Authors: Dr Victor Padilla-Sanchez PhD
Abstract: Macromolecular assemblies like complete viruses are impossible to visualize with regular computers due to the large amount of necessary memory. Complete viruses like bacteriophage t4, hiv-1 and others are so big that regular computers can’t visualize them therefore I have been using supercomputers to analyze these viruses as complete organisms for the last six months. This project started from the need to analyze entire organisms like bacteriophage t4 and hiv-1 viruses. UCSF Chimera molecular visualization software is used in this gpu supercomputers of huge ram memory where I have assembled together an entire hiv-1 infection molecular model, t4 bacteriophage on E. coli membrane and several other visualizations, using pdb structures and cryoEM reconstructions from the PDB and EMDB databanks. The project significance has been to visualize and analyze macromolecular assemblies like entire viruses and parts of cells at atomic resolution for the first time. Only with supercomputers I have achieved this goal of modelling, visualizing and analyzing these huge structural assemblies that can reach ~300 million atoms and beyond. I expect to continue using supercomputers and analyzing these macromolecular complexes at atomic resolution which for example may serve to develop viral display vaccines against diseases.