Brannigan Lab

Computational Biophysics of Membranes, Proteins and Small Molecules


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.


Three Faces

In each image the accessible conformations are represented as a cloud around a representative pose from the respective phase. The three phases are (left to right) bulk POPC membrane, gas, and annihilated. The annihilated phase is like gas phase but all non-bonded interactions have been turned off allowing the lipid to pass through itself.


Image Credit: Ezry Santiago-McRae

Tinker Toys and
Magnetic Balls

A POPC Membrane with two 2 nm gold nanoparticles embedded in it. We observe two polar nanoparticle covered in hydrophobic ligands aggregating. Nanoparticles cause unfavorable membrane conformations due to the exposed regions interacting with water. The membrane rearranges aggregating nanoparticles with ligands splayed open, alleviating unfavorable lipid configurations.


Movie Credit: Jahmal Ennis


Wildtype ELIC colored by contiguous hydrophobicity (blobs), defined by the blobulator. Blob type assignment is a result of blobulation settings chosen to detect transmembrane domains. p- (polar) and s- (short) blobs are colored orange and green, respectively, h-blobs (hydrophobic) are slightly opaque and colored blue.


Image Credit: Connor Pitman

Frame of Reference

The video shows two perspectives on decoupling. The left panel shows the view of the protein/environment while the right panel shows the view of the lipid. The audio is the raw value of the delta E (the difference in energy between adjacent lambda windows); higher volume corresponds to larger values of delta E. The first half of the video is quite tame because only electrostatics are being decoupled - the environment and the lipid still “see” each other for the most part. The Van der Waals interactions are then scaled out over the second half of the video denoted by both a change in volume and the visual fading of either the lipid (left) or environment (right). The last moments of the audio have a rapid increase in volume as we approach the discontinuity between slightly coupled and fully decoupled.


Movie Credit: Ezry Santiago-McRae

For the Love of

A POPC Membrane, both waters and ions hidden.

Image Credit: Jahmal Ennis


The Envelope (E) protein of SARS-CoV-2 (grey) embedded in a thick, poly-unsaturated membrane (magenta). Only the hydrophobic core of the membrane is shown.

Image Credit: Jesse Sandberg

Landscapes of
Alien Nature

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.


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
bilayer membrane!

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.


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