As supercomputers continue to increase power and efficiency, one of the largest benefits of that progress is the ability for scientists to run more simulations on more data in much less time. What once would take weeks now needs only days. Days become hours, hours become minutes – the time from theory to results has never been faster.
So why not use this modern marvel of advanced research computing to learn new answers about one of humanity’s most studied topics: the foundation of life on Earth?
Researchers at the University of Illinois Urbana-Champaign and the Science and Technology Center for Quantitative Cell Biology (QCB) utilized the state-of-the-art Delta supercomputing system at the National Center for Supercomputing Applications to simulate the full life cycle of a bacterial cell.
Using Delta’s powerful graphics processing units (GPUs), QCB Director Zan Luthey-Schulten and her team simulated the complicated, 105-minute cycle of a 4-D model of a minimal cell in six days of computing time. Researchers used one GPU node to simulate only the DNA replication of the cell, while a different GPU node took care of the rest of the cell processes.
“I can’t overstate how hard it is to simulate things that are moving – and doing it in 3D for an entire cell was … triumphant,” said Zane Thornburg, a postdoctoral fellow at the Beckman Institute for Advanced Science and Technology and the Cancer Center at Illinois.
The research findings were published in the journal Cell.
“We have a whole-cell model that predicts many cellular properties simultaneously,” Luthey-Schulten said. “If you want to know what’s going on, say, in nucleotide metabolism, you can also look at what’s going on in DNA replication and the biogenesis of ribosomes. So the simulations can give you the results of hundreds of experiments simultaneously.”
NCSA is a partner of the QCB, a multidisciplinary, multi-institution collaboration led by researchers at the University of Illinois, dedicated to transforming our ability to understand and predict life processes while making quantitative cell biology widely accessible to meet society’s needs. This research was supported by allocations through the U.S. National Science Foundation program ACCESS.
“Delta is a flexible and powerful tool that helps researchers find answers to difficult questions through advanced computing capabilities, including, in this case, running complicated simulations of living organisms,” said Bill Gropp, the principal investigator for Delta and DeltaAI. “We’re excited to see researchers utilize the powerful potential of the largest GPU resource in the NSF ACCESS portfolio to assist their innovative work.”
Find out more about this breakthrough research in the release from the University of Illinois News Bureau.
ABOUT DELTA AND DELTAAI
NCSA’s Delta and DeltaAI are part of the national cyberinfrastructure ecosystem through the U.S. National Science FoundationACCESS program. Delta (OAC 2005572) is a powerful computing and data-analysis resource combining next-generation processor architectures and NVIDIA graphics processors with forward-looking user interfaces and file systems. The Delta project partners with the Science Gateways Community Institute to empower broad communities of researchers to easily access Delta and with the University of Illinois Division of Disability Resources & Educational Services and the School of Information Sciences to explore and reduce barriers to access. DeltaAI (OAC 2320345) maximizes the output of artificial intelligence and machine learning (AI/ML) research. Tripling NCSA’s AI-focused computing capacity and greatly expanding the capacity available within ACCESS, DeltaAI enables researchers to address the world’s most challenging problems by accelerating complex AI/ML and high-performance computing applications running terabytes of data. Additional funding for DeltaAI comes from the State of Illinois.