Scientists Use High-Performance Computing to Understand Cancer Growth

Source: Medical Press | Andrea Schneibel,  | January 12, 2021

Scientists tap the power of high-performance computing in a bet to understand cancer growth
Addressing many important biological questions requires large length- and time-scales, as well as molecular level details. Shown here is a simulation of protein-lipid dynamics for a 1 µm x 1 µm membrane subsection at near-atomistic resolution. The images were acquired using the Multiscale Machine-Learned Modeling Infrastructure (MuMMI). Credit: Tim Carpenter, LLNL

Researchers are running thousands of simulations on Summit to identify how a specific protein triggers up to 30 percent of all human tumors

Summit is part of the Oak Ridge Leadership Computing Facility (OLCF), a US Department of Energy (DOE) Office of Science User Facility located at DOE’s Oak Ridge National Laboratory (ORNL).

The effort is one of several projects awarded hours on the supercomputer by DOE’s Office of Advanced Scientific Computing Research’s (ASCR’s) Leadership Computing Challenge (ALCC) during the 2019–2020 period, and again for 2020–2021.

Led by scientists at Lawrence Livermore National Laboratory (LLNL), the team recently completed 400,000 Summit node-hours of simulations in an attempt to gain knowledge of RAS, a family of proteins that, when mutated, has been found to drive about 30 percent of human tumors, including some of the deadliest ones, such as 95 percent of pancreatic cancers and 45 percent of colorectal cancers.

They did this by running a total of 2,600 simulations, up from their originally planned 600.

“This translates into hundreds of thousands of [computational] jobs, all running simultaneously, tracking different data sets across multiple systems of the supercomputer itself. Without a system like Summit, this would have not been possible,” said Felice Lightstone, Biochemical and Biophysical Systems Group leader in the Biosciences and Biotechnology Division at LLNL.

RAS: a team player, until it’s not

Humans and RAS proteins are no strangers to each other. In fact, RAS proteins are present in all the cells of our bodies, with the exception of red blood cells, and play a significant role in signal transduction, a vital process that affects the biological function of a cell.

“From that perspective, we really need RAS proteins just for normal living,” Lightstone said.

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