NCSI: Molecular Dynamics of the Viral Life Cycle

Status	Completed
Mentor Name	Jodi Hadden-Perilla
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Molecular Dynamics of the Viral Life Cycle
Summary	Student will learn to perform all-atom molecular dynamics simulations and participate in the development of computational methods to investigate processes of the viral life cycle.
Job Description	The student will apply their knowledge of biochemistry and physical chemistry to study the dynamics of viral systems within physiological environments. She will learn to setup and analyze molecular dynamics simulations and participate in the development and testing of computational methods aimed at investigating key processes in the viral life cycle, such as assembly and disassembly. The student will learn to write basic computer code and design analyses for handing molecular dynamics trajectories. The student will utilize NAMD and VMD on hybrid CPU/GPU architectures. The student will have the opportunity to present her work at local and national conferences.
Computational Resources	The student will have access to XSEDE resources, in additional to local resources for high-memory data analysis and visualization.
Contribution to Community	The project will engage a promising young scientist from an underrepresented demographic in computational biophysical chemistry research. The project will provide an opportunity to explore how to better attract undergraduate students with biochemistry backgrounds to computational science.
Position Type	Apprentice
Training Plan	Now that the student has become familiar with Linux computing environments and basic TCL programming, learned to setup basic MD simulations, and carried out her first analyses on biomolecular structures, she will develop a computational tool for post-processing MD simulation trajectories to assess the appropriateness of assigned protonation states for titratable residues. This tool will be relevant to investigating pH dependence during key stages of the viral life cycle. She will have the opportunity to interact closely with a cohort of graduate students carrying out similar research and will be closely guided by a mentor who has 14 years of experience in the field.
Student Prerequisites/Conditions/Qualifications	Student should have taken CHEM 418 and CHEM 419 (Introductory Physical Chemistry I and II for Biochemistry Majors)
Duration	Semester
Start Date	02/07/2022
End Date	05/26/2022