The University of Chicago has received a $1.5 million grant from the National Science Foundation's to develop a computational infrastructure for simulating and studying biomolecular activity.
The grant, awarded by NSF's Centers for Chemical Innovation, will fund the creation of the Center for Multiscale Theory and Simulation, which will span three UChicago research institutes: the Institute for Biophysical Dynamics, the Computation Institute, and the James Franck Institute.
Also, IBM, Genentech, and Schrödinger are listed as industrial collaborators of the new center.
According to the grant abstract, researchers at the university will focus on developing theoretical and computational capabilities to describe biomolecular processes "starting from the molecular scale and ending at the cellular scale."
Specifically, the researchers hope to develop a framework that connects "molecular properties and concepts with key features of cellular biology occurring at much larger length and time scales" in order to understand how the former "define the functional behavior of cellular systems," the abstract states.
The new center will provide a broad array of computational equipment, software, and techniques to support its work, including large allocations of computer time from NSF and from Argonne National Laboratory's Leadership Computing Facility to run calculations.
Using the example of the HIV virion, which spreads AIDS infection from cell to cell, Gregory Voth, a professor of chemistry at UChicago, explained that he and his colleagues are working on a technique that could result in a simpler way to predict molecular motion inside a cell.
"On the molecular scale," the HIV virion is a "huge object that probably involves a billion total atoms," he said in a statement. "You would never get anywhere just by trying to study atom-by-atom, how they all interact with each other.”
UChicago's infrastructure includes a “coarse-graining” approach that the researchers have used to study the HIV virion particle as well as to explore antibodies that are used in pharmaceutical formulations for anti-cancer drugs.
"A coarse-grained model may ... map a billion atoms into an equivalent structure that has a hundred thousand objects that represent what those atoms are doing,” Voth explained. “If you do it right then new important patterns of interactions emerge [and] you begin to learn a lot about the system.”
The researchers believe that these applications could be used in settings outside life sciences such as renewable energy and new materials