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Primeur weekly 2020-05-25

Focus

InsideHPC's Rich Brueckner passes away at 58 ...

Only half of the EuroHPC countries confirmed they will participate in co-funding EuroHPC projects ...

Quantum computing

Atos and CSC empower the Finnish quantum research community with Atos Quantum Learning Machine ...

Quantum Hall effect 'reincarnated' in 3D topological materials ...

University of California Los Angeles physicists develop world's best quantum bits ...

Quantum leap: Photon discovery is a major step toward at-scale quantum technologies ...

Focus on Europe

HPC-AI Advisory Council and ISC Group continue Annual Student Cluster Competition as an online event ...

ELASTIC software architecture advances urban mobility in Florence ...

Middleware

Waste energy of LUMI supercomputer produces 20 percent of the district heat of Kajaani ...

Italy-based Do IT Systems becomes Bright Services Partner ...

Hardware

Microsoft claims to have built new supercomputer for OpenAI ...

New York University and IBM research takes electrons for a spin in moving toward more efficient, higher density data ...

GRC wins Phase I of AFWERX Programme ...

Samsung Electronics expands its foundry capacity with a new production line in Pyeongtaek, Korea ...

HPE reports Q2 results ...

Intersect360 Research invites your input in an all new survey ...

Applications

Scientists seeking therapies for deadly bacterial disease ...

2020 OLCF User Meeting will happen remote together ...

Summit supercomputer is mining for COVID-19 connections ...

A new method for unraveling complex gene interactions ...

ACM honours computing innovators for advances in research, education and industry ...

Discovery about the edge of fusion plasma could help realize fusion power ...

Superconductors with 'zeitgeist' - When materials differentiate between past and future ...

NIST team builds hybrid quantum system by entangling molecule with atom ...

BIOS IT partners with Panasas to deliver ActiveStor Ultra turnkey HPC storage appliances ...

Supercomputer model simulations reveal cause of Neanderthal extinction ...

Pittsburgh Supercomputing Center is supporting COVID-19 research ...

The Cloud

New technique separates industrial noise from natural seismic signals ...

Lyell Immunopharma goes all-in on AWS as its Cloud provider ...

WekaIO furthers Weka AI by integrating with deep learning pipeline management solution from Valohai ...

Pittsburgh Supercomputing Center is supporting COVID-19 research


SARS-CoV-2 visualized using the ChimeraX programme. Spikes consist of three protein subunits, colour-coded by subunit (PDB ID: 6VSB). The model is built around a core from SARS-CoV (EMDB ID: 1423). There are 46 spikes in a core of 100 nm diameter.
21 May 2020 Pittsburgh - From the start the Pittsburgh Supercomputing Center (PSC) has been active in the support of researchers who try to find an answer in the fight against the COVID-19 outbreak. An experimental test for the coronavirus, powered by the Bridges supercomputer, has revealed viral changes and host responses. In addition, Bridges is helping the Catholic University visualize the coronavirus at atomic detail.

A new experimental test to identify the SARS-CoV-2 virus from genetic material is being developed by an international team led by Weill Cornell Medicine scientists. Their new method, combined with a large-scale sequence analysis of the virus, is shedding light on how the COVID-19 outbreak and the virus developed in New York City.

Using the large-memory nodes of PSC's Bridges supercomputing platform the team, led by Christopher Mason, Jonathan Foox, and Cem Meydan of Weill Cornell Medicine, has identified a strain of the virus that developed in the city from March into April 2020, at the peak of the epidemic. Parallel analysis of how the genes in patients' lung cells react to the infection revealed how patient responses to the virus can affect the course of the disease.

The researchers note that their experimental test - called LAMP, or loop-mediated isothermal amplification - confirmed changes in viral presence for clinical samples that offer a broad picture of how the virus has impacted patients. Those data, plus the in-depth analysis of host-cell transcriptomes - which shows which genes are active in a given tissue - performed by Christopher Mason's team also provide clues as to why the virus affects patients with hypertension, heart conditions and diabetes more severely, and how that might affect treatments for COVID-19.

The group has submitted a paper on their findings to a peer-reviewed journal.

In other research, the outer structures of the SARS-CoV-2 virus that causes COVID-19 have now been visualized down to the positions of every atom, also thanks to the power of PSC's Bridges supercomputing platform. Victor Padilla-Sanchez of the Catholic University of America in Washington, DC, has used Bridges' large-memory nodes in the massive task of computing images of the virus via the interactions between 6 million atoms for each virus and 300 million atoms in 16 viruses as they merge with the outer membrane of a human lung cell.

Victor Padilla-Sanchez created a simulated virus based on the "spike" protein of SARS-CoV-2 from a COVID-19 genetic sequence obtained on February 26, 2020. The spike protein is the only one necessary for the virus to invade a host cell. To simplify the massive computational task, he simulated the viral exterior around a core that conforms to the laboratory-measured shape and size of the core of the similar SARS virus, SARS-CoV, from 2002 (EMDB ID: 1423) from laboratory images. The simulation, which will be documented in a research article now in preparation, is meant to provide scientists with a more exact model of the virus upon which to design drugs, vaccines and other clinical interventions.
Source: Pittsburgh Supercomputing Center - PSC

Back to Table of contents

Primeur weekly 2020-05-25

Focus

InsideHPC's Rich Brueckner passes away at 58 ...

Only half of the EuroHPC countries confirmed they will participate in co-funding EuroHPC projects ...

Quantum computing

Atos and CSC empower the Finnish quantum research community with Atos Quantum Learning Machine ...

Quantum Hall effect 'reincarnated' in 3D topological materials ...

University of California Los Angeles physicists develop world's best quantum bits ...

Quantum leap: Photon discovery is a major step toward at-scale quantum technologies ...

Focus on Europe

HPC-AI Advisory Council and ISC Group continue Annual Student Cluster Competition as an online event ...

ELASTIC software architecture advances urban mobility in Florence ...

Middleware

Waste energy of LUMI supercomputer produces 20 percent of the district heat of Kajaani ...

Italy-based Do IT Systems becomes Bright Services Partner ...

Hardware

Microsoft claims to have built new supercomputer for OpenAI ...

New York University and IBM research takes electrons for a spin in moving toward more efficient, higher density data ...

GRC wins Phase I of AFWERX Programme ...

Samsung Electronics expands its foundry capacity with a new production line in Pyeongtaek, Korea ...

HPE reports Q2 results ...

Intersect360 Research invites your input in an all new survey ...

Applications

Scientists seeking therapies for deadly bacterial disease ...

2020 OLCF User Meeting will happen remote together ...

Summit supercomputer is mining for COVID-19 connections ...

A new method for unraveling complex gene interactions ...

ACM honours computing innovators for advances in research, education and industry ...

Discovery about the edge of fusion plasma could help realize fusion power ...

Superconductors with 'zeitgeist' - When materials differentiate between past and future ...

NIST team builds hybrid quantum system by entangling molecule with atom ...

BIOS IT partners with Panasas to deliver ActiveStor Ultra turnkey HPC storage appliances ...

Supercomputer model simulations reveal cause of Neanderthal extinction ...

Pittsburgh Supercomputing Center is supporting COVID-19 research ...

The Cloud

New technique separates industrial noise from natural seismic signals ...

Lyell Immunopharma goes all-in on AWS as its Cloud provider ...

WekaIO furthers Weka AI by integrating with deep learning pipeline management solution from Valohai ...