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Primeur weekly 2016-10-10

Exascale supercomputing

The incredible shrinking particle accelerator ...

Brookhaven Lab to play major role in 2 DOE exascale computing application projects ...

Quantum computing

More stable qubits in perfectly normal silicon ...

Focus on Europe

RSC supercomputers go West ...

Hardware

Allinea tools play vital role in advancing computational research at the VSC, Austria's largest HPC facility ...

Smallest transistor ever ...

Turning to the brain to reboot computing ...

Complex materials can self-organize into circuits, may form basis for multifunction chips ...

Wireless data centre on a chip aims to cut energy use ...

Adapteva announces 28nm 64-core Epiphany-IV microprocessor chip ...

SGI introduces unique scale-out solution for SAP HANA that protects investments when moving to real-time business ...

Applications

Clemson University scientists receive $1.8 million grant to combat Type 2 diabetes ...

Climate change intensifies night-time storms over Lake Victoria ...

Computer simulations explore how Alzheimer's disease starts ...

Rice University lab explores cement's crystalline nature to boost concrete performance ...

Rice University researchers say 2D boron may be best for flexible electronics ...

Large animals, such as the imperious African elephant, most vulnerable to impact of human expansion ...

Computer simulation finds dangerous molecule activity for ageing ...

Tornadogenesis ...

As hurricane heads up coast, a RENCI supercomputer swings into action ...

New drug candidate may reduce deficits in Parkinson's disease ...

XSEDE allocations awarded to 155 research teams across U.S. ...

OSC part of NSF-funded consortium for advancing research computing practices ...

NCSA awarded NSF grant to expand computational science education in food, energy, and water ...

Crosstalk analysis of biological networks for improved pathway annotation ...

The Cloud

Nimbix collaborates with IBM and NVIDIA to launch powerful GPU Cloud offering ...

Computer simulation finds dangerous molecule activity for ageing


Associate Professor Ilia Solov'yov. Credit: Anders Boe/SDU.
3 Oct 2016 Odense - All human organisms are attacked by free radicals - they destroy our cells, and over time they contribute to us ageing. Now, researchers have found out how a particularly dangerous type of free radicals is formed, and it may lead to a better understanding of aging.

Every time we breathe we bring crucial oxygen into the body. However, a very small part of this oxygen may be converted to so-called free radicals, which have an unfailing ability to damage our cells. The older we become, the more our cells are damaged and thereby also our organs, muscles, etc.

Free radicals also have great significance concerning ageing and thus, understandably, attract great scientific interest.

Associate Professor Ilia Solov'yov and postdoc, Ph.D, Peter Husen, University of Southern Denmark (SDU), are two of the scientists who are trying to understand how free radicals form.

Their interest is not only of the medical kind; they are just as much concerned with the opportunities that computer power holds concerning analysis of extremely complex biological systems - such as the formation of the special group of free radicals called superoxides.

"We wanted to find out exactly which factors lead to the formation of these superoxides. We knew as much that the formation occurs in a cluster of proteins but the rest was a mystery. And of course it is interesting to find out the details, because it is only when we know them that we can hope to be able to control and perhaps even prevent the formation of superoxides", stated Ilia Solov'yov who is an associate professor and head of the Quantum Biology and Computational Physics Group at SDU.

Together with postdoc Peter Husen from the same research group he fed the Danish supercomputer Abacus molecular biological data and asked it to make a simulation of what is going on inside the relevant cluster of proteins that leads to the formation of superoxides.

"The simulation showed us that an oxygen molecule can penetrate and reach specific locations in the cluster of proteins where, potentially, it can absorb an extra electron and thus turn into superoxide. This cannot be observed in a regular microscope and therefore this process has so far been unknown."

The scientists' next step is to examine whether it is possible to prevent the oxygen molecule from entering the protein cluster and initiate the formation of the harmful superoxides.

The microscope has led to several major scientific breakthroughs, but there is a limit to how much - or rather; how little - one can see in it. If one wants to study units as small as proteins and molecules, the method of choice today is via computer models in which one can build such things as virtual proteins and examine them on-screen. One can then study the function of the protein in detail through computer simulations.

Free radicals destroy our cells and cause DNA damage - unless they are neutralised by antioxidants. Health food stores sell various products that contain antioxidants, which is found in some vegetables and berries, but we also produce them ourselves. However, we can neither produce nor eat enough to stave off our ageing.

Source: University of Southern Denmark

Back to Table of contents

Primeur weekly 2016-10-10

Exascale supercomputing

The incredible shrinking particle accelerator ...

Brookhaven Lab to play major role in 2 DOE exascale computing application projects ...

Quantum computing

More stable qubits in perfectly normal silicon ...

Focus on Europe

RSC supercomputers go West ...

Hardware

Allinea tools play vital role in advancing computational research at the VSC, Austria's largest HPC facility ...

Smallest transistor ever ...

Turning to the brain to reboot computing ...

Complex materials can self-organize into circuits, may form basis for multifunction chips ...

Wireless data centre on a chip aims to cut energy use ...

Adapteva announces 28nm 64-core Epiphany-IV microprocessor chip ...

SGI introduces unique scale-out solution for SAP HANA that protects investments when moving to real-time business ...

Applications

Clemson University scientists receive $1.8 million grant to combat Type 2 diabetes ...

Climate change intensifies night-time storms over Lake Victoria ...

Computer simulations explore how Alzheimer's disease starts ...

Rice University lab explores cement's crystalline nature to boost concrete performance ...

Rice University researchers say 2D boron may be best for flexible electronics ...

Large animals, such as the imperious African elephant, most vulnerable to impact of human expansion ...

Computer simulation finds dangerous molecule activity for ageing ...

Tornadogenesis ...

As hurricane heads up coast, a RENCI supercomputer swings into action ...

New drug candidate may reduce deficits in Parkinson's disease ...

XSEDE allocations awarded to 155 research teams across U.S. ...

OSC part of NSF-funded consortium for advancing research computing practices ...

NCSA awarded NSF grant to expand computational science education in food, energy, and water ...

Crosstalk analysis of biological networks for improved pathway annotation ...

The Cloud

Nimbix collaborates with IBM and NVIDIA to launch powerful GPU Cloud offering ...