Newcomer Conduit Leverages Frontera to Understand SARS-CoV-2 ‘Budding’

By Oliver Peckham

January 10, 2022

Conduit, created by MIT graduate (and current CEO) Ryan Robinson, was founded in 2017. But it might not have been until a few years later, when the pandemic started, that Conduit may have found its true calling. While Conduit’s commercial division is busy developing a Covid-19 test called nanoSPLASH, its nonprofit arm was granted access to one of the most powerful supercomputers in the world—Frontera, at the Texas Advanced Computing Center (TACC)—to model the “budding” process of SARS-CoV-2.

Budding, the researchers explained, is how the virus’ genetic material is encapsulated in a spherical envelope—and the process is key to the virus’ ability to infect. Despite that, they say, it has hitherto been poorly understood:

The Conduit team—comprised of Logan Thrasher Collins (CTO of Conduit), Tamer Elkholy, Shafat Mubin, David Hill, Ricky Williams, Kayode Ezike and Ankush Singhal—sought to change that, applying for an allocation from the White House-led Covid-19 High-Performance Computing Consortium to model the budding process on a supercomputer.

The allocation was granted, with the team getting access to TACC’s Frontera system, a 23.5-Linpack petaflops Dell system that ranked 13th on the most recent Top500 list. On Frontera, they used the GROMACS molecular dynamics package to run simulations of the viral molecules involved in the budding process—specifically, the virus’ membrane (M) and envelope (E) proteins, along with a cell membrane—with each simulation containing around half a million atoms modeled across 800 million time steps. They simulated a variety of protein configurations, including a membrane-only system; a system with four E protein pentamers; a system with a single M protein dimer; a system with four M protein dimers; and a system with three M protein dimers and one E protein pentamer.

“It was an honor to utilize one of the world’s most powerful high-performance computing machines for our Covid-19 research,” Collins told HPCwire in an email interview. “We were nervous when the Frontera system was temporarily unavailable during the snowstorms last year, but through our determination and organized communication, we completed our simulations in a timely fashion and were able to make our results available to help combat the ongoing pandemic.”

The results in question were detailed in a paper published in the December issue of the Journal of Physical Chemistry Letters. The researchers found that the M and E proteins facilitated different parts of the budding process, with the M protein in particular inducing membrane curvature. “One of the most notable outcomes of our simulations was that the [four M protein dimer] system gained a substantial degree of global curvature over time, while other systems such as mem had very little curvature,” they wrote. Through quantitative analyses comparing the simulations, they concluded that “E proteins likely do not induce substantial curvature, that isolated M proteins create bulges in the membrane, and that many M proteins together can act together to induce larger amounts of curvature.”

The left image shows strong curvature in the M dimer-heavy system, while the right image shows little to no curvature in the membrane-only system. Image courtesy of the authors.

In sum: the curvature caused by the M protein (roughly 300 times more plentiful than the E protein) wraps the cell membrane around the virus’ genetic material, while the E protein, they hypothesized, worked to coordinate the M proteins in this task.

Based on the results of the in silico modeling, the researchers concluded that “the M protein dimer may represent a valuable target for drugs intended to treat Covid-19 and other coronavirus diseases,” validating that suspicion by running the M protein dimer structure through a drug target identification tool and finding several high-scoring target candidates.

“My hope is that our results will provide a foundation for the development of drugs which target the SARS-CoV-2 M protein and thereby interfere with coronavirus budding,” Collins said. “I plan to contact investigators working in adjacent areas and perhaps collaborate with them so as to take further steps towards making such treatments a reality. Because of the high level of evolutionary conservation of the M protein, we anticipate that drugs targeting its function might be active against a wide array of different coronaviruses, including existing and emerging variants of SARS-CoV-2.”

To learn more about the research, read the paper: Elucidation of SARS-Cov-2 Budding Mechanisms through Molecular Dynamics Simulations of M and E Protein Complexes. The paper was published in the Journal of Physical Chemistry Letters and written by Logan Thrasher Collins, Tamer Elkholy, Shafat Mubin, David Hill, Ricky Williams, Kayode Ezike and Ankush Singhal.

To learn more about HPC in the fight against Covid-19, visit HPCwire’s timeline of supercomputing and the pandemic.

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!

Meta’s Massive New AI Supercomputer Will Be ‘World’s Fastest’

January 24, 2022

Fresh off its rebrand last October, Meta (née Facebook) is putting muscle behind its vision of a metaversal future with a massive new AI supercomputer called the AI Research SuperCluster (RSC). Meta says that RSC will b Read more…

Supercomputer Analysis Shows the Atmospheric Reach of the Tonga Eruption

January 21, 2022

On Saturday, an enormous eruption on the volcanic islands of Hunga Tonga and Hunga Haʻapai shook the Pacific Ocean. The explosion, which could be heard six thousand miles away in Alaska, caused tsunamis across the entir Read more…

NSB Issues US State of Science and Engineering 2022 Report

January 20, 2022

This week the National Science Board released its biannual U.S. State of Science and Engineering 2022 report, as required by the NSF Act. Broadly, the report presents a near-term view of S&E based mostly on 2019 data. To a large extent, this year’s edition echoes trends from the last few reports. The U.S. is still a world leader in R&D spending and S&E education... Read more…

Researchers Achieve 99 Percent Quantum Accuracy with Silicon-Embedded Qubits 

January 20, 2022

Researchers in Australia and the U.S. have made exciting headway in the quantum computing arms race. A multi-institutional team including the University of New South Wales and Sandia National Laboratory announced that th Read more…

Trio of Supercomputers Powers Estimate of Carbon in Earth’s Outer Core

January 20, 2022

Carbon is one of the essential building blocks of life on Earth, and it—along with hydrogen, nitrogen and oxygen—is one of the key elements researchers look for when they search for habitable planets and work to unde Read more…

AWS Solution Channel

shutterstock 718231072

Accelerating drug discovery with Amazon EC2 Spot Instances

This post was contributed by Cristian Măgherușan-Stanciu, Sr. Specialist Solution Architect, EC2 Spot, with contributions from Cristian Kniep, Sr. Developer Advocate for HPC and AWS Batch at AWS, Carlos Manzanedo Rueda, Principal Solutions Architect, EC2 Spot at AWS, Ludvig Nordstrom, Principal Solutions Architect at AWS, Vytautas Gapsys, project group leader at the Max Planck Institute for Biophysical Chemistry, and Carsten Kutzner, staff scientist at the Max Planck Institute for Biophysical Chemistry. Read more…

Multiverse Targets ‘Quantum Computing for the Masses’

January 19, 2022

The race to deliver quantum computing solutions that shield users from the underlying complexity of quantum computing is heating up quickly. One example is Multiverse Computing, a European company, which today launched the second financial services product in its Singularity product group. The new offering, Fair Price, “delivers a higher accuracy in fair price calculations for financial... Read more…

Meta’s Massive New AI Supercomputer Will Be ‘World’s Fastest’

January 24, 2022

Fresh off its rebrand last October, Meta (née Facebook) is putting muscle behind its vision of a metaversal future with a massive new AI supercomputer called t Read more…

Supercomputer Analysis Shows the Atmospheric Reach of the Tonga Eruption

January 21, 2022

On Saturday, an enormous eruption on the volcanic islands of Hunga Tonga and Hunga Haʻapai shook the Pacific Ocean. The explosion, which could be heard six tho Read more…

NSB Issues US State of Science and Engineering 2022 Report

January 20, 2022

This week the National Science Board released its biannual U.S. State of Science and Engineering 2022 report, as required by the NSF Act. Broadly, the report presents a near-term view of S&E based mostly on 2019 data. To a large extent, this year’s edition echoes trends from the last few reports. The U.S. is still a world leader in R&D spending and S&E education... Read more…

Multiverse Targets ‘Quantum Computing for the Masses’

January 19, 2022

The race to deliver quantum computing solutions that shield users from the underlying complexity of quantum computing is heating up quickly. One example is Multiverse Computing, a European company, which today launched the second financial services product in its Singularity product group. The new offering, Fair Price, “delivers a higher accuracy in fair price calculations for financial... Read more…

Students at SC21: Out in Front, Alongside and Behind the Scenes

January 19, 2022

The Supercomputing Conference (SC) is one of the biggest international conferences dedicated to high-performance computing, networking, storage and analysis. SC Read more…

Q-Ctrl – Tackling Quantum Hardware’s Noise Problems with Software

January 13, 2022

Implementing effective error mitigation and correction is a critical next step in advancing quantum computing. While a lot of attention has been given to effort Read more…

Nvidia Defends Arm Acquisition Deal: a ‘Once-in-a-Generation Opportunity’

January 13, 2022

GPU-maker Nvidia is continuing to try to keep its proposed acquisition of British chip IP vendor Arm Ltd. alive, despite continuing concerns from several governments around the world. In its latest action, Nvidia filed a 29-page response to the U.K. government to point out a list of potential benefits of the proposed $40 billion deal. Read more…

Nvidia Buys HPC Cluster Management Company Bright Computing

January 10, 2022

Graphics chip powerhouse Nvidia today announced that it has acquired HPC cluster management company Bright Computing for an undisclosed sum. Unlike Nvidia’s bid to purchase semiconductor IP company Arm, which has been stymied by regulatory challenges, the Bright deal is a straightforward acquisition that aims to expand... Read more…

IonQ Is First Quantum Startup to Go Public; Will It be First to Deliver Profits?

November 3, 2021

On October 1 of this year, IonQ became the first pure-play quantum computing start-up to go public. At this writing, the stock (NYSE: IONQ) was around $15 and its market capitalization was roughly $2.89 billion. Co-founder and chief scientist Chris Monroe says it was fun to have a few of the company’s roughly 100 employees travel to New York to ring the opening bell of the New York Stock... Read more…

US Closes in on Exascale: Frontier Installation Is Underway

September 29, 2021

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, held by Zoom this week (Sept. 29-30), it was revealed that the Frontier supercomputer is currently being installed at Oak Ridge National Laboratory in Oak Ridge, Tenn. The staff at the Oak Ridge Leadership... Read more…

AMD Launches Milan-X CPU with 3D V-Cache and Multichip Instinct MI200 GPU

November 8, 2021

At a virtual event this morning, AMD CEO Lisa Su unveiled the company’s latest and much-anticipated server products: the new Milan-X CPU, which leverages AMD’s new 3D V-Cache technology; and its new Instinct MI200 GPU, which provides up to 220 compute units across two Infinity Fabric-connected dies, delivering an astounding 47.9 peak double-precision teraflops. “We're in a high-performance computing megacycle, driven by the growing need to deploy additional compute performance... Read more…

Intel Reorgs HPC Group, Creates Two ‘Super Compute’ Groups

October 15, 2021

Following on changes made in June that moved Intel’s HPC unit out of the Data Platform Group and into the newly created Accelerated Computing Systems and Graphics (AXG) business unit, led by Raja Koduri, Intel is making further updates to the HPC group and announcing... Read more…

Nvidia Buys HPC Cluster Management Company Bright Computing

January 10, 2022

Graphics chip powerhouse Nvidia today announced that it has acquired HPC cluster management company Bright Computing for an undisclosed sum. Unlike Nvidia’s bid to purchase semiconductor IP company Arm, which has been stymied by regulatory challenges, the Bright deal is a straightforward acquisition that aims to expand... Read more…

D-Wave Embraces Gate-Based Quantum Computing; Charts Path Forward

October 21, 2021

Earlier this month D-Wave Systems, the quantum computing pioneer that has long championed quantum annealing-based quantum computing (and sometimes taken heat fo Read more…

Killer Instinct: AMD’s Multi-Chip MI200 GPU Readies for a Major Global Debut

October 21, 2021

AMD’s next-generation supercomputer GPU is on its way – and by all appearances, it’s about to make a name for itself. The AMD Radeon Instinct MI200 GPU (a successor to the MI100) will, over the next year, begin to power three massive systems on three continents: the United States’ exascale Frontier system; the European Union’s pre-exascale LUMI system; and Australia’s petascale Setonix system. Read more…

Three Chinese Exascale Systems Detailed at SC21: Two Operational and One Delayed

November 24, 2021

Details about two previously rumored Chinese exascale systems came to light during last week’s SC21 proceedings. Asked about these systems during the Top500 media briefing on Monday, Nov. 15, list author and co-founder Jack Dongarra indicated he was aware of some very impressive results, but withheld comment when asked directly if he had... Read more…

Leading Solution Providers

Contributors

Lessons from LLVM: An SC21 Fireside Chat with Chris Lattner

December 27, 2021

Today, the LLVM compiler infrastructure world is essentially inescapable in HPC. But back in the 2000 timeframe, LLVM (low level virtual machine) was just getting its start as a new way of thinking about how to overcome shortcomings in the Java Virtual Machine. At the time, Chris Lattner was a graduate student of... Read more…

2021 Gordon Bell Prize Goes to Exascale-Powered Quantum Supremacy Challenge

November 18, 2021

Today at the hybrid virtual/in-person SC21 conference, the organizers announced the winners of the 2021 ACM Gordon Bell Prize: a team of Chinese researchers leveraging the new exascale Sunway system to simulate quantum circuits. The Gordon Bell Prize, which comes with an award of $10,000 courtesy of HPC pioneer Gordon Bell, is awarded annually... Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

Nvidia Defends Arm Acquisition Deal: a ‘Once-in-a-Generation Opportunity’

January 13, 2022

GPU-maker Nvidia is continuing to try to keep its proposed acquisition of British chip IP vendor Arm Ltd. alive, despite continuing concerns from several governments around the world. In its latest action, Nvidia filed a 29-page response to the U.K. government to point out a list of potential benefits of the proposed $40 billion deal. Read more…

Top500: No Exascale, Fugaku Still Reigns, Polaris Debuts at #12

November 15, 2021

No exascale for you* -- at least, not within the High-Performance Linpack (HPL) territory of the latest Top500 list, issued today from the 33rd annual Supercomputing Conference (SC21), held in-person in St. Louis, Mo., and virtually, from Nov. 14–19. "We were hoping to have the first exascale system on this list but that didn’t happen," said Top500 co-author... Read more…

TACC Unveils Lonestar6 Supercomputer

November 1, 2021

The Texas Advanced Computing Center (TACC) is unveiling its latest supercomputer: Lonestar6, a three peak petaflops Dell system aimed at supporting researchers Read more…

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…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire