. My participation in the XSEDE EMPOWER program helped me overcome the challenges. It helps me increase my confidence. In the research, we found reasonable results that can help predict the behavior of the turbulent flow population. The results have created an inclination in me for research and graduate school. The mentor I had was excellent." (written June 2019)
From Hamid Abbasi, Rutgers University (working with a mentor from Hood College), and Christian Wagner, Hood College, participants in summer 2019:
"We co-authored a paper, generated a poster, and participated in a joint formal presentation of our work throughout the summer with our mentor and some of his other interns." (written August 2019)
From Tanya Nesterova, University of Delaware, participant in Summer 2019, Fall 2019, and Summer 2020:
Xu, C., Katyal, N., Nesterova, T., & Perilla, J.R. (2020). Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations. The Journal of Chemical Physics. 153(15). https://doi.org/10.1063/5.0021491
"I attended a National Institutes of Health (NIH) meeting on the structural biology of HIV. I have also produced a poster for a chemistry/biochemistry conference in my university’s department and the Summer Scholars conference. I presented this poster to colleagues in the chemistry and biology field. I also went to the data science symposium in my university and provided a lightning talk and presented my poster in front of other faculty and students who do research in mathematics and computational science. I networked and met people who also do work like mine in chemistry." (written July 2019)
Daniel Norment, California State Polytechnic University, Pomona, participant in summer 2019, created a YouTube video summarizing his project work:
From Lindsey Tam, Pomona College, participant in summer 2019:
(email from mentor) "We released V2.0 of the app that was developed in part with the grant from Shodor/EMPOWER program which is mentioned in About section. Lindsey Tam, a Math major from Pomona College worked on the content last summer and led a group of 6 or so students to develop additional functionality using Pomona College’s Hahn grant the rest of the year. https://apps.apple.com/us/app/hpc-pondr/id1486499863" (written March 2020)
From Mackenzie Tygh, Haverford College, participant in summer 2019:
"I will present my work at the 2020 meeting of the American Astronomical Society."
From Matthew Veter, Portland State University, participant in summer 2019:
"I will presenting the preliminary data I have collected at a computational conference scheduled on August 22 for dissemination of my findings at the NSF-sponsored PacNOW symposium held in Portland, OR." (written August 2019)
From Alfonso Guevara, University of Houston Clear Lake, participant in spring 2019:
Guevara, A., & Kindla, N. (2019, July). Solving the Traveling Salesmen Problem with IBM Q Quantum Computers. Poster presented at PEARC '19: Practice and Experience in Advanced Research Computing, Chicago, IL.
From Rylee Sundermann, South Dakota State University, participant in spring 2019:
Sundermann, R., Stegmeier, N., McClanahan, N., Kimn, J.-H., & Doom, J. (2019, July). 3D Simulations of Biofilms using the Modified Cahn-Hilliard Equation. Poster presented at PEARC '19: Practice and Experience in Advanced Research Computing, Chicago, IL.
From Maritza Anguiano Carrillo, California State University-San Marcos, participant in spring 2019:
(from February 2019 report) "My mentor and I have begun a tutorial session for new students wanting to participate in future research."
From Felix Quintana, participant in spring 2019:
Quintana, F., Kodera A., Horan, B.G., Yamashiro, S., Mittal, J., Watanabe, N., & Vavylonis, D. (2019, March). Mechanism of formin-mediated actin polymerization: alternate delivery of profilin-actin to the barbed end. Poster presented at the 63rd Annual Meeting of the Biophysical Society, Baltimore, MD.
From Bimarsh Sharma, West Virginia University Institute of Technology, participant in fall 2018 and spring 2019:
Sharma, B., Carter, T., & Rai, S. (2019, June 15). Using NetLogo to Simulate Building Occupancy of a University Building Environment. Presented at the 2019 ASEE Annual Conference & Exposition, Tampa, Florida.
Sharma, B., Carter, T., & Rai, S. (2019, February 26). Using NetLogo To Create Building Occupancy Simulation of University Building Environment. Poster presented at the 16th Annual Undergraduate Research Day at the Capitol, Charleston, WV.
Jean Santiago, University of Puerto Rico at Mayagüez, participant in spring and fall 2018, created a visualization:
Araya, G. & Santiago, J. (2018, June 5). Quasi laminarization process induced by Strong Favorable Pressure FPG gradient [Video file]. Retrieved from https://www.youtube.com/watch?v=LaUYJ6NBKwE
He also created a visualization presentation:
Santiago, J., Araya, G., Marin, G., & Cucchietti, F. (2018, November). Symbiosis of quasi-streamwise vortices and low-speed streaks in laminarescent boundary layers. Visualization presented at the Gallery of Fluid Motion at the Annual Meeting of the American Physical Society Division of Fluid Dynamics, Atlanta, GA. https://gfm.aps.org/meetings/dfd-2018/5b97f004b8ac31610362f38b
From David Hughes, California State Polytechnic University-Pomona, participant in summer 2018 through spring 2019:
Hughes, D., & Ji, H. (2019, March 1). Novel Randomized Linear Algebra in Apache Spark. Poster presented at the 2019 Student RCSA Conference, Pomona, CA.
"My major is Computer Science, so academically the program has given me exposure to modern subjects in the field. I had a chance to experience various topics like new programming languages, super-computers, advanced math, etc. that are not part of a normal curriculum. The amount of knowledge and experience I gained through the program directly exceeds what any lecture class could possibly give to a typical undergraduate student. Professionally, the program has greatly improved my public speaking skills and abilities to talk about Computer Science. Due to working with my mentor, I have taken part in giving guest lectures, going to research fairs, and talking to individuals and large groups about my research. In the past I dreaded public speaking, but now the XSEDE EMPOWER program has given me confidence in an area that is not directly related to what was written in the project summary. The XSEDE EMPOWER program was instrumental in helping me be chosen to be my University’s College of Science Valediction; this year there happened to be four perfect GPAs vying for the honor, so student research made an enormous impact on the faculty’s decision. Additionally, the aforementioned effects on public speaking skills made it easy for me to give my speech in front of hundreds of people at commencement." (written June 2019)
From Diego Losada Rubio, participant in summer 2018:
"As first year student I had the opportunity to experience by first hand the world of High Performance Computing and so this was an experience that I will never forget and regret. Thanks to XSEDE EMPOWER Program, apart from learning, working and exploring with my mentor about parallel computing concepts using Little Fe on Physics, I was able to travel to the Petascale Institute and get to know with other students the main ideas of the concepts on parallel computing that I was going to learn right after during that summer and also I was able to go to the PEARC18 and meet lots of passionate and intelligent people that work on the world of High Performance Computing. The XSEDE EMPOWER Program helped me to understand and learn complicated concepts and challenges on parallel computing and simulations. And those challenges that I once overcame are going to help me now in a new summer research experience where I am going to be doing molecular dynamics simulations using a supercomputer." (written May 2019)
From Phan Phu, California State Polytechnic University-Pomona, participant in spring and summer 2018:
Kundu, S., Phu, P.N., Ghosh, P., Kozimor, S.A., Bertke, J.A., Stieber, S.C.E., & Warren, T.H. (2019) Nitrosyl Linkage Isomers: NO Coupling to N2O at a Mononuclear Site. J. Am. Chem. Soc., 141(4), 1415-1419. http://doi.org/10.1021/jacs.8b09769
Phu, P.N., "Quantifying Metal-Nitrosyl Coordination Modes and Oxidation States through X-ray Emission Spectroscopy and Density Functional Theory," COMP Undergraduate Workshop at 255th American Chemical Society National Meeting and Exposition, New Orleans, LA, Mar. 18-22, 2018.
"On January 13, 2018, I presented "Spectroscopic and Computational Studies of Metal Nitrosyl Complexes to Elucidate the Mechanism of Nitrite Reductase" at 30th Annual CSU Biotechnology Symposium in Santa Clara, California"
From Brandon Ubiera, Hood College, participant in fall 2017 and spring 2018:
(email from mentor, 06/04/2018) "First of all, we deeply appreciate this opportunity. This opportunity of the exposure to HPC and computational research means a lot for a small regional institution like Hood College. Our EMPOWER intern Brandon Ubiera was able to learn about parallel computing, deep learning, UNIX administration while helping me with system configuration and out-reaching. We have a student poster accepted by PEARC 18 [...]."
From April Horton, Bluffton University, participant in fall 2017:
(from email from mentor, 03/22/2019) "Last week April Horton received offers from two REU programs in Astronomy: The University of Hawaii, and The University of Wisconsin-Madison. Both had a computational slant—based on her EMPOWER project, a computational science course I taught and other programming courses at Bluffton. The University of Hawaii was her top choice for REU; she’ll be headed there soon after spring semester."
"I presented at Bluffton University’s Research Fair for my XSEDE EMPOWER Program internship entitled “Sonification and Visualization of Scientific Data.” This poster presentation session allowed me to share my research with other Bluffton students while encouraging them to pursue research opportunities they are interested in."
From Brian O. Torres Torres, University of Puerto Rico-Mayagüez, participant in fall 2017:
"I was part of the XSEDE EMPOWER program as a learner for one semester where I worked with my professor Ana Gonzalez on a parallel computing project. This opened up many doors for me since it was my first work experience out of my curriculum related to my major and recruiters seem to be very interested in what I did with my professor. By being part of the program I was able to secure a COOP with NAVSEA in Newport for the upcoming semester. In addition, before starting the program I was not sure if I wanted to pursue a graduate degree and now I have decided to do a Masters on Computer Science and I am considering applying for Georgia Tech’s MS in machine learning. Honestly the program helped professionally and academically and it’s something I will never regret doing." (written June 2018)
From Mark Hisle (Centre College) and Maxwell Meier (Earlham College), participants in summer 2017:
Maxwell gave a presentation of this paper at the PEARC18 conference:
Mark S. Hisle, Maxwell S. Meier, and David M. Toth. 2018. Accelerating AutoDock Vina with Containerization. In Proceedings of the Practice and Experience in Advanced Research Computing (PEARC '18). ACM, New York, NY, USA, Article 36, 5 pages. https://doi.org/10.1145/3219104.3219154
"Using supercomputers to combat Ebola." https://www.newswise.com/articles/using-supercomputers-to-combat-ebola. October 20, 2020
"A Bright Future in Research." https://www.udel.edu/udaily/2020/april/blind-chemistry-student-research/. April 3, 2020.
"SWOSU Students Win Two Firsts at High Performance Computing Competition" https://www.swosu.edu/news/2019/2019-09-30b.php. September 30, 2019.
"Senior and professor collaborate on research." https://www.bluffton.edu/news/_beaversall/Beavers062019ryanoostland.aspx. June 20, 2019.
"College of Science to Honor Two Valedictorians." http://polycentric.cpp.edu/2019/05/college-of-science-to-honor-two-valedictorians/. May 17, 2019.
"Researchers Attempt To Predict & Prevent Suicide Using Deep Learning And Math." https://www.forbes.com/sites/robinseatonjefferson/2019/04/15/researchers-confident-deep-learning-and-math-can-help-end-veteran-suicide. April 15, 2019.
"Paid to learn: Students delve into the world of high performance computing." http://wofford.edu/newsroom/2018/Paid-to-learn/. September 14, 2018.
"#WhyWeLearn: Supercomputing institute ‘surreal’ for Comp Sci major." http://aum.edu/content/whywelearn-supercomputing-institute-%E2%80%98surreal%E2%80%99-comp-sci-major. June 13, 2017.