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Jan. 25, 2023

Untying molecular knots

Making molecular simulations more efficient with LongBondEliminator

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 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.”

Josh Vermaas, assistant professor at the PRL and the Department of Biochemistry and Molecular Biology and the primary investigator on this paper, was working on developing structural models for lignin, a polymer that is important in the plant cell wall. When creating lignin models that he could simulate, he was running into a common problem: In these simulations, the computer didn’t know what to do when one component overlapped with another and pierced the ring of the first, creating a model that would not be possible in reality.

When running into this issue, Vermaas and computational researchers like him would need to go through and fix all the errors by hand. This is a time consuming and tedious process.

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By: Kara Headley