Supercomputers Enable First Holistic Model of SARS-CoV-2, Showing Spike Proteins Move in Tandem

By Oliver Peckham

February 28, 2021

Most models of SARS-CoV-2, the coronavirus that causes COVID-19, hone in on key features of the virus: for instance, the spike protein. Some of this is attributable to the relative importance of those features, but most is attributable to computational necessity – simulating even a single protein in such excruciating resolution is extraordinarily computation-intensive. Now, researchers from the University of Chicago and the University of California, San Diego have developed the first complete model of the coronavirus, finding, among other things, that its spike proteins move cooperatively.

An animation of the entire SARS-CoV-2 virus. Image courtesy of Gregory Voth.

“We wanted to understand how SARS-CoV-2 works holistically as a whole particle,” said Gregory Voth, a professor of chemistry at the University of Chicago and corresponding author of the study, in an interview with Jorge Salazar of the Texas Advanced Computing Center (TACC). “We developed a bottom-up coarse-grained model where we took information from atomistic-level molecular dynamics simulations and from experiments.”

Voth and his colleagues have been using the coarse-grained modeling method, which resolves groups of atoms rather than each individual atom, to study viruses like HIV and the flu for decades. “The benefit of the coarse-grained model is that it can be hundreds to thousands of times more computationally efficient than the all-atom model,” he said. “What you’re left with are the much slower, collective motions. The effects of the higher frequency, all-atom motions are folded into those interactions if you do it well. That’s the idea of systematic coarse-graining.”

From left to right: the spike protein trimer, pentameric envelope protein, membrane dimer protein and nucleocapsid protein. Image courtesy of Gregory Voth.

Using the coarse-graining method, the team simplified and combined atomistic models of SARS-CoV-2’s spike, membrane, nucleocapsid and envelope proteins. Some of these all-atom models were generated by the Amaro Lab (led by Gordon Bell Special Prize winner Rommie Amaro) using the 23.5 Linpack petaflops Frontera supercomputer at TACC, and the remaining models were generated on the Anton 2 system at the Pittsburgh Supercomputing Center (PSC). 

“Frontera and Anton 2 provided the key molecular level input data into this model,” Voth said. “Frontera has been especially useful in providing the molecular dynamics data at the atomistic level for feeding into this model. It’s very valuable.”

The supercomputer-powered coarse-grained model showed some interesting behavior: the virus’ spike proteins, which litter its surface and allow it to infect human cells, move cooperatively. 

“They don’t move independently like a bunch of random, uncorrelated motions. They work together,” Voth said. “The paper we published shows the beginnings of how the modes of motion in the spike proteins are correlated. … The ultimate goal of the model would be, as a first step, to study the initial virion attractions and interactions with ACE2 receptors on cells and to understand the origins of that attraction and how those proteins work together to go on to the virus fusion process.”

To learn more about this research, read the paper here and read the article by TACC’s Jorge Salazar 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!

2022 Road Trip: NASA Ames Takes Off

November 25, 2022

I left Dallas very early Friday morning after the conclusion of SC22. I had a race with the devil to get from Dallas to Mountain View, Calif., by Sunday. According to Google Maps, this 1,957 mile jaunt would be the longe Read more…

2022 Road Trip: Sandia Brain Trust Sounds Off

November 24, 2022

As the 2022 Great American Supercomputing Road Trip carries on, it’s Sandia’s turn. It was a bright sunny day when I rolled into Albuquerque after a high-speed run from Los Alamos National Laboratory. My interview su Read more…

2022 HPC Road Trip: Los Alamos

November 23, 2022

With SC22 in the rearview mirror, it’s time to get back to the 2022 Great American Supercomputing Road Trip. To refresh everyone’s memory, I jumped in the car on November 3rd and headed towards SC22 in Dallas, stoppi Read more…

Chipmakers Looking at New Architecture to Drive Computing Ahead

November 23, 2022

The ability to scale current computing designs is reaching a breaking point, and chipmakers such as Intel, Qualcomm and AMD are putting their brains together on an alternate architecture to push computing forward. The chipmakers are coalescing around the new concept of sparse computing, which involves bringing computing to data... Read more…

QuEra’s Quest: Build a Flexible Neutral Atom-based Quantum Computer

November 23, 2022

Last month, QuEra Computing began providing access to its 256-qubit, neutral atom-based quantum system, Aquila, from Amazon Braket. Founded in 2018, and built on technology developed at Harvard and MIT, QuEra, is one of Read more…

AWS Solution Channel

Shutterstock 1648511269

Avoid overspending with AWS Batch using a serverless cost guardian monitoring architecture

Pay-as-you-go resources are a compelling but daunting concept for budget conscious research customers. Uncertainty of cloud costs is a barrier-to-entry for most, and having near real-time cost visibility is critical. Read more…

 

shutterstock_1431394361

AI and the need for purpose-built cloud infrastructure

Modern AI solutions augment human understanding, preferences, intent, and even spoken language. AI improves our knowledge and understanding by delivering faster, more informed insights that fuel transformation beyond anything previously imagined. Read more…

SC22’s ‘HPC Accelerates’ Plenary Stresses Need for Collaboration

November 21, 2022

Every year, SC has a theme. For SC22 – held last week in Dallas – it was “HPC Accelerates”: a theme that conference chair Candace Culhane said reflected “how supercomputing is continuously changing the world by Read more…

Chipmakers Looking at New Architecture to Drive Computing Ahead

November 23, 2022

The ability to scale current computing designs is reaching a breaking point, and chipmakers such as Intel, Qualcomm and AMD are putting their brains together on an alternate architecture to push computing forward. The chipmakers are coalescing around the new concept of sparse computing, which involves bringing computing to data... Read more…

QuEra’s Quest: Build a Flexible Neutral Atom-based Quantum Computer

November 23, 2022

Last month, QuEra Computing began providing access to its 256-qubit, neutral atom-based quantum system, Aquila, from Amazon Braket. Founded in 2018, and built o Read more…

SC22’s ‘HPC Accelerates’ Plenary Stresses Need for Collaboration

November 21, 2022

Every year, SC has a theme. For SC22 – held last week in Dallas – it was “HPC Accelerates”: a theme that conference chair Candace Culhane said reflected Read more…

Quantum – Are We There (or Close) Yet? No, Says the Panel

November 19, 2022

For all of its politeness, a fascinating panel on the last day of SC22 – Quantum Computing: A Future for HPC Acceleration? – mostly served to illustrate the Read more…

RISC-V Is Far from Being an Alternative to x86 and Arm in HPC

November 18, 2022

One of the original RISC-V designers this week boldly predicted that the open architecture will surpass rival chip architectures in performance. "The prediction is two or three years we'll be surpassing your architectures and available performance with... Read more…

Gordon Bell Special Prize Goes to LLM-Based Covid Variant Prediction

November 17, 2022

For three years running, ACM has awarded not only its long-standing Gordon Bell Prize (read more about this year’s winner here!) but also its Gordon Bell Spec Read more…

2022 Gordon Bell Prize Goes to Plasma Accelerator Research

November 17, 2022

At the awards ceremony at SC22 in Dallas today, ACM awarded the 2022 ACM Gordon Bell Prize to a team of researchers who used four major supercomputers – inclu Read more…

Gordon Bell Nominee Used LLMs, HPC, Cerebras CS-2 to Predict Covid Variants

November 17, 2022

Large language models (LLMs) have taken the tech world by storm over the past couple of years, dominating headlines with their ability to generate convincing hu Read more…

Nvidia Shuts Out RISC-V Software Support for GPUs 

September 23, 2022

Nvidia is not interested in bringing software support to its GPUs for the RISC-V architecture despite being an early adopter of the open-source technology in its GPU controllers. Nvidia has no plans to add RISC-V support for CUDA, which is the proprietary GPU software platform, a company representative... Read more…

RISC-V Is Far from Being an Alternative to x86 and Arm in HPC

November 18, 2022

One of the original RISC-V designers this week boldly predicted that the open architecture will surpass rival chip architectures in performance. "The prediction is two or three years we'll be surpassing your architectures and available performance with... Read more…

AWS Takes the Short and Long View of Quantum Computing

August 30, 2022

It is perhaps not surprising that the big cloud providers – a poor term really – have jumped into quantum computing. Amazon, Microsoft Azure, Google, and th Read more…

Chinese Startup Biren Details BR100 GPU

August 22, 2022

Amid the high-performance GPU turf tussle between AMD and Nvidia (and soon, Intel), a new, China-based player is emerging: Biren Technology, founded in 2019 and headquartered in Shanghai. At Hot Chips 34, Biren co-founder and president Lingjie Xu and Biren CTO Mike Hong took the (virtual) stage to detail the company’s inaugural product: the Biren BR100 general-purpose GPU (GPGPU). “It is my honor to present... Read more…

Tesla Bulks Up Its GPU-Powered AI Super – Is Dojo Next?

August 16, 2022

Tesla has revealed that its biggest in-house AI supercomputer – which we wrote about last year – now has a total of 7,360 A100 GPUs, a nearly 28 percent uplift from its previous total of 5,760 GPUs. That’s enough GPU oomph for a top seven spot on the Top500, although the tech company best known for its electric vehicles has not publicly benchmarked the system. If it had, it would... Read more…

AMD Thrives in Servers amid Intel Restructuring, Layoffs

November 12, 2022

Chipmakers regularly indulge in a game of brinkmanship, with an example being Intel and AMD trying to upstage one another with server chip launches this week. But each of those companies are in different positions, with AMD playing its traditional role of a scrappy underdog trying to unseat the behemoth Intel... Read more…

JPMorgan Chase Bets Big on Quantum Computing

October 12, 2022

Most talk about quantum computing today, at least in HPC circles, focuses on advancing technology and the hurdles that remain. There are plenty of the latter. F Read more…

UCIe Consortium Incorporates, Nvidia and Alibaba Round Out Board

August 2, 2022

The Universal Chiplet Interconnect Express (UCIe) consortium is moving ahead with its effort to standardize a universal interconnect at the package level. The c Read more…

Leading Solution Providers

Contributors

Using Exascale Supercomputers to Make Clean Fusion Energy Possible

September 2, 2022

Fusion, the nuclear reaction that powers the Sun and the stars, has incredible potential as a source of safe, carbon-free and essentially limitless energy. But Read more…

Nvidia, Qualcomm Shine in MLPerf Inference; Intel’s Sapphire Rapids Makes an Appearance.

September 8, 2022

The steady maturation of MLCommons/MLPerf as an AI benchmarking tool was apparent in today’s release of MLPerf v2.1 Inference results. Twenty-one organization Read more…

Not Just Cash for Chips – The New Chips and Science Act Boosts NSF, DOE, NIST

August 3, 2022

After two-plus years of contentious debate, several different names, and final passage by the House (243-187) and Senate (64-33) last week, the Chips and Science Act will soon become law. Besides the $54.2 billion provided to boost US-based chip manufacturing, the act reshapes US science policy in meaningful ways. NSF’s proposed budget... Read more…

SC22 Unveils ACM Gordon Bell Prize Finalists

August 12, 2022

Courtesy of the schedule for the SC22 conference, we now have our first glimpse at the finalists for this year’s coveted Gordon Bell Prize. The Gordon Bell Pr Read more…

Intel Is Opening up Its Chip Factories to Academia

October 6, 2022

Intel is opening up its fabs for academic institutions so researchers can get their hands on physical versions of its chips, with the end goal of boosting semic Read more…

AMD Previews 400 Gig Adaptive SmartNIC SOC at Hot Chips

August 24, 2022

Fresh from finalizing its acquisitions of FPGA provider Xilinx (Feb. 2022) and DPU provider Pensando (May 2022) ), AMD previewed what it calls a 400 Gig Adaptive smartNIC SOC yesterday at Hot Chips. It is another contender in the increasingly crowded and blurry smartNIC/DPU space where distinguishing between the two isn’t always easy. The motivation for these device types... Read more…

Google Program to Free Chips Boosts University Semiconductor Design

August 11, 2022

A Google-led program to design and manufacture chips for free is becoming popular among researchers and computer enthusiasts. The search giant's open silicon program is providing the tools for anyone to design chips, which then get manufactured. Google foots the entire bill, from a chip's conception to delivery of the final product in a user's hand. Google's... Read more…

AMD’s Genoa CPUs Offer Up to 96 5nm Cores Across 12 Chiplets

November 10, 2022

AMD’s fourth-generation Epyc processor line has arrived, starting with the “general-purpose” architecture, called “Genoa,” the successor to third-gen Eypc Milan, which debuted in March of last year. At a launch event held today in San Francisco, AMD announced the general availability of the latest Epyc CPUs with up to 96 TSMC 5nm Zen 4 cores... Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire