Recreating the Molecules of Life
Basic biology textbooks will tell you: all life on Earth is built from four types of molecules. The four molecules of life are proteins, carbohydrates, lipids, and nucleic acids, with each of the four groups vital for every single living organism.
Until a decade ago, conducting research on the evolution and interactions of large collections of atoms and molecules could only be modeled using very simple computer simulation experiments, because the computing power needed to handle the large data-sets to understand life at its most basic form just wasn’t available.
During UF’s 2023 Winter Break, Jinze Xue, a Ph.D. student in the Roitberg Computational Chemistry Group, conducted a large-scale early Earth chemistry experiment utilizing more than 1000 A100 GPUs on HiPerGator. A molecular dynamics experiment was performed on 22 million atoms that identified 12 amino acids, three nucleobases, one fatty acid, and two dipeptides. The discovery of larger molecules, which would not have been possible in smaller computing systems, is a significant achievement.
Dr. Adrian Roitberg, V.T. and Louise Jackson Professor in UF’s Department of Chemistry, and his research group have been exploring the use of Machine Learning (ML) to study chemical reactions for the past six years.
“Our previous success enabled us to use ML/AI to calculate energies and forces on molecular systems, with results that are identical to those of high-level quantum chemistry--but around one million times faster!
The accomplishments empowered us to ask the following question: Can one create ‘molecules of life’, such as amino acids and DNA bases starting from a simple mix of gases and simulating their reactions?
“These questions have been asked before, but due to computational limitations, previous calculations used small numbers of atoms and could not explore the range of time needed to obtain results," Roitberg said. "But with HiPerGator, we can do it!”
Erik Deumens, PhD, senior director in UFIT for Research Computing, explained how this full takeover of HiPerGator was possible.
"HiPerGator is heavily used throughout the year for research and education. But it has the unique capability to run very large `hero’ calculations that use the entire machine with the potential to lead to breakthroughs in science and scholarship," Deumens said. "Such calculations require careful scheduling to not impact the normal business of supporting research and teaching, which is why we do them around quieter times, like Christmas and over the July 4th holidays. When we found out about the work Dr. Roitberg’s group was doing, we approached him to try a `hero’ run with the code he developed.”
The emergence of AI and very powerful GPUs can enable such highly compute and data intensive scientific simulations to be carried out--calculations scientists could only imagine just a few years ago. The combination of AI models that speed up the dynamics of very large collections of atoms and molecules coupled with the power of the University of Florida’s supercomputer (the fastest in U.S. higher education) enabled the experiment to be done.
“Using Machine Learning methods, we created a simulation using the complete HiPerGator set of GPUs," Roitberg said. "We were able to see, in real time, the formations of almost every amino acid (e.g., alanine, glycine, etc.) and a number of very complex molecules. This was very exciting to experience.”
This project is part of the effort to discover how complex molecules can form from basic building blocks, and to make the process automatic through large computer simulations. The molecules of life is one example of this general idea.
Roitberg notes that he and his research group spent many hours working with members of UFIT. Ying Zhang, UFIT’s AI Support Manager, ran point for this experiment.
“Ying put together a team comprised of Research Computing staff and staff from NVIDIA to help scale compute runs, provide invaluable advice and help, and accelerate analysis of the data to the point where the analyses were done in just seven hours, instead of the three days we initially expected it to take. We met every week from initial conception to the final results, in a very fruitful collaboration.”
The results, and the short time in which HiPerGator was able to deliver them is inspiring new lines of inquiry from Roitberg and others who are getting closer every day to answering questions about how complex molecules, such as those seen in life, is formed.
“This is a great opportunity for UF faculty,” Roitberg said. “Having HiPerGator in-house, with the incredible staff willing to go above and beyond to help researchers produce ground-breaking science like this, is something that makes my non-UF colleagues very jealous.”