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	Students will learn how to set up simulations using several tools and run MD using GROMACS simulation package on COMET. They will run multiple replicates of membrane proteins in bilayers with complex composition and study the effect of membrane on the structure of the proteins and the impact of the proteins on the bilayer curvature and thickness. The students will also perform initial analysis on the MD time series using simulation packages and write codes in python for more complex analysis.
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	Apprentice
Training Plan	The students will participate in a workshop held in the lab by the PI to learn about the following topics: 1. MD and its applications in studying proteins 2. Different force-fields in MD; their advantage and disadvantages 3. Different simulations packages 4. How to set up a system including membrane proteins and water molecules in GROMACS 5. How to run MD 6. How to run jobs on super computers 7. How to perform simple analysis on the trajectories obtained from MD 8. How to run simple codes in python
Student Prerequisites/Conditions/Qualifications
Duration	Semester
Start Date	01/02/2019
End Date	05/15/2019