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Primeur weekly 2019-09-09

Quantum computing

New quantum project aims for ultra-secure communication in Europe ...

Schrödinger and Qu & Co announce collaboration to advance quantum mechanical computations on quantum computers ...

Spreading light over quantum computers ...

Focus on Europe

AUBASS' AUTOSAR Adaptive Platform solution ported on Kalray's intelligent processor ...

eScience Center takes part in hackathon to improve tools for analysis of internet therapies ...

At the edge of chaos, powerful new electronics could be created ...

Middleware

2CRSI becomes a Bright reseller in the USA, Europe and Middle East ...

NERSC and ECP host OpenMP Hackathon for energy-efficient architectures ...

Hardware

Shell and PDENH are investing in Dutch sustainable data centre technology scale-up Asperitas ...

Konstantinos Orginos awarded time on world's fastest supercomputer to study Lattice QCD ...

GRC teams with NVIDIA to provide fully optimized liquid-immersion cooled system to support the Texas Advanced Computing Center's Frontera supercomputer ...

Mellanox introduces new LinkX 200G & 400G cables & transceivers at CIOE, Shenzhen, China and ECOC, Dublin, Ireland 2019 ...

Texas boosts U.S. science with fastest academic supercomputer in the world ...

New insulation technique paves the way for more powerful and smaller chips ...

WekaIO awarded three patents ...

Intel Xeon Scalable processors drive advanced research in world's fastest academic supercomputer ...

Applications

Rochester Institute of Technology researchers use Frontera supercomputer to simulate neutron star mergers ...

Researchers use TACC's new Frontera supercomputer to simulate viruses and cells ...

Teaching Neural Networks Quantum Chemistry ...

Building a sunnier energy future ...

Researchers apply increasing computational power to develop predictive models and create patient-specific treatment plans ...

Researchers will simulate high speed turbulent flows on Frontera supercomputer ...

U.S. National Science Foundation awards San Diego Supercomputer Center and partners $5,9 million to host EarthCube Office ...

Researchers uncover role of earthquake motions in triggering a 'surprise' tsunami ...

Artificial Intelligence for Physics Research ...

NCSA machine learning pipeline provides insight into energy-efficient home improvement programmes ...

Eight projects to gain early access to the Frontier supercomputer ...

New Berkeley Lab study uses supercomputers to analyze hydrological changes in a California watershed following a wildfire ...

PPG selected for DOE partnership to speed development, testing of adhesives for lightweight vehicles ...

Sum of three cubes for 42 finally solved - using real life planetary computer ...

Researchers use TACC's new Frontera supercomputer to simulate viruses and cells


This scientific image shows influenza viral proteins (green) beginning the process of merging the viral envelope with a model of the cell membrane, a key step in viral infection. Credit: Peter Kasson, University of Virginia.
3 Sep 2019 Austin - Emerging viruses have been with us for hundreds of years and will be with us for hundreds more. If you follow the news, we are continually concerned about whether there will be another outbreak of influenza or increasing incidence of Ebola or other viruses that threaten our health.

An emerging virus is a term applied to a newly discovered virus, one that is increasing in incidence or has the potential to spread. HIV is the clearest example of a previously unknown virus that has now produced one of the largest pandemics in history.

Peter Kasson, an associate professor of Molecular Physiology and Biomedical Engineering at the University of Virginia, has combined computer science and biology throughout his educational and professional career.

"We work to understand viral infections such as influenza and Zika", Peter Kasson stated. "What we do guides the development of new antiviral therapies, and also helps us assess how well vaccines work and how well people's immunity can prevent new viral threats from causing widespread disease in the United States."

Peter Kasson and his team observe viruses experimentally by tagging them with fluorescent proteins and using microscopy to understand how they affect cells.

However, the experiments provide them with a very limited level of detail. "To be able to really study the mechanisms of viral infection, we have to combine experiments with computer models where we build a model of the virus, one atom at a time, and then simulate the mechanics of how the atoms interact", Peter Kasson stated. "It's a challenge that requires the fastest supercomputers in the world."

The new Frontera supercomputer at the Texas Advanced Computing Center (TACC) is the fastest academic supercomputer in the world. Its hundreds of thousands of closely linked computational cores are well-suited for the kinds of simulations Peter Kasson's team needs to run. Their research uses experimental data to refine their simulations, and has the potential to serve as a test case for and also develop large-scale adaptive ensemble methods - programmes that run many simulations, examine the results, and decide what to run next so that the process of deciding what simulations to do is automated as well as the simulations themselves.

Peter Kasson leads one of the 34 research groups selected to participate in the Frontera early user period. "The initial experience has been extremely smooth. We've been able to get some exciting preliminary results that we're very eager to run further", Peter Kasson stated. "In the time we've been using Frontera, our simulations are proceeding two or three times faster than on the prior supercomputers we've had access to."

Stopping viruses in their tracks in Peter Kasson's ultimate goal. "Viruses are these really tiny packages that encode a lot of complexity. We can observe the function experimentally, but taking them apart and achieving a mechanistic understanding is something that we need the simulations to help with - that really gets me excited."

In addition to enabling simulations on a massive scale, Frontera offers the opportunity to train young scientists on a cutting-edge system. "They learn best practices, advance science, and do this on the best supercomputer the country has to offer to prepare us for the future", Peter Kasson stated.

This award by the National Science Foundation (NSF) Office of Advanced Cyberinfrastructure is jointly supported by the Division of Chemistry within the NSF Directorate for Mathematical and Physical Sciences and the Division of Chemical, Bioengineering, Environmental, and Transport Systems within the NSF Directorate for Engineering. The Award abstract is no. 1835780 - Collaborative Research: NSCI Framework - Software: SCALE-MS - Scalable Adaptive Large Ensembles of Molecular Simulations.
Source: University of Texas at Austin, Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2019-09-09

Quantum computing

New quantum project aims for ultra-secure communication in Europe ...

Schrödinger and Qu & Co announce collaboration to advance quantum mechanical computations on quantum computers ...

Spreading light over quantum computers ...

Focus on Europe

AUBASS' AUTOSAR Adaptive Platform solution ported on Kalray's intelligent processor ...

eScience Center takes part in hackathon to improve tools for analysis of internet therapies ...

At the edge of chaos, powerful new electronics could be created ...

Middleware

2CRSI becomes a Bright reseller in the USA, Europe and Middle East ...

NERSC and ECP host OpenMP Hackathon for energy-efficient architectures ...

Hardware

Shell and PDENH are investing in Dutch sustainable data centre technology scale-up Asperitas ...

Konstantinos Orginos awarded time on world's fastest supercomputer to study Lattice QCD ...

GRC teams with NVIDIA to provide fully optimized liquid-immersion cooled system to support the Texas Advanced Computing Center's Frontera supercomputer ...

Mellanox introduces new LinkX 200G & 400G cables & transceivers at CIOE, Shenzhen, China and ECOC, Dublin, Ireland 2019 ...

Texas boosts U.S. science with fastest academic supercomputer in the world ...

New insulation technique paves the way for more powerful and smaller chips ...

WekaIO awarded three patents ...

Intel Xeon Scalable processors drive advanced research in world's fastest academic supercomputer ...

Applications

Rochester Institute of Technology researchers use Frontera supercomputer to simulate neutron star mergers ...

Researchers use TACC's new Frontera supercomputer to simulate viruses and cells ...

Teaching Neural Networks Quantum Chemistry ...

Building a sunnier energy future ...

Researchers apply increasing computational power to develop predictive models and create patient-specific treatment plans ...

Researchers will simulate high speed turbulent flows on Frontera supercomputer ...

U.S. National Science Foundation awards San Diego Supercomputer Center and partners $5,9 million to host EarthCube Office ...

Researchers uncover role of earthquake motions in triggering a 'surprise' tsunami ...

Artificial Intelligence for Physics Research ...

NCSA machine learning pipeline provides insight into energy-efficient home improvement programmes ...

Eight projects to gain early access to the Frontier supercomputer ...

New Berkeley Lab study uses supercomputers to analyze hydrological changes in a California watershed following a wildfire ...

PPG selected for DOE partnership to speed development, testing of adhesives for lightweight vehicles ...

Sum of three cubes for 42 finally solved - using real life planetary computer ...