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!

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows users to virtually “walk” around the massive supercomputer Read more…

By Oliver Peckham

Supercomputer Simulations Examine Changes in Chesapeake Bay

August 8, 2020

The Chesapeake Bay, the largest estuary in the continental United States, weaves its way south from Maryland, collecting waters from West Virginia, Delaware, DC, Pennsylvania and New York along the way. Like many major e Read more…

By Oliver Peckham

Student Success from ‘Scratch’: CHPC’s Proof is in the Pudding

August 7, 2020

Happy Sithole, who directs the South African Centre for High Performance Computing (SA-CHPC), called the 13th annual CHPC National conference to order on December 1, 2019, at the Birchwood Conference Centre in Kempton Pa Read more…

By Elizabeth Leake

New GE Simulations on Summit to Advance Offshore Wind Power

August 6, 2020

The wind energy sector is a frequent user of high-power simulations, with researchers aiming to optimize wind flows and energy production from the massive turbines. Now, researchers at GE are preparing to undertake a lar Read more…

By Oliver Peckham

Research: A Survey of Numerical Methods Utilizing Mixed Precision Arithmetic

August 5, 2020

Within the past years, hardware vendors have started designing low precision special function units in response to the demand of the machine learning community and their demand for high compute power in low precision for Read more…

By Hartwig Anzt and Jack Dongarra

AWS Solution Channel

AWS announces the release of AWS ParallelCluster 2.8.0

AWS ParallelCluster is a fully supported and maintained open source cluster management tool that makes it easy for scientists, researchers, and IT administrators to deploy and manage High Performance Computing (HPC) clusters in the AWS cloud. Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

Implement Photonic Tensor Cores for Machine Learning?

August 5, 2020

Researchers from George Washington University have reported an approach for building photonic tensor cores that leverages phase change photonic memory to implement a neural network (NN). Their novel architecture, reporte Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows use Read more…

By Oliver Peckham

Research: A Survey of Numerical Methods Utilizing Mixed Precision Arithmetic

August 5, 2020

Within the past years, hardware vendors have started designing low precision special function units in response to the demand of the machine learning community Read more…

By Hartwig Anzt and Jack Dongarra

Implement Photonic Tensor Cores for Machine Learning?

August 5, 2020

Researchers from George Washington University have reported an approach for building photonic tensor cores that leverages phase change photonic memory to implem Read more…

By John Russell

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

Machines, Connections, Data, and Especially People: OAC Acting Director Amy Friedlander Charts Office’s Blueprint for Innovation

August 3, 2020

The path to innovation in cyberinfrastructure (CI) will require continued focus on building HPC systems and secure connections between them, in addition to the Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

PEARC20 Plenary Introduces Five Upcoming NSF-Funded HPC Systems

July 30, 2020

Five new HPC systems—three National Science Foundation-funded “Capacity” systems and two “Innovative Prototype/Testbed” systems—will be coming onlin Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

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

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

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

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 i Read more…

By Doug Black

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

Leading Solution Providers

Contributors

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

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

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

‘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

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and in Read more…

By Oliver Peckham

John Martinis Reportedly Leaves Google Quantum Effort

April 21, 2020

John Martinis, who led Google’s quantum computing effort since establishing its quantum hardware group in 2014, has left Google after being moved into an advi Read more…

By John Russell

$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

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

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