Due to the COVID-19 pandemic in 2020, our lab is doing some research to aid in understanding the mechanism of virus attachment to the host, proteins associated with virus virulence, and virus-induced blood clotting. This work is all done in collaboration with experimental labs at UMD (Dr. Sergei Sukharev/Biology) and Dr. Bryan Berger (UVA).
Cell Membrane Modeling
One emphasis on research in the lab is modeling cellular membranes. We have modelled membranes from bacteria and yeast and their organelles. We are currently interested in outer membranes of gram negative bacteria and how these can result in autoimmune diseases attacking the nerve membranes. Membrane models of human cell membranes, e.g. the mylenin sheath, skin, and ocular lens, are also of current interest.
Force Field Development
To accurately model cell membranes, the mathematical function used to describe molecule-molecule interaction must be accurate. Our lab is a leader in the field to develop an accurate and diverse force field for lipids (CHARMM36 and CHARMM36UA). We continue to add to diversity of this force field and fix current deficiencies.
Peripheral Membrane Proteins (PMPs)
PMPs are proteins that bind to the surface of the cell membrane to perform their funciton. We currently study a protein involved in lipid exchange between cellular organelles, known as the Osh4 protein of yeast. This protein has been shown to form membrane contact sites (MCS) and this function is believed to facilitate lipid exchange. Our simulations are probing the mechanism for lipid and cholesterol exchange within the cell.
Transmembrane proteins are proteins that span the cell membrane. Some of these are important proteins that transport molecules, such as drugs, across the rather impermeable membrane. We currently study various secondary active transporters that are involved in drug transport. We also have interest in proteins that are involved in recognizing serotonin at the neuron synapse and large signaling proteins involved in growth (plexins).
Traditional Chemical Engineering
We also do reserach outside the biological area applied to traditional areas of chemical engineering, e.g., asphaletene aggregration, gas hydrates, and self-assembly formatoin. Our current interests in gas hydrates is understanding the molecule-scale growth of hydrates for use in separating and purifying gasses. We also are interested in quantifying the ability to use gas hydrates to squester carbon dioxide.