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 industy updates delivered to you every week!

ISC Keynote: The Algorithms of Life – Scientific Computing for Systems Biology

June 19, 2019

Systems biology has existed loosely under many definitions for a couple of decades. It’s the notion of describing living systems using first-principle physics and mathematics to capture life in equations that are both Read more…

By John Russell

Summit Achieves 445 Petaflops on New ‘HPL-AI’ Benchmark

June 19, 2019

Summit -- the world's top-ranking supercomputer -- has been used to test-drive a new mixed-precision Linpack benchmark, which for now is being called HPL-AI. Traditionally, supercomputer performance is measured using the High-Performance Linpack (HPL) benchmark, which is the basis for the Top500 list that biannually ranks world's fastest supercomputers. Read more…

By Oliver Peckham

By the Numbers: For the HPC Industry, These Are the Good Old Days

June 18, 2019

For technology vendors in HPC and HPC-related markets driven by increased demand for AI, enterprise and exascale solutions, this is the best of times – with better times likely in the offing. HPC analyst firm Hyperion Research took the occasion of its semi-annual HPC market update breakfast today in Frankfurt... Read more…

By Doug Black

HPE Extreme Performance Solutions

HPE and Intel® Omni-Path Architecture: How to Power a Cloud

Learn how HPE and Intel® Omni-Path Architecture provide critical infrastructure for leading Nordic HPC provider’s HPCFLOW cloud service.

For decades, HPE has been at the forefront of high-performance computing, and we’ve powered some of the fastest and most robust supercomputers in the world. Read more…

IBM Accelerated Insights

Avoid AI Redo’s by Starting with the Right Infrastructure

Do you know if you have the right infrastructure for AI? Many organizations don’t have it. In a recent IDC survey, “77.1% of respondents say they ran into one or more limitations with their AI infrastructure on-premise and 90.3% ran into compute limitations in the cloud.” Read more…

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafloppers only. The entry point for the new list is 1.022 petaf Read more…

By Tiffany Trader

ISC Keynote: The Algorithms of Life – Scientific Computing for Systems Biology

June 19, 2019

Systems biology has existed loosely under many definitions for a couple of decades. It’s the notion of describing living systems using first-principle physics Read more…

By John Russell

Summit Achieves 445 Petaflops on New ‘HPL-AI’ Benchmark

June 19, 2019

Summit -- the world's top-ranking supercomputer -- has been used to test-drive a new mixed-precision Linpack benchmark, which for now is being called HPL-AI. Traditionally, supercomputer performance is measured using the High-Performance Linpack (HPL) benchmark, which is the basis for the Top500 list that biannually ranks world's fastest supercomputers. Read more…

By Oliver Peckham

By the Numbers: For the HPC Industry, These Are the Good Old Days

June 18, 2019

For technology vendors in HPC and HPC-related markets driven by increased demand for AI, enterprise and exascale solutions, this is the best of times – with better times likely in the offing. HPC analyst firm Hyperion Research took the occasion of its semi-annual HPC market update breakfast today in Frankfurt... Read more…

By Doug Black

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl Read more…

By Tiffany Trader

Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

Jack Wells Joins OpenACC; Arm Support Coming

June 17, 2019

Perhaps the most significant ISC19 news for OpenACC wasn’t in its official press release yesterday which touted growing user traction and the notable addition Read more…

By John Russell

DDN Launches EXA5 for AI, Big Data, HPC Workloads

June 17, 2019

DDN, for two decades competing at the headwaters of high performance storage, this morning announced an enterprise-oriented end-to-end high performance storage Read more…

By Doug Black

Final Countdown to ISC19: What to See

June 13, 2019

If you're attending the International Supercomputing Conference, taking place in Frankfurt next week (June 16-20), you're either packing, in transit, or are alr Read more…

By Tiffany Trader

High Performance (Potato) Chips

May 5, 2006

In this article, we focus on how Procter & Gamble is using high performance computing to create some common, everyday supermarket products. Tom Lange, a 27-year veteran of the company, tells us how P&G models products, processes and production systems for the betterment of consumer package goods. Read more…

By Michael Feldman

Cray, AMD to Extend DOE’s Exascale Frontier

May 7, 2019

Cray and AMD are coming back to Oak Ridge National Laboratory to partner on the world’s largest and most expensive supercomputer. The Department of Energy’s Read more…

By Tiffany Trader

Graphene Surprises Again, This Time for Quantum Computing

May 8, 2019

Graphene is fascinating stuff with promise for use in a seeming endless number of applications. This month researchers from the University of Vienna and Institu Read more…

By John Russell

Why Nvidia Bought Mellanox: ‘Future Datacenters Will Be…Like High Performance Computers’

March 14, 2019

“Future datacenters of all kinds will be built like high performance computers,” said Nvidia CEO Jensen Huang during a phone briefing on Monday after Nvidia revealed scooping up the high performance networking company Mellanox for $6.9 billion. Read more…

By Tiffany Trader

AMD Verifies Its Largest 7nm Chip Design in Ten Hours

June 5, 2019

AMD announced last week that its engineers had successfully executed the first physical verification of its largest 7nm chip design – in just ten hours. The AMD Radeon Instinct Vega20 – which boasts 13.2 billion transistors – was tested using a TSMC-certified Calibre nmDRC software platform from Mentor. Read more…

By Oliver Peckham

It’s Official: Aurora on Track to Be First US Exascale Computer in 2021

March 18, 2019

The U.S. Department of Energy along with Intel and Cray confirmed today that an Intel/Cray supercomputer, "Aurora," capable of sustained performance of one exaf Read more…

By Tiffany Trader

Deep Learning Competitors Stalk Nvidia

May 14, 2019

There is no shortage of processing architectures emerging to accelerate deep learning workloads, with two more options emerging this week to challenge GPU leader Nvidia. First, Intel researchers claimed a new deep learning record for image classification on the ResNet-50 convolutional neural network. Separately, Israeli AI chip startup Hailo.ai... Read more…

By George Leopold

The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

It’s not easy to be a physicist. Richard Feynman (basically the Jimi Hendrix of physicists) once said: “The first principle is that you must not fool yourse Read more…

By Ben Criger

Leading Solution Providers

SC 18 Virtual Booth Video Tour

Advania @ SC18 AMD @ SC18
ASRock Rack @ SC18
DDN Storage @ SC18
HPE @ SC18
IBM @ SC18
Lenovo @ SC18 Mellanox Technologies @ SC18
NVIDIA @ SC18
One Stop Systems @ SC18
Oracle @ SC18 Panasas @ SC18
Supermicro @ SC18 SUSE @ SC18 TYAN @ SC18
Verne Global @ SC18

TSMC and Samsung Moving to 5nm; Whither Moore’s Law?

June 12, 2019

With reports that Taiwan Semiconductor Manufacturing Co. (TMSC) and Samsung are moving quickly to 5nm manufacturing, it’s a good time to again ponder whither goes the venerable Moore’s law. Shrinking feature size has of course been the primary hallmark of achieving Moore’s law... Read more…

By John Russell

Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

Intel Launches Cascade Lake Xeons with Up to 56 Cores

April 2, 2019

At Intel's Data-Centric Innovation Day in San Francisco (April 2), the company unveiled its second-generation Xeon Scalable (Cascade Lake) family and debuted it Read more…

By Tiffany Trader

Cray – and the Cray Brand – to Be Positioned at Tip of HPE’s HPC Spear

May 22, 2019

More so than with most acquisitions of this kind, HPE’s purchase of Cray for $1.3 billion, announced last week, seems to have elements of that overused, often Read more…

By Doug Black and Tiffany Trader

Arm Unveils Neoverse N1 Platform with up to 128-Cores

February 20, 2019

Following on its Neoverse roadmap announcement last October, Arm today revealed its next-gen Neoverse microarchitecture with compute and throughput-optimized si Read more…

By Tiffany Trader

Announcing four new HPC capabilities in Google Cloud Platform

April 15, 2019

When you’re running compute-bound or memory-bound applications for high performance computing or large, data-dependent machine learning training workloads on Read more…

By Wyatt Gorman, HPC Specialist, Google Cloud; Brad Calder, VP of Engineering, Google Cloud; Bart Sano, VP of Platforms, Google Cloud

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl Read more…

By Tiffany Trader

In Wake of Nvidia-Mellanox: Xilinx to Acquire Solarflare

April 25, 2019

With echoes of Nvidia’s recent acquisition of Mellanox, FPGA maker Xilinx has announced a definitive agreement to acquire Solarflare Communications, provider Read more…

By Doug Black

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This