NCSI: Unveiling Dynamics of Membrane Proteins in Multi-component Lipid Bilayers

Status	Completed
Mentor Name	Afra Panahi
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	Less than 1 year
Project Title	Unveiling Dynamics of Membrane Proteins in Multi-component Lipid Bilayers
Summary	1. Setting up and running molecular dynamic (MD) simulation for membrane proteins in large and complex lipid bilayers 2. Analyzing the data generated by MD and working with large scale data sets to gain information about the conformations and the secondary structures of the proteins embedded in the bilayers
Job Description	The students have strong background in setting up membrane proteins system and run simulations in any bilayer composition. They have experience in handling extensive data generated by MD on COMET and analyzing it using python and/or R to gain information about the role of membrane composition on the protein conformation. They can develop and optimize their code for their analysis and write scripts to perform long calculations on COMET or other computational resources available to the lab.
Computational Resources	Since California State University, San Marcos, currently does not house any HPC servers, we rely heavily on COMET (maintained by XSEDE and San Diego Super Computer) to run our simulations. The funding through EMPOWER will encourage the students to participate in the research and the financial help will allow them to spend more time in the lab.
Contribution to Community
Position Type	Intern
Training Plan	The students at the intern level will have extensive background in running MD and developing analyzing tools and visualization of MD trajectories. They have already participated in the lab workshop held by the PI of the project and has worked in the lab for at least 3 months.
Student Prerequisites/Conditions/Qualifications
Duration	Semester
Start Date	01/02/2019
End Date	05/15/2019