NCSI: Molecular Mechanisms of HIV-1 Infection

Status	Completed
Mentor Name	Juan Perilla
Mentor's XSEDE Affiliation	Research allocation, education allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Molecular Mechanisms of HIV-1 Infection
Summary	Develop large-scale analysis tools for molecular dynamics simulations. Perform molecular dynamics simulations of HIV-1 relevant systems. Collaborate with biophysical scientist in the design of experiments for the validation of the discoveries.
Job Description	The student will be working on developing tools for the study of large-scale biomedical systems. In particular, the student will be using deep learning and statistical analysis. The computational architectures includes multi-core, multi-GPU and multi-node workloads. The resulting work will be primarily based on the two widely used programs NAMD and VMD. The student will have the opportunity to present her/his work at local and national meetings.
Computational Resources	Simulations will be performed using our allocation on Bridges and Stampede2. Novel analysis tools are currently being developed that take advantage of the capabilities offered by PSC's DGX-2 and AI-cluster. The analysis of large data sets will be facilitated by the high I/O provided by the Lustre system availabe in both PSC and TACC.
Contribution to Community
Position Type	Intern
Training Plan	Hands-on learning is expected from the student. The studend will have the opportunity to interact with graduate students and post-docs whose solely work is performed in XSEDE platforms. The student will have the opportunity to gain experience in software engineering and code development aimed to solve biophysical chemistry problems in widely used software like NAMD and VMD.
Student Prerequisites/Conditions/Qualifications	Newark, Delaware, Perilla group, Chemistry and biochemistry, University of Delaware
Duration	Semester
Start Date	06/01/2020
End Date	08/31/2020