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World's Most Powerful Supercomputer Fights Coronavirus

(Image credit: HPC Wire)

Just a few days ago we asked you to contribute your PC's leftover horsepower to help fight the Coronavirus, and while every bit matters, it looks like the Arnold Schwarzenegger of supercomputers is joining the fight: The Oak Ridge National Laboratory (ORNL) just announced that it's bringing in the big guns, tasking Summit with accelerating the process of finding a protein that can bind to the spikes found on the Coronavirus, as reported by HPC Wire. Blocking these spikes would stop the virus from being able to infect lung cells.

Summit employs 220,800 CPU cores, 188,416,000 CUDA cores, 9.2PB of memory, and 250PB of mixed NVRAM/storage for the task. 

“Summit was needed to rapidly get the simulation results we needed. It took us a day or two whereas it would have taken months on a normal computer,” said Jeremy Smith, director of UT/ORNL CMB. “Our results don’t mean that we have found a cure or treatment for the Wuhan coronavirus. We are very hopeful, though, that our computational findings will both inform future studies and provide a framework that experimentalists will use to further investigate these compounds. Only then will we know whether any of them exhibit the characteristics needed to mitigate this virus.” 

(Image credit: Oak Ridge National Laboratory)

The Summit supercomputer is built by IBM, and currently holds the number one place as the most powerful (publicly ranked) supercomputer in the world. It packs a total of 4,608 nodes, each containing two IBM Power9 CPUs and Six Nvidia Volta GV100 GPUs. For a full technical overview of Summit, you can check out our cheat sheet here.

What's The Science Behind Protein Simulations?

The 2019-nCoV has proteins on its surface called spikes, which trick the ACE2 lung cell surface receptor into letting the virus into the cell and starting a viral infection. One way to stop infection is to find a way to block this protein that resides on the virus, preventing the virus from binding to our cells, and thus rendering it unable to establish an infection. Blocking this protein can be accomplished by binding another protein onto it. 

However, proteins can come in an unimaginable amount of shapes, and it will take a very specific protein to bind to the 2019-nCov's spikes. 

Thus far, researcher Micholas Smith from the University of Tennessee and ORNL, has used earlier studies to sequence the virus and a virtual model of the Spike protein on the virus. “We were able to design a thorough computational model based on information that has only recently been published in the literature on this virus,” said Micholas Smith.

Using Summit, Smith and his colleagues are simulating the behavior of over 8000 different protein compounds and their ability to bind to the spikes, however, this takes a lot of computer power. Whereas on a powerful computer this process could take months, Summit is able to complete the simulations in mere days. 

Up until now, Smith has found 77 different small-molecule drug compounds that are worth further study. 

"Using Summit, we ranked these compounds based on a set of criteria related to how likely they were to bind to the S-protein spike,” Smith explained.

Eventually, once a protein is found that can bind to the 2019-nCov's spikes with a high success rate, it can be synthesized into a vaccine.

  • Integr8d
    Coronavirus is way closer to a cold than it is to the flu (which kills vastly more people every year). It's nothing more than media-driven hysteria. You can take off your masks now and breathe the air. If you get a small chest cough, it'll be gone in a week.
    Reply
  • mwestall
    Do stop talking uninformed nonsense. Flu kills 0.1% of those who catch it, so far covid 19 has a mortality of 3%, that's 30 times greater. It's nothing like a cold.
    Reply
  • Deicidium369
    Well not hard to figure out who you support and what "news" outlets you read.
    Reply
  • Deicidium369
    mwestall said:
    Do stop talking uninformed nonsense. Flu kills 0.1% of those who catch it, so far covid 19 has a mortality of 3%, that's 30 times greater. It's nothing like a cold.
    South Korea has revised that 3% down to like 0.65% mortality. The 3% was that high because the people who died from COVID was from a small sample of people who tested positive.
    Reply
  • spongiemaster
    Deicidium369 said:
    Well not hard to figure out who you support and what "news" outlets you read.
    John Hopkins? What agenda do they have in this?

    Reply
  • Zizo007
    No reason to panic unless you live in China or work there. Ebola was far worst with 60% death rate. Just wash your hands and food more often. I personally stopped eating asian food to avoid corona virus.
    Reply
  • 13thmonkey
    Zizo007 said:
    No reason to panic unless you live in China or work there. Ebola was far worst with 60% death rate. Just wash your hands and food more often. I personally stopped eating asian food to avoid corona virus.
    You somehow think its food borne? or that Chinese people where you live have some kind of connection with the Chinese general population that means that disease flows between them no matter how far apart they are, kind of like entanglement?
    Reply
  • derekullo
    Zizo007 said:
    No reason to panic unless you live in China or work there. Ebola was far worst with 60% death rate. Just wash your hands and food more often. I personally stopped eating asian food to avoid corona virus.
    According to the graph to be completely safe you should also avoid food that originated or passed through the United States, Italy, Iran, France, Japan, Spain, UK, Netherlands, South Korea and Switzerland.
    Reply
  • Mandark
    Coronavirus is completely over blown the flu kills more people what a waste of computing resources

    https://weather.com/health/cold-flu/news/2020-01-28-flu-more-deadly-than-coronavirus
    Reply
  • Zizo007
    13thmonkey said:
    You somehow think its food borne? or that Chinese people where you live have some kind of connection with the Chinese general population that means that disease flows between them no matter how far apart they are, kind of like entanglement?
    If they visit China to see family or work they have a chance of getting infected but now idk if they test people going out of China and if the receiving country test passengers. Here in QC Canada we only have 1 confirmed case where an Iranian passenger wasn't tested until she got to several clinics with corona virus symptoms. I miss sushis so much, I haven't eaten sushis since last year before the corona virus outbreak. I was with some of my friends and they kicked us out of the all-you-can-eat sushi buffet because we ate more than 300 sushis lol
    Reply