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Fighting the flu with high-performance computing

Image courtesy US Army Corps of Engineers Europe District, Flickr (CC BY 2.0).

Researchers are tackling the seasonal flu bug using supercomputing resources offered through PRACE, the Partnership for Advanced Computing in Europe.

Researchers are using PRACE supercomputing resources to tackle the seasonal flu bug. By modeling the process through which viruses insert their genetic material into our cells, they hope to further development of vaccines.

Viruses may circulate in our bodies for some time before causing us to become ill. As a flu virus infects the cell, it is enveloped by a lipid bilayer to form a vesicle, which is essentially a small cell membrane, around it. There are proteins on the vesicle's surface, and if these proteins hook on to the cell membrane in one of our cells, the virus will be able to deliver its RNA contents, thus enabling it to reproduce rapidly and causing us to fall ill.

Peter Kasson of the University of Virginia, US, and Erik Lindahl of Stockholm University, Sweden, have been studying this process of membrane fusion at the molecular level. "Today we roughly know how virus infection works but we are interested in uncovering exactly what happens when two membranes are fused together, and how this anchoring process unfolds," explains Lindahl. "But it is very difficult to simulate a membrane fusion at a molecular level as the particles are moving around all the time like oil. That makes it impossible to do in a laboratory."

Lindahl's research team was able to model interaction between an influenza virus and a target cell membrane at an atomic resolution using the HECToR supercomputer at the Edinburgh Parallel Computing Centre (EPCC) in the UK. They used 6.2m core hours on the machine, which formed part of the Distributed European Computing Initiative supported by the PRACE-2IP Project.

HECToR was recently replaced at the EPCC by the 1.56-petaFLOPS supercomputer ARCHER. Read more about this here.

The most likely way of combating membrane fusion is to attack the anchor itself. "The problem is that the proteins of the virus particles contain changes all the time. And in doing so, they make it difficult for medicines or vaccines to target the virus particles," says Lindahl. "If we manage to find the absolute heart of the anchor we will be able to design molecules that can attach to these parts and make it impossible for them to fuse."

Read the original, longer version of this articlein the latest issue of the PRACE Digest. The publication also features articles on how PRACE supercomputing resources are being used to further research in the fields of high-energy physics, climate modelling, engineering, and much more.

- Lena Barner-Rasmussen

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