Manufacturing Bits: March 9

Finding cures for coronavirus
The Department of Energy’s Oak Ridge National Laboratory (ORNL) is using the world’s most powerful supercomputer to identify drug compounds and cures for the coronavirus.

Summit supercomputer. Source: Oak Ridge National Laboratory

The supercomputer, called Summit, has identified 77 small-molecule drug compounds that might warrant further study in order to battle the COVID-19 disease outbreak. To date, though, there is no vaccine treatment for COVID-19.
The IBM-built Summit supercomputer consists of 4,608 IBM Power Systems AC922 server nodes. Each node is equipped with two IBM POWER9 CPUs and six Nvidia Tensorcore V100 GPUs, giving it a peak performance of 200 petaflops, making it more powerful than one million high-end laptops.

Not long ago, the coronavirus appeared in China and then it spread to other nations. Soon after that, the Wuhan Institute of Virology sequenced the genome of the coronavirus. Researchers discovered that the coronavirus had a 79.6% sequence identity and the same mechanisms as Severe Acute Respiratory Syndrome (SARS).

In 2003, SARS hit China and Hong Kong, creating such panic that no one would touch crates on shipping docks. Ultimately, it erased an estimated $40 billion from the global economy and effectively shut down the Chinese semiconductor industry for several months.

With the coronavirus, meanwhile, researchers are trying to determine the root cause of the virus. A virus can infect cells by binding to them, according to IBM. Viruses use a spike to inject their genetic material into the host cell, according to IBM.

“2019-nCoV makes use of a densely glycosylated spike (S) protein to gain entry into host cells. The S protein is a trimeric class I fusion protein that exists in a metastable prefusion conformation that undergoes a dramatic structural rearrangement to fuse the viral membrane with the host-cell membrane. This process is triggered when the S1 subunit binds to a host-cell receptor,” said Daniel Wrapp and others from The University of Texas at Austin in Science, a technology journal. The National Institute of Allergy and Infectious Diseases also contributed to the report.

Needless to say, the goal is to look for compounds that “are most likely to bind to the main ‘spike’ protein of the coronavirus, rendering it unable to infect host cells, according to ORNL.

Using Summit, researchers from ORNL performed simulations on more than 8,000 compounds. They found 77 small-molecule compounds, such as medications and natural compounds, that may be of value.

“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 C. Smith, Governor’s Chair at the University of Tennessee and director of the UT/ORNL Center for Molecular Biophysics. “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.”

Nanoparticles
A group of scientists are exploring different ways to battle the COVID-19 outbreak, including the use of nanoparticles.

The virus behind COVID-19 consists of a tiny structures or nanoparticles. Researchers are exploring the use of tiny nanoparticles that could attach to the virus. This in turn could disrupt their structure with a combination of infrared light.

That structural change would halt the ability of the virus to survive. The virus would also not reproduce in the body, according to Northeastern University.

Researchers are using what they call theranostics to solve the problem. “You have to think in this size range,” said Thomas Webster, Art Zafiropoulo Chair of chemical engineering at Northeastern. “In the nanoscale size range, if you want to detect viruses, if you want to deactivate them. It’s not just having one approach to detect whether you have a virus and another approach to use it as a therapy, but having the same particle (and) the same approach for both your detection and therapy.”

Researchers are contributing these ideas to the Centers for Disease Control and Prevention.

Disease models
Separately, Northeastern University has also demonstrated how the models currently used to predict social trends can also forecast the spread of contagious diseases. Find the report here.