Students: Amanda Rubin and Stephen Gee
Project: The Study of 19 Biological Membrane Types using All-Atom Molecular Simulations
View: Research Poster (PDF)
Institution: Lehigh University
Major: Bioengineering
Advisor: Wonpil Im
Abstract
Molecular dynamics simulations provide scientists with the ability to observe and analyze the interactions and properties of chemical systems at a molecular level. CHARMM-GUI is an easily accessible online resource that uses CHARMM programming to generate and simulate biological systems. One of the most commonly used modules within CHARMM-GUI for drug development is the bilayer membrane builder. As such, certain common membranes are constructed on an individual basis by independent researchers across the globe. In order to streamline the research process for common membranes, the Im lab has worked on compiling a standardized lipid composition for 19 notable membrane types. Following a literature search and utilization of the Orientations of Proteins in Membranes database, the Im lab identified and recorded a standardized lipid composition for each of those systems. The Im lab has since equilibrated and simulated 1000 nanoseconds of each all-atom model as well as conducted system size, hydrophobic thickness, component density, and area per lipid analyses for those systems. Once compiled, the data collected will be formatted and made accessible on the CHARMM-GUI website for scientific use.
About Stephen Gee
Stephen Gee, a sophomore biocomputational engineering student, is an undergraduate researcher in the Im lab. The Im lab develops and maintains CHARMM-GUI, an online interface for biomolecular simulations. Using CHARMM-GUI, they conduct molecular dynamics experiments to explore a variety of biological interactions at the atomic level. Stephen has been a member of the Im lab since the summer of 2020 and has constructed the triacylglycerol (TAG) library in CHARMM-GUI’s membrane builder module. In addition to research, Stephen is also a gryphon, an executive board member of Biomedical Engineering Society, and a member of Lehigh Debate Society.
About Amanda Rubin
Amanda Rubin is a junior in biopharmaceutical engineering with a minor computer science at Lehigh University. She began her research in the summer of 2020 studying lipid membrane types using biomolecular simulations along with a team of undergraduates in the IM lab as part of the Data for Impact Institute. Additionally, around campus Amanda serves as a Consultant for TAMID group, a Facilitator for Break the Silence, and as a member of the Rossin Junior Fellows. Overall, she is passionate about helping others and her community, and hoping her research will help contribute to medical advancements in pharmaceuticals and biotechnology.