A catalyst for scientific breakthroughs: Cryo-EM and HPC

By Suzanne Tracy, HPC Product Marketing Senior Manager, Dell EMC

December 3, 2018

With the combined power of cryo-electron microscopy and high performance computing, scientists are opening up new frontiers in biochemistry.

In the fall of 2017, three distinguished scientists shared a Nobel Prize in Chemistry for pioneering a microscope technology that promises to revolutionize biochemistry. This technology, cryo-electron microscopy, or cryo-EM, opens the door to new levels of scientific discovery, including the visualization of proteins at a near-atomic level.

In simple terms, cryo-EM allows researchers to freeze biomolecules in mid-movement and produce three-dimensional structures of them. These 3D simulations help scientists visualize and understand how biomolecules function and interact — processes that would otherwise be impossible to see.

In announcing the award, the Royal Swedish Academy of Sciences noted that current scientific literature is filled with images of everything from proteins that cause antibiotic resistance to the surface of the Zika virus, and  that “biochemistry is now facing an explosive development and is all set for an exciting future.”[1]

There are a wide range of use cases for cryo-EM.  It is now seen as one of the keys to developing new pharmaceuticals and therapies, including innovations in cancer immunotherapy and precision medicine. The publication Chemistry World notes that, during an outbreak of the Zika virus in Brazil, a group of researchers used cryo-EM to generate a high-resolution 3D image of the virus structure, a view that provided a starting point in the search for sites that could be targeted by drugs to prevent the spread of the virus.[2]

Cryo-EM alone, of course, doesn’t provide all the insights that researchers seek. Those insights come from the combination of cryo-EM and high performance computing (HPC) simulations, which churn through massive amounts of data to yield detailed 3D models of biological structures at sub-cellular and molecular scales.

Let’s look at a few examples of the way cryo-EM and HPC are serving as a catalyst for scientific discovery.

The Rockefeller University

At The Rockefeller University, the Evelyn Gruss Lipper Cryo-Electron Microscopy Resource Center makes sophisticated cryo-EM tools available to university researchers. These tools allow researchers to visualize the 3D structures of molecules and macromolecular complexes in solution.

Over the past four years, the use of cryo-EM has led to dozens of research breakthroughs at the university. In particular, cryo-EM has helped scientists understand the configurations and choreography of a range of previously intractable biological molecules. Some of these molecules are trademarks of deadly diseases, including cystic fibrosis, which make them important targets for new therapies.[3]

Peking University

At Peking University, researchers are leveraging the processing power of HPC clusters from Dell EMC to further cryo-EM cooperative research with Harvard University. These clusters, with 144 nodes and about 2 petabytes of storage with Lustre, enable researchers to map the 3D structure of biological macromolecules to design inhibitors and develop new drugs to treat or cure patients of cancer and other diseases.

“The HPC clusters from Dell EMC are critical to our research missions that highly depend on the analysis of big data generated from highly automated cryo-electron microscopes,” notes Dr. Youdong “Jack” Mao, assistant professor of biophysics at Peking University, in a news release highlighting the research effort. “The HPC systems facilitate the development of state-of-the-art algorithms in pursuit of structural solutions to those grand biomedical problems, which would deliver innovations in cancer immunotherapy and precision medicine.” [4]

Texas Advanced Computing Center

A team of researchers from four universities is using cryo-EM and supercomputing simulations run at Texas Advanced Computing Center (TACC) to model a vital molecular machine known as the human pre-initiation complex (PIC). The goal of this massive scientific investigation, which has involved millions of processor-core hours of simulations, is to produce atomic models that tell the full story of the structure and function of the protein complex of molecules.

A researcher on the project notes that this work lays the foundation for the development of future cures, which wouldn’t be possible without an understanding of the how PIC and other complex molecular machines function. [5]

Revolutionizing medical research

As examples like these show, the combination of cryo-EM and HPC is revolutionizing biochemistry and medical research. It is helping researchers make the fundamental scientific discoveries that create fertile ground for the development of life-saving pharmaceuticals and therapies, like immunotherapy and precision medicine.

And at the end of the day, that’s what really matters — saving lives.

For a closer look at the simulations made possible by cryo-electron microscopy and high performance computing, watch the Cryo-EM demo on Dell PowerEdge servers.


[1] Royal Swedish Academy of Sciences news release, “The Nobel Prize in Chemistry 2017,” October 4, 2017.

[2] Chemistry World, “Explainer: What is cryo-electron microscopy,” 2017.

[3] The Rockefeller University, “Third Rockefeller cryo-EM to help tame poorly behaved proteins,” August 30, 2018.

[4] Dell EMC news release, “Dell EMC Expands High Performance Computing Portfolio with Advances in Cloud, Software and System,” November 15, 2016.

[5] Texas Advanced Computing Center, “How To See Living Machines,” Published on November 21, 2016 by Jorge Salazar.

 

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industry updates delivered to you every week!

Q&A with Nvidia’s Chief of DGX Systems on the DGX-GB200 Rack-scale System

March 27, 2024

Pictures of Nvidia's new flagship mega-server, the DGX GB200, on the GTC show floor got favorable reactions on social media for the sheer amount of computing power it brings to artificial intelligence.  Nvidia's DGX Read more…

Call for Participation in Workshop on Potential NSF CISE Quantum Initiative

March 26, 2024

Editor’s Note: Next month there will be a workshop to discuss what a quantum initiative led by NSF’s Computer, Information Science and Engineering (CISE) directorate could entail. The details are posted below in a Ca Read more…

Waseda U. Researchers Reports New Quantum Algorithm for Speeding Optimization

March 25, 2024

Optimization problems cover a wide range of applications and are often cited as good candidates for quantum computing. However, the execution time for constrained combinatorial optimization applications on quantum device Read more…

NVLink: Faster Interconnects and Switches to Help Relieve Data Bottlenecks

March 25, 2024

Nvidia’s new Blackwell architecture may have stolen the show this week at the GPU Technology Conference in San Jose, California. But an emerging bottleneck at the network layer threatens to make bigger and brawnier pro Read more…

Who is David Blackwell?

March 22, 2024

During GTC24, co-founder and president of NVIDIA Jensen Huang unveiled the Blackwell GPU. This GPU itself is heavily optimized for AI work, boasting 192GB of HBM3E memory as well as the the ability to train 1 trillion pa Read more…

Nvidia Appoints Andy Grant as EMEA Director of Supercomputing, Higher Education, and AI

March 22, 2024

Nvidia recently appointed Andy Grant as Director, Supercomputing, Higher Education, and AI for Europe, the Middle East, and Africa (EMEA). With over 25 years of high-performance computing (HPC) experience, Grant brings a Read more…

Q&A with Nvidia’s Chief of DGX Systems on the DGX-GB200 Rack-scale System

March 27, 2024

Pictures of Nvidia's new flagship mega-server, the DGX GB200, on the GTC show floor got favorable reactions on social media for the sheer amount of computing po Read more…

NVLink: Faster Interconnects and Switches to Help Relieve Data Bottlenecks

March 25, 2024

Nvidia’s new Blackwell architecture may have stolen the show this week at the GPU Technology Conference in San Jose, California. But an emerging bottleneck at Read more…

Who is David Blackwell?

March 22, 2024

During GTC24, co-founder and president of NVIDIA Jensen Huang unveiled the Blackwell GPU. This GPU itself is heavily optimized for AI work, boasting 192GB of HB Read more…

Nvidia Looks to Accelerate GenAI Adoption with NIM

March 19, 2024

Today at the GPU Technology Conference, Nvidia launched a new offering aimed at helping customers quickly deploy their generative AI applications in a secure, s Read more…

The Generative AI Future Is Now, Nvidia’s Huang Says

March 19, 2024

We are in the early days of a transformative shift in how business gets done thanks to the advent of generative AI, according to Nvidia CEO and cofounder Jensen Read more…

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, codenamed Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from Read more…

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. Wh Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the fi Read more…

Alibaba Shuts Down its Quantum Computing Effort

November 30, 2023

In case you missed it, China’s e-commerce giant Alibaba has shut down its quantum computing research effort. It’s not entirely clear what drove the change. Read more…

Nvidia H100: Are 550,000 GPUs Enough for This Year?

August 17, 2023

The GPU Squeeze continues to place a premium on Nvidia H100 GPUs. In a recent Financial Times article, Nvidia reports that it expects to ship 550,000 of its lat Read more…

Shutterstock 1285747942

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed it Read more…

DoD Takes a Long View of Quantum Computing

December 19, 2023

Given the large sums tied to expensive weapon systems – think $100-million-plus per F-35 fighter – it’s easy to forget the U.S. Department of Defense is a Read more…

Synopsys Eats Ansys: Does HPC Get Indigestion?

February 8, 2024

Recently, it was announced that Synopsys is buying HPC tool developer Ansys. Started in Pittsburgh, Pa., in 1970 as Swanson Analysis Systems, Inc. (SASI) by John Swanson (and eventually renamed), Ansys serves the CAE (Computer Aided Engineering)/multiphysics engineering simulation market. Read more…

Choosing the Right GPU for LLM Inference and Training

December 11, 2023

Accelerating the training and inference processes of deep learning models is crucial for unleashing their true potential and NVIDIA GPUs have emerged as a game- Read more…

Intel’s Server and PC Chip Development Will Blur After 2025

January 15, 2024

Intel's dealing with much more than chip rivals breathing down its neck; it is simultaneously integrating a bevy of new technologies such as chiplets, artificia Read more…

Baidu Exits Quantum, Closely Following Alibaba’s Earlier Move

January 5, 2024

Reuters reported this week that Baidu, China’s giant e-commerce and services provider, is exiting the quantum computing development arena. Reuters reported � Read more…

Leading Solution Providers

Contributors

Comparing NVIDIA A100 and NVIDIA L40S: Which GPU is Ideal for AI and Graphics-Intensive Workloads?

October 30, 2023

With long lead times for the NVIDIA H100 and A100 GPUs, many organizations are looking at the new NVIDIA L40S GPU, which it’s a new GPU optimized for AI and g Read more…

Shutterstock 1179408610

Google Addresses the Mysteries of Its Hypercomputer 

December 28, 2023

When Google launched its Hypercomputer earlier this month (December 2023), the first reaction was, "Say what?" It turns out that the Hypercomputer is Google's t Read more…

AMD MI3000A

How AMD May Get Across the CUDA Moat

October 5, 2023

When discussing GenAI, the term "GPU" almost always enters the conversation and the topic often moves toward performance and access. Interestingly, the word "GPU" is assumed to mean "Nvidia" products. (As an aside, the popular Nvidia hardware used in GenAI are not technically... Read more…

Shutterstock 1606064203

Meta’s Zuckerberg Puts Its AI Future in the Hands of 600,000 GPUs

January 25, 2024

In under two minutes, Meta's CEO, Mark Zuckerberg, laid out the company's AI plans, which included a plan to build an artificial intelligence system with the eq Read more…

Google Introduces ‘Hypercomputer’ to Its AI Infrastructure

December 11, 2023

Google ran out of monikers to describe its new AI system released on December 7. Supercomputer perhaps wasn't an apt description, so it settled on Hypercomputer Read more…

China Is All In on a RISC-V Future

January 8, 2024

The state of RISC-V in China was discussed in a recent report released by the Jamestown Foundation, a Washington, D.C.-based think tank. The report, entitled "E Read more…

Intel Won’t Have a Xeon Max Chip with New Emerald Rapids CPU

December 14, 2023

As expected, Intel officially announced its 5th generation Xeon server chips codenamed Emerald Rapids at an event in New York City, where the focus was really o Read more…

IBM Quantum Summit: Two New QPUs, Upgraded Qiskit, 10-year Roadmap and More

December 4, 2023

IBM kicks off its annual Quantum Summit today and will announce a broad range of advances including its much-anticipated 1121-qubit Condor QPU, a smaller 133-qu Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire