NCSI: Assessing the Knotting and Unknotting Mechanism of Proteins

Status	Completed
Mentor Name	Luiz Oliveira
Mentor's XSEDE Affiliation	Startup Allocation (Planning to submit a larger Research Allocation request during the Sep 15 - Oct 15 submission period)
Mentor Has Been in XSEDE Community	3-4 years
Project Title	Assessing the Knotting and Unknotting Mechanism of Proteins
Summary	Identified in approximately 1% of the Protein Data Bank (PDB) entries, knotted proteins have been connected to diseases, such as Alzheimer's disease and Parkinson's disease. Therefore, understanding how the primary structure of proteins folds and knots into a unique configuration has been a challenge in the biophysical community. As a first step towards the goal of better understanding the knotting/unknotting mechanism in proteins, the student will learn basic computational molecular science techniques.
Job Description	With the PI supervision, the student will complete GROMACS tutorials and learn how to perform molecular dynamics (MD) simulations. She will also complete VMD and python tutorials to learn how to post-process the results from MD simulations. It is also expected that she will actively communicate with the PI and prepare monthly reports showing the progress of the tutorials and activities she will be completing. Finally, at the end of the semester, she will prepare a poster highlighting the main concepts learned throughout the 12 weeks of the program. This poster should include the analysis of a simulation of a simple system, and it will be presented at a local symposium for undergraduate research.
Computational Resources	This project will initially utilize resources from an XSEDE Startup allocation (CHE190029)
Contribution to Community	This project will stimulate the interest of students in computational molecular science. Students will expand their knowledge by learning and utilizing molecular modeling, programming languages, and high-performance computing techniques. Dr. Oliveira plans to submit a proposal to promote the learner to apprentice in Spring 2022. Furthermore, the results from the Spring 2022 semester are expected to be presented at the 2022 Molecular Education and Research Consortium in Undergraduate computational chemistRY (MERCURY) conference, and at the 52nd Midwest Theoretical Chemistry Conference (MWTCC). A long-term contribution is to attract more undergraduate students from MVNU to be part of the XSEDE community in the future.
Position Type	Learner
Training Plan	The following is the training plan over the 12 weeks of the program: Week 1 - Week 3: Complete Linux and VMD tutorials. Read and summarize papers on general molecular dynamics theory. Week 4 - Week 6: Complete GROMACS and python tutorials. Start to get familiar with HPC resources. Week 7 - Week 9: Submit simulations to EXPANSE. Week 10 - Week 12: Analyze simulations from previous weeks and submit further simulations if necessary. Prepare poster.
Student Prerequisites/Conditions/Qualifications	Background in Chemistry and Mathematics and willingness to learn computational molecular science.
Duration	Semester
Start Date	08/16/2021
End Date	11/05/2021