Supercomputer Unleashes ‘Hero’ Calculations to Unlock the Secrets of Life’s Building Blocks

In a groundbreaking scientific endeavor, researchers at the University of Florida have harnessed the power of the HiPerGator, the fastest supercomputer in U.S. higher education, to explore the natural formation of life’s essential building blocks. Using advanced molecular dynamics experiments, the team, led by UF Ph.D. student Jinze Xue from the Roitberg Computational Chemistry Group, achieved a major breakthrough during a large-scale early Earth chemistry experiment.

HiPerGator’s prowess, equipped with over 1,000 A100 GPUs and cutting-edge AI models, allowed Xue to delve into the evolution and interactions of a staggering 22 million atoms. This computational feat identified 12 amino acids, three nucleobases, one fatty acid, and two dipeptides—larger molecules that were previously unattainable with smaller computing systems.

Adrian Roitberg, Ph.D., a professor in UF’s Department of Chemistry, highlighted the significance of the project, stating, “Our previous success enabled us to use Machine Learning and AI to calculate energies and forces on molecular systems, with results that are identical to those of high-level quantum chemistry but around 1 million times faster.”

Machine Learning methods facilitated a real-time simulation showcasing the formation of almost every amino acid and several complex molecules. The project aims to understand how complex molecules can form from basic building blocks, moving towards automating the process through large-scale computer simulations.

Erik Deumens, Ph.D., the senior director for UFIT Research Computing, explained how HiPerGator’s unique capabilities allowed for a full takeover, leading to potential breakthroughs in science and scholarship. This project exemplifies the capacity of HiPerGator to support “hero runs” or “moonshot calculations,” advancing scientific, engineering, and scholarly projects.

The collaboration between Roitberg’s group and UFIT staff, spearheaded by Ying Zhang, UFIT’s AI support manager, showcased the synergy between academic research and cutting-edge technology. The accelerated analysis of data, completed in seven hours instead of the anticipated three days, underscored the efficiency of this collaboration.

The research, aiming to unravel the mysteries of life’s molecular foundations, highlights UF’s commitment to supporting groundbreaking science. Roitberg expressed his gratitude, stating, “Having HiPerGator in-house—with the incredible staff willing to go above and beyond to help researchers produce groundbreaking science like this—is something that makes my non-UF colleagues very jealous.”

This groundbreaking use of HiPerGator demonstrates the potential of supercomputing and AI in advancing our understanding of fundamental scientific questions and propels the University of Florida into the forefront of cutting-edge research.