TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

By Staff report

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 illuminate COVID-19, as well as other virus and DNA replication tasks. TACC’s Jorge Salazar highlighted the research, which was conducted by a group of researchers from Boston University, the University of California San Diego and the University of Wisconsin-Madison.

The research comprised two studies, with the first focusing on cell membranes. When viruses like COVID-19 invade, they force host cells to bend and set free the copies of the virus created within the cell (a process known as “budding”). The researchers examined these cell membranes, zeroing in on a specific protein that is suspected to be largely responsible for the budding process. With experimental techniques too low-resolution to study the necessary interactions, the researchers turned to supercomputer-powered simulation.

Using atomistic molecular dynamics simulations, the researchers carefully examined the filaments of the target protein. The goal: to establish whether the atomistic forces within the protein were responsible for the bending, and thus, the budding. These simulations, which included up to two million atoms, were allotted supercomputing time through the NSF’s Extreme Science and Engineering Discovery Environment (XSEDE) program. They ran on TACC’s Stampede2 system, a Dell EMC system equipped with Intel Xeon Phi CPUs that delivers 10.7 Linpack petaflops and ranked 18th on the latest Top500 list of the world’s fastest supercomputers.

“Supercomputers with massive parallelization are very much required to push the boundary of biomolecular simulations,” Qiang Cui, a professor of chemistry, physics and biomedical engineering at Boston University who worked on both studies, told Salazar. “Stampede2 has been crucial for us to set up these relatively large-scale membrane simulations.”

The results of the simulations lent new insight into how the bending occurs, including a “clear intrinsic twist” in the protein.

“Membrane remodeling is an important process that underlies many crucial cellular functions and events, such as synaptic transmission and virus infection,” Cui said. “Understanding the mechanism of membrane remodeling will help propose new strategies for battling human diseases due to impaired membrane fusion activities – or preventing viral infection – a timely topic these days given the quick spread of the new coronavirus.”

The second study also used supercomputer simulations – this time, to examine the chemical processes that govern how nucleotide bases are added to strands of DNA. 

“Our role was to do these molecular dynamics simulations and test different models for how the atoms are moving around during the reaction and test different interactions that are helping that along,” explained Daniel Roston, an assistant project scientist at the University of California San Diego. To run these simulations, they used 500,000 CPU hours on the Comet system at the San Diego Supercomputer Center (SDSC). Comet’s 1,944 Intel Haswell nodes and 72 Nvidia GPU nodes deliver 2.76 peak petaflops.

“One of the great things about XSEDE is that we can take advantage of a ton of computational power,” Roston said. “DNA replication is what life is about. We’re getting at the heart of how that happens, the really fundamental process to life as we know it on Earth. This is so important, we should really understand how it works at a deep level.”

About the research

The first study was written by Taraknath Mandal, Wilson Lough, Saverio E. Spagnolie, Anjon Audhya and Qiang Cui. It was published as “Molecular Simulation of Mechanical Properties and Membrane Activities of the ESCRT-III Complexes” in the February 2020 issue of Biophysical Journal and can be found here.

The second study was written by Daniel Roston, Darren Demapan and Qiang Cui. It was published as “Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase” in the December 2019 issue of PNAS and can be accessed here

To read Jorge Salazar’s original article covering this research, click here.

Header image: Virus budding. Image courtesy of Mandal et al.

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!

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been instrumental to AMD’s datacenter market resurgence. Nanomet Read more…

By Doug Black

Supercomputer-Powered Protein Simulations Approach Lab Accuracy

June 1, 2020

Protein simulations have dominated the supercomputing conversation of late as supercomputers around the world race to simulate the viral proteins of COVID-19 as accurately as possible and simulate potential bindings in t Read more…

By Oliver Peckham

HPC Career Notes: June 2020 Edition

June 1, 2020

In this monthly feature, we'll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it's a promotion, new company hire, or even an accolade, we've got Read more…

By Mariana Iriarte

Supercomputer Modeling Shows How COVID-19 Spreads Through Populations

May 30, 2020

As many states begin to loosen the lockdowns and stay-at-home orders that have forced most Americans inside for the past two months, researchers are poring over the data, looking for signs of the dreaded second peak of t Read more…

By Oliver Peckham

SODALITE: Towards Automated Optimization of HPC Application Deployment

May 29, 2020

Developing and deploying applications across heterogeneous infrastructures like HPC or Cloud with diverse hardware is a complex problem. Enabling developers to describe the application deployment and optimising runtime p Read more…

By the SODALITE Team

AWS Solution Channel

Computational Fluid Dynamics on AWS

Over the past 30 years Computational Fluid Dynamics (CFD) has grown to become a key part of many engineering design processes. From aircraft design to modelling the blood flow in our bodies, the ability to understand the behaviour of fluids has enabled countless innovations and improved the time to market for many products. Read more…

What’s New in HPC Research: Astronomy, Weather, Security & More

May 29, 2020

In this bimonthly feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

By Oliver Peckham

COVID-19 HPC Consortium Expands to Europe, Reports on Research Projects

May 28, 2020

The COVID-19 HPC Consortium, a public-private effort delivering free access to HPC processing for scientists pursuing coronavirus research – some utilizing AI Read more…

By Doug Black

$100B Plan Submitted for Massive Remake and Expansion of NSF

May 27, 2020

Legislation to reshape, expand - and rename - the National Science Foundation has been submitted in both the U.S. House and Senate. The proposal, which seems to Read more…

By John Russell

IBM Boosts Deep Learning Accuracy on Memristive Chips

May 27, 2020

IBM researchers have taken another step towards making in-memory computing based on phase change (PCM) memory devices a reality. Papers in Nature and Frontiers Read more…

By John Russell

Hats Over Hearts: Remembering Rich Brueckner

May 26, 2020

HPCwire and all of the Tabor Communications family are saddened by last week’s passing of Rich Brueckner. He was the ever-optimistic man in the Red Hat presiding over the InsideHPC media portfolio for the past decade and a constant presence at HPC’s most important events. Read more…

Nvidia Q1 Earnings Top Expectations, Datacenter Revenue Breaks $1B

May 22, 2020

Nvidia’s seemingly endless roll continued in the first quarter with the company announcing blockbuster earnings that exceeded Wall Street expectations. Nvidia Read more…

By Doug Black

Microsoft’s Massive AI Supercomputer on Azure: 285k CPU Cores, 10k GPUs

May 20, 2020

Microsoft has unveiled a supercomputing monster – among the world’s five most powerful, according to the company – aimed at what is known in scientific an Read more…

By Doug Black

HPC in Life Sciences 2020 Part 1: Rise of AMD, Data Management’s Wild West, More 

May 20, 2020

Given the disruption caused by the COVID-19 pandemic and the massive enlistment of major HPC resources to fight the pandemic, it is especially appropriate to re Read more…

By John Russell

AMD Epyc Rome Picked for New Nvidia DGX, but HGX Preserves Intel Option

May 19, 2020

AMD continues to make inroads into the datacenter with its second-generation Epyc "Rome" processor, which last week scored a win with Nvidia's announcement that Read more…

By Tiffany Trader

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

[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

[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

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

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do 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

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 (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

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

Contributors

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

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

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

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

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k 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

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

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