"A new multiscale coarse-grained model of the complete SARS-CoV-2 virion, its core genetic material and virion shell, has been developed for the first time using supercomputers."
"A coarse-grained model resolves only groups of atoms, versus all-atom simulations, where every single atomic interaction is resolved." "If you do that well, which is always a challenge, you maintain the physics in the model."
"The early results of the study show how the spike proteins on the surface of the virus move cooperatively." "They don't move independently like a bunch of random, uncorrelated motions. They work together."
"This cooperative motion of the spike proteins is informative of how the coronavirus explores and detects the ACE2 receptors of a potential host cell."
The researchers combined a number of statistical approaches to come to the correlation conclusion. They used principal component analysis, a dimensionality-reduction technique, on a subset of the coarse-grained particles to examine collective modes of motion of the virion. From that they computed a covariance matrix. This analysis included membrane, nucleocapsid, and envelope proteins, as well as the spike proteins, which were all part of the coarse-grained simulation. The analysis showed correlated modes of motion with the spike proteins.First complete coronavirus model shows cooperation
Frontera, Anton 2 supercomputers simulate holistic model of SARS-CoV-2 virionwww.tacc.utexas.edu