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 next submission period)
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Assessing the Knotting and Unknotting Mechanism of Proteins
Summary	This is a continuation of the project approved during Fall-2021. It entails the understanding of how the primary structure of knotted proteins folds and how they form knots into a unique configuration.
Job Description	The students sought for this position have already learned basic computational molecular science techniques during Fall/2021. They master several computational molecular tools, e.g. VMD, python, the Linux operating system, and are familiar with HPC. As apprentices, they will start molecular dynamics (MD) simulations utilizing GROMACS to achieve the goal described above. Moreover, within MD, the students will use the metadynamics family of methods to accelerate their simulations.
Computational Resources	XSEDE-Expanse. Local servers and desktops. The Ohio Supercomputer Center.
Contribution to Community	Results of this project, from Fall 2021 and Spring 2022 semesters, 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).
Position Type	Apprentice
Training Plan	The students sought for this position has already acquired most of the skills necessary for this project.
Student Prerequisites/Conditions/Qualifications	The students should be familiar with MD simulations, the Linux operating systems, python programming language and Gromacs.
Duration	Semester
Start Date	01/10/2022
End Date	04/15/2022