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Primeur weekly 2018-08-13

Focus

DEEP-EST project is exploring the nuts and bolts of mildly disruptive modular supercomputing architecture ...

Gidel's FPGAs only use 1% of their capacity for lossless compression and encryption ...

German HPC and EuroHPC, a question of competitive collaboration benefiting science ...

Quantum computing

NSF launches effort to create practical quantum computer ...

The Rigetti 128-qubit chip and what it means for quantum ...

Quantum chains in graphene nanoribbons ...

Tying electrons down with nanoribbons ...

Focus on Europe

Falling moons: When proto-Earth met its makers - German and Israeli supercomputers spend 100 weeks crunching astronomical numbers ...

PRACE SHAPE Programme supports three further SMEs ...

High Performance Computing for a better agriculture ...

ExCAPE: developing new medicines with high performance computing ...

RDA Grants for Early Careers and Experts - Join the 12th RDA Plenary, 5-8 November 2018, Botswana as part of the International Data Week 2018 ...

Middleware

NetApp and NVIDIA supercharge deep learning with new AI architecture ...

Ohio Supercomputer Center hosting sixth meeting of the MVAPICH Users Group ...

Julia 1.0 has now been released ...

Hardware

Supermicro opens new era of petascale computing with a family of all-flash NVMe 1U systems scalable up to a petabyte of high performance storage ...

DDN building new flash enterprise virtualisation and analytics division with 100 new hires planned through September ...

Co-construction of the future university: Sugon signs with XJTLU ...

Intel launches world's densest, totally silent solid state drive ...

Intel's vision for the future of memory and storage with Optane + QLC ...

University of Texas at Arlington researcher working to use computer cache to speed up memory access ...

Applications

Blue Waters professor Kaiyu Guan receives AGU Early Career Award ...

NCSA Brown Dog project wins Best Technical Paper at PEARC18 ...

2018 NCSA Blue Waters Symposium presentations now available ...

Supercomputer simulations show new target in HIV-1 replication ...

Supercomputer simulations show new target in HIV-1 replication


The naturally-occurring compound IP6 (red) facilitates the formation and assembly of HIV-1 structural proteins, results from XSEDE Stampede2 and Anton2 systems show. Image courtesy of Perilla et al.
9 Aug 2018 Austin - HIV-1 replicates in ninja-like ways. The virus slips through the membrane of vital white blood cells. Inside, HIV-1 copies its genes and scavenges parts to build a protective bubble for its copies. Scientists don't understand many of the details of how HIV-1 can fool our immune system cells so effectively. The virus infects 1.2 million people in the U.S. and 37 million people worldwide in 2018. Supercomputers helped model a key building block in the HIV-1 protective capsid, which could lead to strategies for potential therapeutic intervention in HIV-1 replication.

Scientists found the naturally-occurring compound a hexakisphosphate (IP6) promotes both assembly and maturation of HIV-1. "We discovered, in collaboration with other researchers, that HIV uses this small molecule to complete its function", stated Juan R. Perilla, Department of Chemistry and Biochemistry, University of Delaware. "This is a molecule that's extremely available in human cells and in other mammalian cells. HIV has evolved to make use of these small molecules present in our cells to essentially be infectious." Juan R. Perilla co-authored the study in the journalNaturein August 2018.

Juan R. Perilla ran simulations of inositol phosphate interactions with HIV structural proteins CA-CTD-SP1 using NAMD through allocations on XSEDE, the Extreme Science and Engineering Environment, funded by the National Science Foundation (NSF). "XSEDE provides a unique framework which allows us to use computational resources that are tailored to the needs of a particular scientific problem. In addition, we benefit from the HPC training opportunities provided by XSEDE which allows us to develop novel analysis tools", Juan R. Perilla stated.

The allocation included time on the Anton2 system of the Pittsburgh Supercomputing Center to run atomistic simulations of bound IP6. "Anton2 enabled us to perform long-scale simulations to test the stability of the immature capsid assembly and IP6", Juan R. Perilla stated.

Through XSEDE, the Stampede2 system at the Texas Advanced Computing Center ran NAMD simulations of the Inositol phosphates IP3, IP4, IP5 and their interactions with HIV proteins CA-CTD-SP1. "What Stampede2 allowed us to do is establish what the molecular interactions are between the HIV proteins and this small molecule and to test the hypothesis that it was stabilizing a particular part of the protein using molecular dynamics", stated Juan R. Perilla.

"I think Stampede2 is a great machine, and it's extremely beneficial to the scientific community to have a resource like that available on a merit-based system. What I would like the public to know is that it's important that these large-scale machines are available. They are not just a replacement of a small cluster. These machines really enable new science. If you didn't have machines of this scale, you couldn't do the kind of science that we do because our problems are larger than what you can have on a campus cluster. We really need to have the scale of these machines available to the scientific community to enable the kind of science that we do", Juan R. Perilla stated.

Juan R. Perilla described the increasing use of the 'computational microscope', the combination of supercomputers with laboratory data. "With the computational microscope, you can see how things move. Many experimental techniques are just a snapshot. With the computational microscope, you can actually see how things are moving", he stated.

Supercomputer modeling of how building blocks of HIV-1 move in time made a difference in this study. "That discovery opens a door for development of new treatments. It's a therapeutic target. Because of that, it makes it very appealing for drug development and therapeutic development", Juan R. Perilla stated.

There remains much to be learned about HIV-1 behaves, said Juan R. Perilla. "We're basic scientists. NSF's mission is to understand these systems as living organisms. The overall idea is that we want to understand the virus as a biological problem and ultimately this knowledge will be used to derive therapeutics", Juan R. Perilla stated.

The study, " Inositol phosphates are assembly cofactors for HIV-1 ", was published in the journalNatureon August 1, 2018. The study authors are Robert A. Dick and Volker M. Vogt of Cornell University; Kaneil K. Zadrozny, Jonathan M. Wagner, Barbie K. Ganser-Pornillos, and Owen Pornillos of the University of Virginia; Chaoyi Xu and Juan R. Perilla of the University of Delaware; Florian K. M. Schur of the European Molecular Biology Laboratory and the Institute of Science and Technology Austria; Terri D. Lyddon, Marc C. Johnson, and Clifton L. Ricana of the University of Missouri. The National Institutes of Health funded the research. This work used the Extreme Science and Engineering Discovery Environment, which is supported by National Science Foundation grant number OCI-1053575.

Source: University of Texas at Austin, Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2018-08-13

Focus

DEEP-EST project is exploring the nuts and bolts of mildly disruptive modular supercomputing architecture ...

Gidel's FPGAs only use 1% of their capacity for lossless compression and encryption ...

German HPC and EuroHPC, a question of competitive collaboration benefiting science ...

Quantum computing

NSF launches effort to create practical quantum computer ...

The Rigetti 128-qubit chip and what it means for quantum ...

Quantum chains in graphene nanoribbons ...

Tying electrons down with nanoribbons ...

Focus on Europe

Falling moons: When proto-Earth met its makers - German and Israeli supercomputers spend 100 weeks crunching astronomical numbers ...

PRACE SHAPE Programme supports three further SMEs ...

High Performance Computing for a better agriculture ...

ExCAPE: developing new medicines with high performance computing ...

RDA Grants for Early Careers and Experts - Join the 12th RDA Plenary, 5-8 November 2018, Botswana as part of the International Data Week 2018 ...

Middleware

NetApp and NVIDIA supercharge deep learning with new AI architecture ...

Ohio Supercomputer Center hosting sixth meeting of the MVAPICH Users Group ...

Julia 1.0 has now been released ...

Hardware

Supermicro opens new era of petascale computing with a family of all-flash NVMe 1U systems scalable up to a petabyte of high performance storage ...

DDN building new flash enterprise virtualisation and analytics division with 100 new hires planned through September ...

Co-construction of the future university: Sugon signs with XJTLU ...

Intel launches world's densest, totally silent solid state drive ...

Intel's vision for the future of memory and storage with Optane + QLC ...

University of Texas at Arlington researcher working to use computer cache to speed up memory access ...

Applications

Blue Waters professor Kaiyu Guan receives AGU Early Career Award ...

NCSA Brown Dog project wins Best Technical Paper at PEARC18 ...

2018 NCSA Blue Waters Symposium presentations now available ...

Supercomputer simulations show new target in HIV-1 replication ...