Credit: CC0 Public Domain.
Basic biology textbooks will tell you that all life on Earth is made up of four molecules: proteins, carbohydrates, lipids, and nucleic acids. Every group is vital to every living organism.
But what if humans could really prove that these "molecules of life", such as amino acids and DNA bases, can form naturally in the right environment? Researchers at the University of Florida are testing the experiment using Hipergator, the fastest supercomputer in higher education in the United States.
HiperGator, with its AI models and huge graphics processing unit (GPU) capacity, dedicated processors designed to accelerate graphics rendering, is changing the molecular research game.
Until a decade ago, the study of the evolution and interaction of a large number of atoms and molecules could only be done using simple computer simulation experiments; The computing power required to process the dataset is not available.
Now, thanks to the Hipergator. Using a supercomputer, UF PhD student Jinze Xue (from the Roitberg Computational Chemistry group) was able to conduct large-scale early geochemistry experiments during the 2023 winter break.
Xue used more than 1,000 A100 GPUs on HiperGator, performed molecular dynamics experiments on 22 million atoms, and identified 12 amino acids, 3 nucleobases, 1 fatty acid, and 2 dipeptides. The discovery of larger molecules, which would not be possible in smaller computational systems, is a major achievement.
Our previous successes have allowed us to use machine learning and artificial intelligence to calculate energy and forces on molecular systems with the same results as those of advanced quantum chemistry, but about a million times faster," said Dr. Adrian Rotberg, a professor in the Department of Chemistry at UF who has been using machine learning to study chemical reactions for six years.
These questions have been asked before, but due to computational limitations, previous calculations used a small number of atoms and could not explore the time frame required to obtain the results. But with Hipergator, we can do it.
Dr. Erik Deumens, Senior Director at UFIT Research Computing, explains how to fully acquire Hipergator.
The Hipergator has the unique ability to run very large using the entire machine'Heroes'computing, it is possible to make breakthroughs in science and scholarship," said Deumens. "When we found out that Dr. Roitberg's team was doing the work, we approached him and tried to do it with the ** he developed'Heroes'Run. ”
The advent of artificial intelligence and powerful GPUs has made it possible to carry out such data-intensive scientific simulations that scientists could only imagine calculations a few years ago.
Using a machine learning approach, we created a simulation using the full set of Hipergator GPUs," says Roitberg. "We were able to see the formation of almost all amino acids (alanine, glycine, etc.) and many very complex molecules in real time. It's so exciting.
The project is part of an ongoing effort to discover how complex molecules form from fundamental building blocks and automate the process through large-scale computer simulations. Roitberg and his research team spend a lot of time working with members of UFIT. Ying Zhang, UFIT's AI support manager, provided points for the experiment.
"Ying assembled a team of research compute and NVIDIA staff to help scale compute runs, provide valuable advice and assistance, and speed up data analysis in just seven hours instead of the three days we initially expected," Roitberg said. "From the initial idea to the final result, we met every week and the collaboration was very productive. ”
These results, and Hipergator's ability to deliver them in a fraction of the time, are groundbreaking, bringing researchers one step closer to answering questions about how complex molecules are formed. The fact that Roitberg was able to run such calculations suggests that the UF has the ability to support "Hero Runs" or "Bold Innovative Program Computing" that would advance science, engineering, and academic projects.
This is a great opportunity for UF teachers," Roitberg said. "Having Hipergator inside – incredible staff willing to go above and beyond to help researchers produce breakthrough science like this – made my non-UF colleagues very jealous.