Russian Supercomputer and Three Chinese Universities Join the Good Hope Net Project to Combat Coronavirus

May 28, 2020

MOSCOW, Russia and HUNAN, Shanghai, Xiamen (China), May 28, 2020 — The China’s Hunan University, Shanghai Jiao Tong University and Xiamen University have joined an international science group named The Good Hope Net. The scientists from Russia, Finland, Italy, Canada and China have a high priority access to RSC Tornado supercomputer deployed at Joint Supercomputing Center of Russian Academy of Sciences (JSCC RAS) for studying methods to fight against the COVID-19 coronavirus infection. This project aims to develop medicine for diagnostics and therapy against the coronavirus contagious disease that became the cause of the global pandemic.

Image courtesy of RSC Group.

The Good Hope Net team uses a recently upgraded cluster system based on 2nd Generation Intel Xeon Scalable processors, which has been deployed by RSC Group, the leading Russian and worldwide well known solution provider for high-performance computing and data storage-on-demand.

The coronavirus pandemic in 2020 threatens lives of many people and hinders economic and social activity in multiple countries all over the world. As a result, it attracted significant attention of many research groups. Finding treatments to prevent and mitigate the negative impact of COVID-19 is the highest priority in the worldwide scientific community now. The international and multidisciplinary The Good Hope Net project takes advantages of the latest advances in experimental physics, chemistry, and biology to investigate the life cycle of the virus and to target specifically its specific proteins.

Sophisticated simulation methods require supercomputing power to study all details of the interaction between the Spike-protein on coronavirus surface and the human protein ACE2 which is known to be the entry point for SARS and SARS-2 coronaviruses. It will help to complete all research stages within a limited amount of time.

International project to fight the global pandemic

“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. One of the obvious shortcomings is the lack of technologies for quick development of medicines for diagnostics and therapy. To help solving this problem, an international team of scientists – from Russia, Finland, Italy and Canada – was formed. We all have different competences, knowledge, skills and resources. 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. We hope that our research will actually help to fight spread of such infections,” explains Anna Kichkailo, Head of Laboratory For Digital Controlled Drugs and Theranostics at the Krasnoyarsk Federal Science Center of RAS, Head of the Laboratory for Biomolecular and Medical Technology of the V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University.

The Good Hope Net project team consists of:

  • Laboratory for Digital Controlled Drugs and Theranostics and Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics at the Federal Science Center, Siberian Branch of Russian Academy of Sciences (KIP FSC SB RAS, Krasnoyarsk, Russia),
  • Laboratory for Biomolecular and Medical Technology, V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University (KSMU, Krasnoyarsk, Russia) – project coordinator,
  • Laboratory of Chemical Cybernetics, Department of Chemistry at Lomonosov Moscow State University (MSU, Moscow, Russia),
  • Laboratory for Computer Simulation of Biomolecular Systems and Nanomaterials at N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences (IBCP RAS, Moscow, Russia),
  • Organic Synthesis Laboratory, Institute of Chemical Biology and Fundamental Medical Science, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS, Novosibirsk, Russia),
  • Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä (Finland),
  • Institute for Experimental Endocrinology and Oncology (IEOS), part of National Research Council (CNR), Naples (Italy),
  • Department of Molecular Medicine and Medical Biotechnologies, Department of Pharmacy, Federico II University of Naples (Italy),
  • The Bioanalytical and Molecular Interaction Laboratory, Department of Chemistry and Biomolecular Sciences, University of Ottawa (Canada),
  • The Molecular Science and Biomedicine Laboratory, Hunan University (China),
  • School of Medicine, Institute of Molecular Medicine, Shanghai Jiao Tong University (China),
  • Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian (China).

Computer design of medicine against COVID-19

“We aim to use molecular simulation to create a computer model of a medical drug with selective interaction with receptor-binding domain of Spike protein of SARS-CoV-2 coronavirus strain. The most promising specific binding agents to be used for diagnostics (identification of virus particles in saliva) and development of virus treatment drugs preventing ingress of infection. The results of theoretical calculations and computer simulation will be experimentally tested on proteins, viruses and cells,” summarizes Anna Kichkailo.

Image courtesy of RSC Group.

Supercomputer simulations are used to study details of interaction between Spikeprotein on coronavirus surface and the human protein ACE2 (angiotensin converting enzyme 2). ACE2 is known to be the entry point for SARS and SARS-2 coronaviruses. By blocking its interaction with the spike protein, it is possible to reduce virus activity in human body. Massive molecular dynamics and quantum chemistry calculations of virus and human proteins are using to estimate protein binding energies. The results of simulations will be used to design aptamers that will bind with virus proteins better than ACE2. Molecular docking and molecular dynamics methods will be used to create a library of promising aptamers and to estimate the strength of their interaction with virus proteins. Binding energies for the most promising aptamers will be refined with quantumchemistry methods. A lot of supercomputing resources is required to complete all these research stages within limited amount of time.

The need for supercomputers

Developing drugs to mitigate the disease and reduce the risk of the severe complications is one of the most important tasks before coronavirus vaccine will be widely adopted. Computer simulations deliver valuable information on the viral activity on atomic level and they can be used to predict the efficiency of potential drugs. Such calculations are extremely demanding and can be done only with the most powerful supercomputers.

HPC systems are widely used in simulations of biochemical processes. The simulations help to reduce the number of experiments that would otherwise be needed to get same results. Leading global pharmaceutical and research centers use molecular modeling at the initial steps of drug development, when a massive number of chemical substances have to be investigated for specific activity.

Experimental data about the coronavirus activity on molecular level is very limited and have been produced in vitro. For example, the viral protein structure corresponds tothe crystallized protein and not to a virus in solution. Moreover, there is not enough experimental data on complexes between virus and human proteins or virus proteins and potential drugs. On the other hand, supercomputer calculations can give all the structural data and the details of binding process. Therefore, the computing part is critically important, as well as subsequent experimental verification.

Upgraded MVS-10P OP supercomputer at JSCC RAS

The Joint Supercomputer Center of the Russian Academy of Sciences is one of the most powerful Russian supercomputing centers in the fields of science and education. JSCC RAS staff includes qualified scientists, programmers and engineers. Over 150 groups of researches use JSCC resources for fundamental and applied research tasks. Total peak performance of JSCC RAS computing facilities exceeds 1.3 Petaflops (petaflops – quadrillion of floating-point operations per second, or 1000 teraflops). Five JSCC RAS cluster systems are included in the Top50 list of the most powerful Russian supercomputers.

After the recent upgrade of MVS-10P OP at the end of 2019 completed by the Ministry of Science and Highest Education of the Russian Federation, its peak performance reached 771 Teraflops (teraflops – trillion of floating-point operations per second). Adding a new segment based on the modern high-performance 2nd Generation Intel Xeon Scalable processors allowed to achieve the significant performance increase of y 209 Teraflops. MVS-10P OP is based on RSC Tornado, an universal ultrahigh-dense and energy efficient platform developed by RSC Group (Russia).

“By regularly upgrading JSCC RAS computing resources we get new R&D opportunities, provide RAS and academic researches with powerful resources for various complex fundamental and applied tasks and improve overall efficiency of Russian scientists,” said Gennady Savin, Academician of RAS and Science Head of the Joint Supercomputer Center of the Russian Academy of Sciences.

Researchers access resources of JSCC RAS using the National Research Network (NICS) of the Ministry of Science and Highest Education of the Russian Federation.


Source: RSC Group 

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!

What’s New in Computing vs. COVID-19: SC20 Edition

November 30, 2020

Supercomputing, big data and artificial intelligence are crucial tools in the fight against the coronavirus pandemic. Around the world, researchers, corporations and governments are urgently devoting their computing reso Read more…

By Oliver Peckham

GENCI Supercomputer Simulation Illuminates the Dark Universe

November 30, 2020

What we can see and touch are, in the scheme of the universe, relatively minor components, with visible matter and tangible mass constituting just 16 percent of the universe’s mass and 30 percent of its energy, respect Read more…

By Oliver Peckham

The Present and Future of AI: A Discussion with HPC Visionary Dr. Eng Lim Goh

November 27, 2020

As HPE’s chief technology officer for artificial intelligence, Dr. Eng Lim Goh devotes much of his time talking and consulting with enterprise customers about how AI can benefit their business operations and products. Read more…

By Todd R. Weiss

SC20 Panel – OK, You Hate Storage Tiering. What’s Next Then?

November 25, 2020

Tiering in HPC storage has a bad rep. No one likes it. It complicates things and slows I/O. At least one storage technology newcomer – VAST Data – advocates dumping the whole idea. One large-scale user, NERSC storage architect Glenn Lockwood sort of agrees. The challenge, of course, is that tiering... Read more…

By John Russell

Exscalate4CoV Runs 70 Billion-Molecule Coronavirus Simulation

November 25, 2020

The winds of the pandemic are changing – for better and for worse. Three viable vaccines now teeter on the brink of regulatory approval, which will pave the way for broad distribution by April or May. But until then, COVID-19 cases are skyrocketing across the U.S. and Europe... Read more…

By Oliver Peckham

AWS Solution Channel

Add storage to your high-performance file system with a single click and meet your scalability needs

Many organizations have on-premises, high-performance workloads burdened with complex management and scalability challenges. Scaling data-intensive workloads on-premises typically involves purchasing more hardware, which can slow time to production and require high upfront investment. Read more…

Intel® HPC + AI Pavilion

Intel Keynote Address

Intel is the foundation of HPC – from the workstation to the cloud to the backbone of the Top500. At SC20, Intel’s Trish Damkroger, VP and GM of high performance computing, addresses the audience to show how Intel and its partners are building the future of HPC today, through hardware and software technologies that accelerate the broad deployment of advanced HPC systems. Read more…

Azure Scaled to Record 86,400 Cores for Molecular Dynamics

November 20, 2020

A new record for HPC scaling on the public cloud has been achieved on Microsoft Azure. Led by Dr. Jer-Ming Chia, the cloud provider partnered with the Beckman Institute for Advanced Science and Technology at the Universi Read more…

By Oliver Peckham

The Present and Future of AI: A Discussion with HPC Visionary Dr. Eng Lim Goh

November 27, 2020

As HPE’s chief technology officer for artificial intelligence, Dr. Eng Lim Goh devotes much of his time talking and consulting with enterprise customers about Read more…

By Todd R. Weiss

SC20 Panel – OK, You Hate Storage Tiering. What’s Next Then?

November 25, 2020

Tiering in HPC storage has a bad rep. No one likes it. It complicates things and slows I/O. At least one storage technology newcomer – VAST Data – advocates dumping the whole idea. One large-scale user, NERSC storage architect Glenn Lockwood sort of agrees. The challenge, of course, is that tiering... Read more…

By John Russell

Exscalate4CoV Runs 70 Billion-Molecule Coronavirus Simulation

November 25, 2020

The winds of the pandemic are changing – for better and for worse. Three viable vaccines now teeter on the brink of regulatory approval, which will pave the way for broad distribution by April or May. But until then, COVID-19 cases are skyrocketing across the U.S. and Europe... Read more…

By Oliver Peckham

Azure Scaled to Record 86,400 Cores for Molecular Dynamics

November 20, 2020

A new record for HPC scaling on the public cloud has been achieved on Microsoft Azure. Led by Dr. Jer-Ming Chia, the cloud provider partnered with the Beckman I Read more…

By Oliver Peckham

Gordon Bell Prize Winner Breaks Ground in AI-Infused Ab Initio Simulation

November 20, 2020

The race to blend deep learning and first-principle simulation to speed up solutions and scale up problems tackled is one of the most exciting research areas in computational science today. This year’s ACM Gordon Bell Prize winner announced today at SC20 makes significant progress in that direction. Read more…

By John Russell

Gordon Bell Special Prize Goes to Massive SARS-CoV-2 Simulations

November 19, 2020

2020 has proven a harrowing year – but it has produced remarkable heroes. To that end, this year, the Association for Computing Machinery (ACM) introduced the Read more…

By Oliver Peckham

SC20 Keynote: Climate, Exascale & the Ultimate Answer

November 19, 2020

SC20’s keynote was delivered by renowned meteorologist and climatologist Bjorn Stevens, a director at the Max Planck Institute for Meteorology since 2008 and a professor at the University of Hamburg. In his keynote, Stevens traced the history of climate science from its earliest days through... Read more…

By Oliver Peckham

EuroHPC Exec. Dir. Talks Procurement, EPI, and Europe’s Efforts to Control its HPC Destiny

November 19, 2020

While much of the HPC community’s attention is fixed on SC20’s flood of news and new product announcements, Anders Dam Jensen, the newly-minted executive di Read more…

By Steve Conway

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Azure Scaled to Record 86,400 Cores for Molecular Dynamics

November 20, 2020

A new record for HPC scaling on the public cloud has been achieved on Microsoft Azure. Led by Dr. Jer-Ming Chia, the cloud provider partnered with the Beckman I Read more…

By Oliver Peckham

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

NICS Unleashes ‘Kraken’ Supercomputer

April 4, 2008

A Cray XT4 supercomputer, dubbed Kraken, is scheduled to come online in mid-summer at the National Institute for Computational Sciences (NICS). The soon-to-be petascale system, and the resulting NICS organization, are the result of an NSF Track II award of $65 million to the University of Tennessee and its partners to provide next-generation supercomputing for the nation's science community. Read more…

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Leading Solution Providers

Contributors

Aurora’s Troubles Move Frontier into Pole Exascale Position

October 1, 2020

Intel’s 7nm node delay has raised questions about the status of the Aurora supercomputer that was scheduled to be stood up at Argonne National Laboratory next year. Aurora was in the running to be the United States’ first exascale supercomputer although it was on a contemporaneous timeline with... Read more…

By Tiffany Trader

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Top500: Fugaku Keeps Crown, Nvidia’s Selene Climbs to #5

November 16, 2020

With the publication of the 56th Top500 list today from SC20's virtual proceedings, Japan's Fugaku supercomputer – now fully deployed – notches another win, Read more…

By Tiffany Trader

Texas A&M Announces Flagship ‘Grace’ Supercomputer

November 9, 2020

Texas A&M University has announced its next flagship system: Grace. The new supercomputer, named for legendary programming pioneer Grace Hopper, is replacing the Ada system (itself named for mathematician Ada Lovelace) as the primary workhorse for Texas A&M’s High Performance Research Computing (HPRC). Read more…

By Oliver Peckham

At Oak Ridge, ‘End of Life’ Sometimes Isn’t

October 31, 2020

Sometimes, the old dog actually does go live on a farm. HPC systems are often cursed with short lifespans, as they are continually supplanted by the latest and Read more…

By Oliver Peckham

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

Microsoft Azure Adds A100 GPU Instances for ‘Supercomputer-Class AI’ in the Cloud

August 19, 2020

Microsoft Azure continues to infuse its cloud platform with HPC- and AI-directed technologies. Today the cloud services purveyor announced a new virtual machine Read more…

By Tiffany Trader

Nvidia-Arm Deal a Boon for RISC-V?

October 26, 2020

The $40 billion blockbuster acquisition deal that will bring chipmaker Arm into the Nvidia corporate family could provide a boost for the competing RISC-V architecture. As regulators in the U.S., China and the European Union begin scrutinizing the impact of the blockbuster deal on semiconductor industry competition and innovation, the deal has at the very least... Read more…

By George Leopold

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This