Our research group is located in the Physics Department and Center for Computational and Integrative Biology (CCIB) at Rutgers University - Camden. We use high performance computing and Molecular Dynamics Simulation to investigate biophysical interactions of proteins, membranes, and small molecules. Many of our research topics involve using concepts and methods from physics to understand complex signaling mechanisms in the central nervous system. Our group members come from a range of backgrounds, including biology, pharmacology, physical chemistry, engineering and physics.
The image shows 5 nanometer gold nanoparticles
embedded in a POPC membrane. The POPC headgroups are shown in a iceblue, tails are in purple, GNP’s are shown in cyan, and ligands are hidden. These GNP’s bend the membrane into various shapes leading to areas of high curvature.
VMD CONTEST WINNER 2022
Image Credit: Jahmal Ennis
Envelope protein of
SARS-CoV-2 wearing a ruffled skirt
The pleats of the skirt represent the trajectory-averaged height of the outer membrane C1A/B beads as a function of r and theta. Coloring indicates mean curvature of the membrane surface. Positive curvature is shown in blue; and negative curvature is shown in red.
Image Credit: Jesse Sandberg
The most colorful lipid
The lilac beads represent the phosphate head groups. The multicolor chains represent POPC and the purple-ish secondary structure protein is Gramicidin A (warning: Gramicidin A is not a protein, it is a peptide). The bubbles represent water beads.
VMD CONTEST WINNER 2022
Image Credit: Mariadelia Arguello Acuna
SDS Micelles getting
to know each other
SDS micelles coming into contact just before fusing together! The negatively charged headgroups are shown in red, and hydrophobic tails are shown in yellow.
Image Credit: Connor Pitman
A Protein Subunit Gone Wrong
The F0F1 ATP Synthase is a highly conserved mitochondrial membrane protein, responsible for ATP synthesis. It synthesizes ATP using a proton gradient across the membrane. Ice worms have a unique Histidine-rich extension in the APT6 subunit (shown in cyan) that is hypothesized to accelerate proton flow across the membrane, thus producing more ATP levels than the energetic demand of ice worms. Shown in pink and cyan is the predicted structure of the ice worm F0 domain embedded in a POPC bilayer.
Image Credit: Noureen Abdelrahman
Membrane Lipid in a Pocket
The Erwinia ligand-gated ion channel (ELIC) is a bacterial homolog and model system for important neuronal membrane proteins. Ligand-gated ion channels typically only open after binding a ligand. Membrane lipids, however, can have a tremendous impact of the function of these membrane proteins. POPG is shown in pink; transmembrane helix 1 (M1) in blue; M2 in orange; M3 in green; M4 in yellow. Portions of the protein not immediately relevant to the binding pocket are shown in gray.
Image Credit: Ezry Santiago-McRae