NCSI: Quantifying Binding Strength in Bacterial Nanowires through Non-Equilibrium Simulations

Status	Completed
Mentor Name	Josh Vermaas
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Quantifying Binding Strength in Bacterial Nanowires through Non-Equilibrium Simulations
Summary	Some bacteria use heme-rich protein assemblies called nanowires to move electron excitations long distances. We aim to probe these nanowire components through molecular simulation, building on current simulations ongoing in the laboratory to calculate the binding affinity between individual monomers within the nanowires.
Job Description	With faculty and postdoc supervision, the student will use the molecular simulation tools VMD and NAMD to set up steered molecular dynamics simulations designed to pull apart protein dimers found in bacterial nanowires. Upon completion, these simulations will be analyzed to determine the weakest interactions along different crystal axes within the nanowire. The simulation design largely follows previous protein-protein interaction literature. At the end of the semester, the student is expected to have produced a research poster, suitable for a local or national conference on their efforts during the semester.
Computational Resources	The PI has obtained an XSEDE allocation for this specific project as part of his larger research allocation. As proposed, the simulations would be carried out on the CPU partition of Expanse, with setup and analysis happening on workstations on local campus workstations within the PIs laboratory. Testing run configurations will occur on local HPC resources here on campus to derisk the simulations for user error in input.
Contribution to Community	The larger XSEDE community depends on a pipeline of exceptional scientists from a diverse set of backgrounds and lived experiences coming into computational sciences. This project has been tailored specifically to the research interests of an exceptional undergraduate biochemistry student who does not fit into traditional HPC or computational chemistry stereotypes. Bringing in underrepresented groups into the computational sciences training is imperative to maintaining a robust workforce of American scientists.
Position Type	Apprentice
Training Plan	The student is expected to come into lab for at minimum 4-5 hours per week during normal business hours to receive realtime feedback from other group members, and to participate in group meetings to see the full breadth of possibilities for molecular simulation. An additional 4-5 hours per week can be worked remotely or in lab, depending on student preference. At the assigned workstation, the tools needed to conduct the research are all preinstalled.
Student Prerequisites/Conditions/Qualifications	Completed the VMD and NAMD tutorials, prior experience analyzing unbiased nanowire simulations. Prior experience analyzing molecular simulation with python-based tools.
Duration	Semester
Start Date	09/01/2021
End Date	12/12/2021