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Understanding the Membrane Disruption Mechanism of Antimicrobial Peptides Using Molecular Simulations
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Mentor NameKevin Jose Cheng
Mentor's XSEDE AffiliationResearch Allocation
Mentor Has Been in XSEDE Community1-2 years
Project TitleUnderstanding the Membrane Disruption Mechanism of Antimicrobial Peptides Using Molecular Simulations
SummaryThis project seeks to understand how eukaryotic organisms use antimicrobial peptides to defend themselves against bacterial infections Specifically, you would simulate and analyze how the antimicrobial peptides interact with bacterial membranes using the latest software developed at the University of Illinois.
Job DescriptionThis position will include performing Molecular Dynamics simulations, and analyze the data using computer programming, then interpret the data considering what has been previously reported about the biological mechanism in the scientific literature
Computational ResourcesStampede2 (via XSEDE)
PSC (Via XSEDE)
Local cluster at School of Chemical Sciences
Contribution to CommunityThis research has the potential to further our understanding of our own defenses against infection which could contribute to medicine development.
Position TypeApprentice
Training PlanThe training plan can be split up into smaller milestones.
The only resources necessary is a laptop that can use a linux terminal.
Goal 1: Generate the full-tail system 5 copies of POPC, POPS, then mixture
Goal 2: Convert these full -tailed to HMMM using Muyun’s script generating a PDB & PSF file
Goal 3: Run Simulations Using XSEDE
Goal 4: Analyze simulations using Python Packages
Student Prerequisites/Conditions/QualificationsThere no required technical skills, but having any background knowledge in biology, physics, or computer science will certainly give you a head start. Since the research is highly interdisciplinary, expect to learn a lot initially. The only requirement I have is an eagerness for learning and willingness to put in the extra effort that is necessary for successful scientific research.
DurationSemester
Start Date01/10/2022
End Date05/25/2022
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