Petaflops help scientists understand why some COVID-19 variants are more contagious
(2023/02/23)
- Reference: 1677159607
- News link: https://www.theregister.co.uk/2023/02/23/petaflops_covid/
- Source link:
Supercomputer-power calculations have helped to uncover how certain variants of the COVID-19 virus "improve" – ie, become more contagious – through their binding energy with human cells.
A lab at Ohio’s University of Toledo has specialized in understanding molecular recognition, the process by which two molecules find each other, and bind together to act-out a biological function.
At the start of the pandemic, Xiche Hu, associate professor at the department of chemistry and biochemistry, thought the work might be well placed to help explain the way the nefarious virus spreads among humans.
[1]
Through a COVID-inspired scheme, he bid for resources from the [2]Ohio Supercomputer Center (OSC) to cut the time taken for calculation set to describe the coronavirus's binding processes. Collectively, OSC supercomputers provide a peak computing performance of 7.5 Petaflops. The center also offers approximately 16 petabytes of disk storage capacity distributed over several file systems, plus more than 14 PB of available backup tape storage.
[3]
[4]
“We immediately realized that there were many molecular recognition issues, so we felt duty-bound to study this,” Hu [5]said . “The Ohio Supercomputer Center (OSC) had called for researchers studying the coronavirus, offering a special grant. We applied and were granted priority access and an unlimited budget for 18 months.”
Joined by two doctoral students, Pawan Bhatta and Majed Aljohani, he began looking at differences between the original SARS-CoV-2 and new so-called variants of concern (VoC) at the atomic level. VoC are those strains which health orgs consider problematic because of their increased transmissibility, morbidity or mortality rates.
[6]
Using supercomputing resources, the team were able to perform high-level calculations at an accelerated rate.
“If we did one of these calculations in our lab, we are talking about weeks or months, but when we do it at OSC we can finish it within days,” Hu said.
[7]Foxconn expands Vietnam factories, perhaps to help Apple diversify beyond China
[8]Singapore pulls plug on COVID tracking program
[9]No, AI can't tell if you've got COVID-19 by listening to your coughs
[10]Corporate execs: Get back, get back, to the office where you once belonged
“We often need to do multiple calculations in parallel, so the OSC resources are instrumental to this research.”
The mission was to find the binding energy between COVID-19’s spike proteins and the human receptors within the cell, because higher binding energy means the virus becomes more contagious.
The results showed that four out of five variants studied exhibited a common mutation, N501Y, which increased the binding energy between parts of the human cell and the virus. Meanwhile, the mutation also helps the virus to create a network of water molecules that could increase infection rates.
[11]
The hope is the findings could help the scientists develop methods to fight the COVID-19 pandemic by “screening a library of compounds to find which molecules can block out the binding site, preventing infection,” Hu said. ®
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[7] https://www.theregister.com/2023/02/16/foxconn_expands_vietnam/
[8] https://www.theregister.com/2023/02/09/singapore_pulls_plug_on_covid/
[9] https://www.theregister.com/2023/01/05/ai_covid_cough/
[10] https://www.theregister.com/2022/12/16/return_to_office/
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[12] https://whitepapers.theregister.com/
A lab at Ohio’s University of Toledo has specialized in understanding molecular recognition, the process by which two molecules find each other, and bind together to act-out a biological function.
At the start of the pandemic, Xiche Hu, associate professor at the department of chemistry and biochemistry, thought the work might be well placed to help explain the way the nefarious virus spreads among humans.
[1]
Through a COVID-inspired scheme, he bid for resources from the [2]Ohio Supercomputer Center (OSC) to cut the time taken for calculation set to describe the coronavirus's binding processes. Collectively, OSC supercomputers provide a peak computing performance of 7.5 Petaflops. The center also offers approximately 16 petabytes of disk storage capacity distributed over several file systems, plus more than 14 PB of available backup tape storage.
[3]
[4]
“We immediately realized that there were many molecular recognition issues, so we felt duty-bound to study this,” Hu [5]said . “The Ohio Supercomputer Center (OSC) had called for researchers studying the coronavirus, offering a special grant. We applied and were granted priority access and an unlimited budget for 18 months.”
Joined by two doctoral students, Pawan Bhatta and Majed Aljohani, he began looking at differences between the original SARS-CoV-2 and new so-called variants of concern (VoC) at the atomic level. VoC are those strains which health orgs consider problematic because of their increased transmissibility, morbidity or mortality rates.
[6]
Using supercomputing resources, the team were able to perform high-level calculations at an accelerated rate.
“If we did one of these calculations in our lab, we are talking about weeks or months, but when we do it at OSC we can finish it within days,” Hu said.
[7]Foxconn expands Vietnam factories, perhaps to help Apple diversify beyond China
[8]Singapore pulls plug on COVID tracking program
[9]No, AI can't tell if you've got COVID-19 by listening to your coughs
[10]Corporate execs: Get back, get back, to the office where you once belonged
“We often need to do multiple calculations in parallel, so the OSC resources are instrumental to this research.”
The mission was to find the binding energy between COVID-19’s spike proteins and the human receptors within the cell, because higher binding energy means the virus becomes more contagious.
The results showed that four out of five variants studied exhibited a common mutation, N501Y, which increased the binding energy between parts of the human cell and the virus. Meanwhile, the mutation also helps the virus to create a network of water molecules that could increase infection rates.
[11]
The hope is the findings could help the scientists develop methods to fight the COVID-19 pandemic by “screening a library of compounds to find which molecules can block out the binding site, preventing infection,” Hu said. ®
Get our [12]Tech Resources
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[2] https://www.osc.edu/
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[7] https://www.theregister.com/2023/02/16/foxconn_expands_vietnam/
[8] https://www.theregister.com/2023/02/09/singapore_pulls_plug_on_covid/
[9] https://www.theregister.com/2023/01/05/ai_covid_cough/
[10] https://www.theregister.com/2022/12/16/return_to_office/
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[12] https://whitepapers.theregister.com/
Re: Two sides of the coin
Charlie Clark
This kind of processing is not really suitable for molecular design; the idea is to help develop a kind of early warning system. Other systems for this have already been developed and tools like CRISPR-CAS9 are already being used to make them.
Re: Two sides of the coin
b0llchit
It is not the the genetic structure that you optimize with calculation nor do you use it to splice and construct. It is its effect of the genetics on the molecules you want to look at. And that can be calculated using proposed and used methods from this research.
From energetic optimization of the molecule you can conclude which genetic makeup you must construct. Then you use that to create the strand and CRISPR-CAS9 to implant it into a new virus.
Re: Two sides of the coin
Throatwarbler Mangrove
That's science for you; almost every discovery can be used for beneficial purposes or harmful ones, as illustrated by this ancient parable:
"Build a man a fire, and you keep him warm for a night. Set a man on fire, and you keep him warm for the rest of his life."
Two sides of the coin
It is nice to see how biology can be explained by the molecular interactions when enough calculation power is committed. It surely has good uses.
However, the other side is that it also opens up for creating specific molecules to do one's bidding. This is biological warfare at a whole new level.
The problem is that the undesirable side of this work will be done in hiding and will haunt us sooner or later. And that is regardless the treaties about banning biological warfare.