From Summit to [email protected], global supercomputing is continuing to mobilize against the coronavirus pandemic by crunching massive problems like epidemiology, therapeutic development and vaccine development. The latest addition to the arsenal is a supercomputer at the Joint Supercomputer Center of the Russian Academy of Sciences (RAS), which is working to develop drugs to fight against COVID-19.
“Rapid global spread of COVID-19 coronavirus infection pandemic has shown that there are no clear global emergency response plans against threats to humankind caused by new viruses,” said Anna Kichkailo, head of the Laboratory for Digital Controlled Drugs and Theranostics at RAS’ Krasnoyarsk Federal Science Center and head of the Laboratory for Biomolecular and Medical Technology at V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University. “One of the obvious shortcomings is the lack of technologies for quick development of medicines for diagnostics and therapy.”
To help bridge this gap, RAS employed its MVS-10P cluster supercomputer. MVS-10P (which was manufactured by Russian supercomputing firm RSC Group) comprises 208 nodes, each equipped with dual Intel Xeon E5-2690 CPUs and dual Intel Xeon Phi SE10X coprocessors, and contains an aggregate 13.2 TB of memory. Overall, MVS-10P delivers 375.7 Linpack teraflops. According to RAS, a recent upgrade at the end of 2019 raised its peak performance from 524 teraflops to 771 teraflops.
MVS-10P was put in the hands of an international research team consisting of scientists from a dozen institutions across Russia, Finland, Italy, China, Japan and Canada. “We all have different competences, knowledge, skills and resources,” Kichkailo explained. “Our geographically distributed team includes virologists, biologists, chemists, mathematicians and physical scientists. The international cooperation is extremely important to achieve quick progress and rapidly react to the ever-changing situation with global COVID-19 pandemic.”
The research team is studying COVID-19’s notorious “spike” protein that is widely considered the key to the virus’ ability to infect humans – and thus, the key to disabling it. Massive molecular dynamics and quantum chemistry simulations run on MVS-10P are examining interactions between the spike protein and the human protein ACE2, which serves as the entry point for SARS-class viruses. The researchers are hoping to use the results of these simulations to design aptamers (molecules that bind to specific target molecules) that would be more attractive binding targets for COVID-19 than ACE2. Then, the research team will refine the aptamers with further supercomputer simulations.
“We hope that our research will actually help to fight spread of such infections,” Kichkailo concluded.