Self-Aggregation of Functionalized Capsids Using Coarse Grained Molecular Dynamics

Viral capsids, the protein shells of a virus, have been the subject of significant amount of research in a variety of fields. Their potential relevance to biomedical science arises from their ability to encapsulate or carry drugs and deliver them to targeted sites in the body. The capsids can be decorated with polymers, long chains of hydrocarbons, to target specific sites or promote controlled aggregation for creating novel materials. Since viral capsids are within the same scale as nanoparticles, a cluster of them have a larger surface area, which is more area for the drugs to be attached to the capsids. We used coarse-grained molecular dynamics to model and simulate the aggregation of the Cow-Pea Mosaic Virus (CPMV) capsids decorated with polyethylene glycol (PEG), our polymer. Additional variations of the system includes changing the polymer density on the capsids and the capsid volume fraction, to show how these changes affect the self-assembled structures. We analyzed the systems to find the overall shape of the clusters, using the cluster size, the number of neighbors for each capsid, the effective radius of the cluster, and the moments of inertia. Our observations suggest that (a) the excluded volume of the capsids and (b) the polymer density on the capsids play the largest role on the aggregation dynamics when compared to other variants. Our findings can help further the research of targeted drug delivery systems using nanoparticles decorated with polymers.