Nano Visualizations are essential for unlocking the mysteries of the nanoscale, offering detailed and accurate representations that drive innovation in nanotechnology, materials science and medicine.

The goal of this project was not only to create an accurate atomistic model of the coronavirus particle, including its insides, but also do it in a way that the model can be easily updated. The frequency with which new knowledge is discovered made us chose algorithmic approaches instead of traditional manual modeling. In this way, our model is rather calculated than handcrafted, and by changing the input parameters, we can update it to reflect the latest theories and discoveries made by biologists.

What exactly is a virion made of cannot be seen in any microscope. Microscopes show us the overall shape of the virion, but the exact molecular composition has to be determined through various other techniques. Once biologists figure out which molecules the virion is made of, how these molecules look like, and how they are organized, we can use computer algorithms to create a 3D model which correspond to all the findings biologists have discovered.

Building of such model typically starts with defining the overall shape. Electron microscopes can only show us pictures of cross-sections of individual virus particles. These contours can give us a pretty good idea of how the virion looks like in 3D. Once we build the 3D model of the overall shape using statistical methods based on the electron microscopy images, we can populate it with many copies of models of the individual molecules which make up the virus.

We can get the protein models from PDB, a database of atomic models of proteins and other organic molecules. They describe the positions of individual atoms, from which the molecule of the given protein is composed. However, there were no models for SARS-CoV-2 proteins available yet, so biologists had to prepare them for us according to their most current research.

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