During lockdown, two things were on everyone’s mind: When is the vaccine going to come out, and while I’m waiting, what can I do to occupy my time? Some got into baking, others knitting. Researchers from the Vermaas lab at the MSU-DOE Plant Research Laboratory (PRL) combined these two questions and tried their hand at the puzzle that is vaccine molecular simulation. This had its challenges and led the researchers to create a more efficient tool to solve the problem of ring piercings in molecular simulations.
Molecular simulations use the power of computing to create a computational microscope which can observe biological structures on the atomic level. Researchers take structures they have observed in the lab and create computer models, which can involve fitting thousands of atoms together in just the right spots. It’s like working on a puzzle: With each new piece put into place, the overall picture of what the system is and what it can do becomes clearer.
“We have a general idea where the puzzle pieces, which means our molecular components, need to go,” said Martin Kulke, postdoc in the Vermaas lab, describing how these simulations are created. “But we use computer tools to automatically place the pieces, which leads to components overlapping. In the overlap of these puzzle pieces, we get the problem of these ring piercings.”
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