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Molecular Dynamics of the Viral Life Cycle


Shodor > NCSI > XSEDE EMPOWER > XSEDE EMPOWER Positions > Molecular Dynamics of the Viral Life Cycle

Status
Completed
Mentor NameJodi Hadden-Perilla
Mentor's XSEDE AffiliationResearch Allocation
Mentor Has Been in XSEDE Community4-5 years
Project TitleMolecular Dynamics of the Viral Life Cycle
SummaryStudent 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 DescriptionThe 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 ResourcesThe student will have access to XSEDE resources, in additional to local resources for high-memory data analysis and visualization.
Contribution to CommunityThe 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 TypeLearner
Training PlanThe student will complete NAMD and VMD tutorials and become familiarized with Linux computing environments. She will learn TCL and receive hands-on training on setup and analysis of molecular dynamics simulations. She will perform a literature review to learn about virus biology and the viral life cycle. She will have the opportunity to interact closely with a cohort of graduate students carrying out similar research. She will be closely guided by the mentor with 14 years of experience in the field to perform calculations, simulations, and analyses relevant to investigation of the viral life cycle.
Student Prerequisites/Conditions/QualificationsStudent should have taken CHEM 418 and CHEM 419 (Introductory Physical Chemistry I and II for Biochemistry Majors)
DurationSemester
Start Date08/31/2021
End Date12/18/2021

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