Blue Waters Supercomputer Helps Tackle Pandemic Flu Simulations

By Staff report

February 26, 2020

While not the novel coronavirus that is now sweeping across the world, the 2009 H1N1 flu pandemic (pH1N1) infected up to 21 percent of the global population and killed over 200,000 people. Now, a team of researchers from the University of California San Diego have applied supercomputing power to pH1N1 simulations in order to better understand that pandemic, manage its annual recurrences – and prepare for the next one.

The UC San Diego team built an all-atom, solvated and experimentally based integrative model of pH1N1, using this simulation to examine two binding sites on the flu’s viral proteins. While most viral simulations simplify in order to precisely model one target area for a drug, this simulation broke new ground by modeling the entire viral envelope of pH1N1 – over 160 million atoms – without sacrificing detail.

“Even just building this system from the ground up was quite challenging as it required us to integrate different types of experimental data, at different resolutions,” said Rommie Amaro, the UC San Diego professor of chemistry and biochemistry who led the study, in an interview with UC San Diego. “This model itself was useful to understand the physical arrangement of molecules in the virus, which had never been done before at this level of detail.”

To successfully run the mesoscale simulation of pH1N1 – one of the largest biological systems ever to be simulated on this level – the researchers turned to the Blue Waters supercomputer hosted by the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. Blue Waters, now in its final year of operations, is a hybrid CPU-GPU Cray system with more than 1.5 petabytes of memory and approximately 26 petabytes of storage that delivers around 13 peak petaflops.

A video of the simulation, courtesy of Lorenzo Casalino, UC San Diego.

The powerful simulation allowed researchers to better understand how flu proteins interacted with one another on the surface of the virus. They also used the many protein copies throughout the simulation to conduct a statistical analysis of viral protein movement. “This was useful because it allowed us, for the first time, to characterize how quickly one particular loop known as the ‘150-loop’ opened and closed,” Amaro explained. “We care about the motion of this loop because the loop is right up next to where drugs, like Tamiflu, bind to deactivate the protein.”

Crucially, the study may have opened the door for new anti-influenza therapeutics. “Our study also provides new evidence that an often-overlooked so-called ‘secondary site’ may be the first place the natural substrate of the flu binds,” Amaro said. “Thus a novel viable therapeutic strategy may be to design molecules that effectively block that site.”

“We are thrilled Blue Waters, both the computer and the support staff, was able to contribute to this groundbreaking success,” said William Kramer, director of Blue Waters. “To our knowledge, a molecular dynamics simulation on so grand a scale has never been attempted, let alone completed.”

Funding for the work was provided in part by the National Institutes of Health and the National Science Foundation.

About the research 

The research discussed in this article was published as “Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism” in the February 2020 issue of ACS Central Science. It was written by Jacob D. Durrant, Sarah E. Kochanek, Lorenzo Casalino, Pek U leong, Abigail C. Dommer and Rommie E. Amaro and can be accessed here.

To read the article by UC San Diego’s Cythia Dillon discussing this research, click here.

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!

Alibaba Highlights COVID-19 Research Enabled by Its Cloud HPC

April 8, 2020

Many supercomputer centers are fast-tracking COVID-19-related proposals and prioritizing COVID-19-related jobs on their systems. For the researchers whose access to these systems is limited (or for whom time is too limit Read more…

By Oliver Peckham

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing ( Read more…

By John Russell

Ethernet Technology Consortium Launches 800 Gigabit Ethernet Specification

April 7, 2020

The newly rebranded Ethernet Technology Consortium (ETC), formerly known as the 25 Gigabit Ethernet Consortium, announced a new 800 Gigabit Ethernet specification and an expanded scope aimed at meeting the needs of perfo Read more…

By Tiffany Trader

Spanish Researchers Introduce HPC-Ready COVID-19 Spread Simulator

April 7, 2020

With governments in a mad scramble to identify the policies most likely to curb the spread of the pandemic without unnecessarily crippling the global economy, researchers are turning to AI and high-performance computing Read more…

By Oliver Peckham

Stony Brook Researchers to Run COVID-19 Simulations on Supercomputers

April 6, 2020

A wide range of supercomputers are crunching the infamous “spike” protein of the novel coronavirus, from Summit more than a month ago to [email protected] to a Russian cluster just a week ago. Read more…

By Staff report

AWS Solution Channel

Amazon FSx for Lustre Update: Persistent Storage for Long-Term, High-Performance Workloads

Last year I wrote about Amazon FSx for Lustre and told you how our customers can use it to create pebibyte-scale, highly parallel POSIX-compliant file systems that serve thousands of simultaneous clients driving millions of IOPS (Input/Output Operations per Second) with sub-millisecond latency. Read more…

What’s New in Computing vs. COVID-19: Fast-Tracked Research, Susceptibility Study, Antibodies & More

April 6, 2020

Supercomputing, big data and artificial intelligence are crucial tools in the fight against the coronavirus pandemic. Around the world, researchers, corporations and governments are urgently devoting their computing reso Read more…

By Oliver Peckham

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems Read more…

By John Russell

Ethernet Technology Consortium Launches 800 Gigabit Ethernet Specification

April 7, 2020

The newly rebranded Ethernet Technology Consortium (ETC), formerly known as the 25 Gigabit Ethernet Consortium, announced a new 800 Gigabit Ethernet specificati Read more…

By Tiffany Trader

ECP Milestone Report Details Progress and Directions

April 1, 2020

The Exascale Computing Project (ECP) milestone report issued last week presents a good snapshot of progress in preparing applications for exascale computing. Th Read more…

By John Russell

Pandemic ‘Wipes Out’ 2020 HPC Market Growth, Flat to 12% Drop Expected

March 31, 2020

As the world battles the still accelerating novel coronavirus, the HPC community has mounted a forceful response to the pandemic on many fronts. But these efforts won't inoculate the HPC industry from the economic effects of COVID-19. Market watcher Intersect360 Research has revised its 2020 forecast for HPC products and services, projecting... Read more…

By Tiffany Trader

LLNL Leverages Supercomputing to Identify COVID-19 Antibody Candidates

March 30, 2020

As COVID-19 sweeps the globe to devastating effect, supercomputers around the world are spinning up to fight back by working on diagnosis, epidemiology, treatme Read more…

By Staff report

Weather at Exascale: Load Balancing for Heterogeneous Systems

March 30, 2020

The first months of 2020 were dominated by weather and climate supercomputing news, with major announcements coming from the UK, the European Centre for Medium- Read more…

By Oliver Peckham

Q&A Part Two: ORNL’s Pooser on Progress in Quantum Communication

March 30, 2020

Quantum computing seems to get more than its fair share of attention compared to quantum communication. That’s despite the fact that quantum networking may be Read more…

By John Russell

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

Julia Programming’s Dramatic Rise in HPC and Elsewhere

January 14, 2020

Back in 2012 a paper by four computer scientists including Alan Edelman of MIT introduced Julia, A Fast Dynamic Language for Technical Computing. At the time, t Read more…

By John Russell

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Steve Scott Lays Out HPE-Cray Blended Product Roadmap

March 11, 2020

Last week, the day before the El Capitan processor disclosures were made at HPE's new headquarters in San Jose, Steve Scott (CTO for HPC & AI at HPE, and former Cray CTO) was on-hand at the Rice Oil & Gas HPC conference in Houston. He was there to discuss the HPE-Cray transition and blended roadmap, as well as his favorite topic, Cray's eighth-gen networking technology, Slingshot. Read more…

By Tiffany Trader

Fujitsu A64FX Supercomputer to Be Deployed at Nagoya University This Summer

February 3, 2020

Japanese tech giant Fujitsu announced today that it will supply Nagoya University Information Technology Center with the first commercial supercomputer powered Read more…

By Tiffany Trader

Tech Conferences Are Being Canceled Due to Coronavirus

March 3, 2020

Several conferences scheduled to take place in the coming weeks, including Nvidia’s GPU Technology Conference (GTC) and the Strata Data + AI conference, have Read more…

By Alex Woodie

Leading Solution Providers

SC 2019 Virtual Booth Video Tour

AMD
AMD
ASROCK RACK
ASROCK RACK
AWS
AWS
CEJN
CJEN
CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
IBM
IBM
MELLANOX
MELLANOX
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
SIX NINES IT
SIX NINES IT
VERNE GLOBAL
VERNE GLOBAL
WEKAIO
WEKAIO

Cray to Provide NOAA with Two AMD-Powered Supercomputers

February 24, 2020

The United States’ National Oceanic and Atmospheric Administration (NOAA) last week announced plans for a major refresh of its operational weather forecasting supercomputers, part of a 10-year, $505.2 million program, which will secure two HPE-Cray systems for NOAA’s National Weather Service to be fielded later this year and put into production in early 2022. Read more…

By Tiffany Trader

Exascale Watch: El Capitan Will Use AMD CPUs & GPUs to Reach 2 Exaflops

March 4, 2020

HPE and its collaborators reported today that El Capitan, the forthcoming exascale supercomputer to be sited at Lawrence Livermore National Laboratory and serve Read more…

By John Russell

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

IBM Unveils Latest Achievements in AI Hardware

December 13, 2019

“The increased capabilities of contemporary AI models provide unprecedented recognition accuracy, but often at the expense of larger computational and energet Read more…

By Oliver Peckham

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

IBM Debuts IC922 Power Server for AI Inferencing and Data Management

January 28, 2020

IBM today launched a Power9-based inference server – the IC922 – that features up to six Nvidia T4 GPUs, PCIe Gen 4 and OpenCAPI connectivity, and can accom Read more…

By John Russell

Summit Joins the Fight Against the Coronavirus

March 6, 2020

With the coronavirus sweeping the globe, tech conferences and supply chains are being hit hard – but now, tech is hitting back. Oak Ridge National Laboratory Read more…

By Staff report

CINECA’s Carlo Cavazzoni Describes the Supercomputing Battle Against COVID-19

March 17, 2020

The latest episode of the This Week in HPC podcast features Carlo Cavazzoni, a senior staff member at CINECA, one of the leading supercomputing organizations in Europe. Intersect360 Research's Addison Snell spoke to Cavazzoni to discuss both CINECA's work using supercomputing to combat COVID-19 and Cavazzoni's personal experience living near the epicenter... Read more…

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