Mark Maupin and Team Publish in ‘Molecules’

Mark Maupin, a computational and data scientist at Pacific Northwest National Laboratory (PNNL), was the team lead for a paper published in the journal Molecules.

The paper, “ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling,” outlines the methodology and examines the effectiveness of the software tool. The paper was published in July.

The tool is designed to convert complex molecular structures from a simplified representation to a more detailed representation. This conversion process is crucial for effectively leveraging multiscale modeling in molecular dynamics simulations.

The research team validated ezAlign against other methods for converting lipid membrane systems from coarse-grained molecular structures to atomistic resolution.

“One significant advantage of ezAlign that the research team found is its ease of use, where adding new molecules is a trivial and automatable task,” said W.F. Drew Bennett of Lawrence Livermore National Laboratory. “Also, ezAlign does not require training data or human knowledge of chemistry and can back map complex membrane-protein systems.”

The paper was the result of a Cooperative Research and Development Agreement that Maupin ran between Lawrence Livermore National Laboratory and Procter & Gamble, his employer for nearly six years before arriving at PNNL in February 2023.

In addition to Maupin and Bennett, the research team included Austen Bernardi, Tugba Nur Ozturk, Heidi Ingólfsson, and Delin Sun of Lawrence Livermore National Laboratory; and Stephen Fox of Proctor & Gamble.