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Primeur weekly 2017-07-24

Focus

20th Birthday celebrating OpenMP still welcoming new members ...

Fujitsu's processor roadmap is hitting new targets for Deep Learning ...

Focus on Europe

New FPGA programming method delivers five times more computing power ...

Gazprom Neft to utilise capacity at the St Petersburg Polytechnic University supercomputer ...

Tenfold connectivity increase between Ukraine and European research and education network ...

Newly improved Brain Simulation Platform now online ...

Joeri van Leeuwen received a grant and in-kind expertise from the eScience Center for his astronomy project AA-ALERT ...

Middleware

Bright Computing and Brazil-based AMT sign partnership agreement ...

Hardware

7th International Women in HPC workshop ...

IBM scientists observe elusive gravitational effect in solid-state physics ...

New Supermicro Rack Scale Design (RSD) supports high-density, high-performance pooled NVMe storage ...

Inspur announced the new M5 series servers to get businesses ready for the new era of intelligent computing ...

Women, leadership and Flash - Panel and networking event ...

Applications

3D models help scientists gauge flood impact ...

Pulses of electrons manipulate nanomagnets and store information ...

Flashes of light on the dark matter ...

Titan simulations show importance of close 2-way coupling between human and Earth systems ...

A firefly's flash inspires new nanolaser light ...

Simulation reveals universal signature of chaos in ultracold reactions ...

Massive simulation shows HIV capsid interacting with its environment ...

ANSYS, Saudi Aramco and KAUST shatter supercomputing record ...

Scientists use "Piz Daint" simulations to track heavy summer precipitation from the Mediterranean ...

Fernanda Foertter elected SIG HPC Education Vice Chair ...

The Cloud

IBM expands global Cloud data centre presence with four new facilities ...

The Cloud comes to you: AT&T to power self-driving cars, AR/VR and other future 5G applications through edge computing ...

Teradata acquires San Diego-based start-up StackIQ to strengthen Teradata Everywhere and IntelliCloud capabilities ...

IBM mainframe ushers in new era of data protection ...

Solarflare lets server racks match connectivity of a human neuron ...

New high speed interface connects IBM Z to IBM storage systems ...

Oracle significantly expands Cloud at Customer with PaaS and SaaS services to help customers in their journey to the Cloud ...

Massive simulation shows HIV capsid interacting with its environment


Physics professor Klaus Schulten and postdoctoral researcher Juan R. Perilla conducted a 64-million-atom simulation of the HIV capsid. Video shows simulation of HIV capsid. Yellow and blue particles are ions flowing into and out of the capsid. The genetic material of the HIV virus is encased in multiple structures that hide it from the host immune system. The capsid, in blue, protects the virus after it enters a cell and shuttles it to the nucleus, where it completes the process of infection. Graphic by Juan Perilla.
19 Jul 2017 Champaign - It took two years on a supercomputer to simulate 1.2 microseconds in the life of the HIV capsid, a protein cage that shuttles the HIV virus to the nucleus of a human cell. The 64-million-atom simulation offers new insights into how the virus senses its environment and completes its infective cycle. The findings are reported in the journalNature Communications.

"We are learning the details of the HIV capsid system, not just the structure but also how it changes its environment and responds to its environment", stated University of Illinois research scientist Juan R. Perilla, who led the study with University of Illinois physics professor Klaus Schulten. Such details could help scientists find new ways to defeat the virus, Juan R. Perilla said.

Klaus Schulten, who died in October 2016, pioneered the application of molecular dynamics simulations to study large biological systems. He called the method "computational microscopy".

The capsid simulation was performed on the Department of Energy's Titan supercomputer. Analyzing the data required a second supercomputer, Blue Waters, at the National Center for Supercomputing Applications at the University of Illinois.

The HIV capsid is made up of hundreds of identical proteins arrayed in a network of six-sided and five-sided structures, each with a tiny pore at its centre. The capsid contains the virus's genetic material, hiding it from host cell defenses. It also transports the virus to the cell nucleus, which it must infiltrate to complete infection.

The new study revealed several properties that likely enhance the capsid's ability to sense its environment and find its way to the nucleus, Perilla said. It showed, for example, that different parts of the capsid oscillate at different frequencies. These oscillations likely transmit information from one part of the capsid to another, he said.

The study also revealed that ions flow into and out of the capsid pores. Negative ions accumulate on the positively charged surface inside the capsid, while positive ions adhere to the outside, which carries a negative charge.

"If you can break this electrostatic balance that the capsid is trying to keep together, you may be able to force it to burst prematurely", Juan R. Perilla stated.

The positively charged interior also could help facilitate the influx of DNA building blocks. The virus needs these molecules from the host to convert its own RNA into DNA, Juan R. Perilla said. These DNA building blocks, called nucleotides, carry a negative charge and are small enough to pass through the capsid's pores, he said.

The researchers also found that stress propagates through the capsid in patterns. The stresses align in regions that experiments have shown are most susceptible to bursting.

These data reveal potential vulnerabilities that could be exploited to develop new drugs to defeat the HIV virus by targeting its capsid, Juan R. Perilla said.

Juan R. Perilla and Klaus Schulten are associated with the Beckman Institute for Advanced Science and Technology at the University of Illinois.

The National Science Foundation and the National Institutes of Health support this research.

The paper titled " Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations " is available online - DOI: 10.1038/ncomms15959.

Physics professor Klaus Schulten and postdoctoral researcher Juan R. Perilla conducted a 64-million-atom simulation of the HIV capsid. The video shows the simulation of the HIV capsid. Yellow and blue particles are ions flowing into and out of the capsid. Photo by L. Brian Stauffer/Background image by Juan Perilla and Klaus Schulten/Video by Juan Perilla.
Source: University of Illinois

Back to Table of contents

Primeur weekly 2017-07-24

Focus

20th Birthday celebrating OpenMP still welcoming new members ...

Fujitsu's processor roadmap is hitting new targets for Deep Learning ...

Focus on Europe

New FPGA programming method delivers five times more computing power ...

Gazprom Neft to utilise capacity at the St Petersburg Polytechnic University supercomputer ...

Tenfold connectivity increase between Ukraine and European research and education network ...

Newly improved Brain Simulation Platform now online ...

Joeri van Leeuwen received a grant and in-kind expertise from the eScience Center for his astronomy project AA-ALERT ...

Middleware

Bright Computing and Brazil-based AMT sign partnership agreement ...

Hardware

7th International Women in HPC workshop ...

IBM scientists observe elusive gravitational effect in solid-state physics ...

New Supermicro Rack Scale Design (RSD) supports high-density, high-performance pooled NVMe storage ...

Inspur announced the new M5 series servers to get businesses ready for the new era of intelligent computing ...

Women, leadership and Flash - Panel and networking event ...

Applications

3D models help scientists gauge flood impact ...

Pulses of electrons manipulate nanomagnets and store information ...

Flashes of light on the dark matter ...

Titan simulations show importance of close 2-way coupling between human and Earth systems ...

A firefly's flash inspires new nanolaser light ...

Simulation reveals universal signature of chaos in ultracold reactions ...

Massive simulation shows HIV capsid interacting with its environment ...

ANSYS, Saudi Aramco and KAUST shatter supercomputing record ...

Scientists use "Piz Daint" simulations to track heavy summer precipitation from the Mediterranean ...

Fernanda Foertter elected SIG HPC Education Vice Chair ...

The Cloud

IBM expands global Cloud data centre presence with four new facilities ...

The Cloud comes to you: AT&T to power self-driving cars, AR/VR and other future 5G applications through edge computing ...

Teradata acquires San Diego-based start-up StackIQ to strengthen Teradata Everywhere and IntelliCloud capabilities ...

IBM mainframe ushers in new era of data protection ...

Solarflare lets server racks match connectivity of a human neuron ...

New high speed interface connects IBM Z to IBM storage systems ...

Oracle significantly expands Cloud at Customer with PaaS and SaaS services to help customers in their journey to the Cloud ...