Tag Archives: supercomputer

supercomputer study

Supercomputer study unlocks secrets of brain

In the seven-year study just released, RMIT University researchers – led by Professor Toby Allen and including Dr Bogdan Lev and Dr Brett Cromer – modelled how protein “switches” are activated by binding molecules to generate electrical signals in the brain. 

The findings, which involved hundreds of millions of computer processing hours, pave the way for understanding how brain activity can be controlled by existing and new drugs, including anaesthetics.

General anaesthetics work by blocking “on” switches and enhancing “off” switches in the brain, leading to loss of sensation and the ability to feel pain. 

“Even though anaesthetics have been used for more than 150 years, scientists still don’t know how they work at the molecular level,” says Allen.

“General anaesthetics are a mainstay of modern medicine, but have a small safety margin, requiring skilled anaesthetists for their safe use. They may also have long-term effects on brain function in both newborns and the elderly.

“Our study has uncovered details of the switching mechanism that will help in the design of new anaesthetics that are safer, both immediately and for long-term brain function, as well as more effective and more targeted use of anaesthetics.”

Allen says the computer models, using the Victorian Life Sciences Computation Initiative, provide an unprecedented level of understanding of the nervous system.

“These protein switches, called ligand-gated ion channels, are primary electrical components of our nervous systems. Understanding how they work is one of the most important questions in biology,” he says.

“Our computer models show something that’s never been seen before. We have discovered how ion channels bind molecules, such as neurotransmitters, and are activated to generate electrical signals in neurons.

“We are now using these models to make important predictions for how the binding of drugs and anaesthetics may control electrical signalling.”

The findings also unlock a range of other potential applications including understanding how ion channel mutations cause diseases like epilepsy and startle disease, as well as new treatments for anxiety, alcoholism, chronic pain, stroke and other neural conditions.

And because all living organisms share similar proteins, the findings could also open up possibilities for safer and more effective insecticides and anti-parasitics, while the computer modelling developed in the study reduces the need to test new drugs on animals.

The study was funded by the National Health and Medical Research Council, as well as the Medical Advances Without Animals Trust.

The findings have been published this month in Proceedings of the National Academy of Sciences USA.

This article was first published by RMIT on 22 May 2017. Read the original article here.

supercomputer

Supercomputer empowers scientists

Creating commercial drugs these days seems to require more time at the keyboard than in the lab as these drugs can be designed on a computer long before any chemicals are combined.

Computer-based simulations test the design created by the theoretical chemist and quickly indicate any potential problems or enhancements.

This process generates data, and lots of it. So in order to provide University of Western Australia (UWA) chemistry researchers with the power to perform these big data simulations the university built its own supercomputer, Pople.

Dr Amir Karton, head of UWA’s computational chemistry lab says the supercomputer is named after Sir John Pople who was one of the pioneers of computational chemistry for which he won a Nobel Prize in 1998.

“We model very large systems ranging from enzymes to nano materials to design proteins, drugs and catalysts, using multi-scale theoretical procedures, and Pople was designed for such simulations,” Karton says.

“These simulations will tell you how other drugs will interact with your design and what modifications you will need to do to the drug to make it more effective.”

Pople was designed by UWA and while it is small compared to Magnus at the Pawsey Supercomputing Centre it gives the researchers exactly what they want.

That being a multi-core processor, a large and very fast local disk as well as 512 GB of memory in which to run the simulations.

Magnus’ power equivalent to 6 million iPads

While Magnus has nearly 36,000 processors—processing power equivalent to six million iPads running at once—Pople has just 2316 processors.

But, Magnus was designed with large computational projects like the Square Kilometre Array in mind whereas Pople provides such services to individual users.

Dr Dean Taylor, the faculty’s systems administrator says the total amount of memory available to Pople amounts to 7.8 TB, and the total amount of disk space is 153 TB, which could fill almost two thousand 80 GB Classic iPods.

By comparison a top-of-the-range gaming PC might have four processors, 16 GB of memory and a 2 TB disk drive.

A large portion of the Intel Xeon processors (1896 cores) were donated by Perth-based geoscience company DownUnder GeoSolutions.

DownUnder GeoSolutions’ managing director Dr Matthew Lamont says it is the company’s way of investing in the future.

Pople will also assist physics and biology research involving the nature of gravitational waves and the combustion processes that generate compounds important for seed germination.

– Chris Marr

This article was first published by ScienceNetwork Western Australia on 30 April 2016. Read the original article here.

innovation in western australia

Innovation in Western Australia

Science is fundamental for our future social and economic wellbeing.

In Western Australia we’re focusing on areas where we have natural advantages, and an appropriate base of research and industrial capacity. Western Australia’s Science Statement, released by Premier Barnett in April 2015, represents a capability audit of relevant research and engagement expertise in our universities, research institutes, State Government agencies and other organisations. Mining and energy, together with agriculture, are traditional powerhouses, but the science priorities also reflect the globally significant and growing capabilities in medicine and health, biodiversity and marine science, and radio astronomy. It’s a great place to begin exciting new collaborations.

The Science Statement has also helped to align efforts across research organisations and industry. For instance, in 2015 an industry-led “Marine Science Blueprint 2050” was released, followed by the Premier commissioning a roundtable of key leaders from industry, Government, academia and community to develop a long-term collaborative research strategy. These meetings highlighted critical areas of common interest such as decommissioning, marine noise, community engagement and sharing databases.


“Opportunities abound for science and industry to work together to translate research into practical, or commercial, outcomes.”


Science, innovation and collaboration are integral to many successful businesses in Western Australia. In the medical field, a range of technological innovations have broadened the economy and created new jobs. Some of these success stories include Phylogica, Admedus, Orthocell, iCeutica, Dimerix, Epichem and Proteomics International. Another example in this space is the Phase I clinical trial facility, Linear Clinical Research, which was established with support from the State Government – 75% of the trials conducted to date come from big pharmaceutical and biotechnology companies in the USA.

Opportunities abound for science and industry to work together to translate research into practical, or commercial, outcomes. For example, the field of big data analytics is rapidly permeating many sectors. Perth’s Pawsey Centre, the largest public research supercomputer in the southern hemisphere, processes torrents of data delivered by many sources, including radioastronomy as the world’s largest radio telescope, the Square Kilometre Array, is being developed in outback WA. In addition, local company DownUnder GeoSolutions has a supercomputer five times the size of Pawsey for massive geophysical analyses. In such a rich data environment, exciting new initiatives like the CISCO’s Internet of Everything Innovation Centre, in partnership with Woodside, is helping to drive innovation and growth.

Leading players in the resources and energy sector are also taking innovative approaches to enhance efficiency and productivity. Rio Tinto and BHP Billiton use remote-controlled driverless trucks, and autonomous trains, to move iron ore in the Pilbara. Woodside has an automated offshore facility, while Shell is developing its Prelude Floating Liquefied Natural Gas facility soon to be deployed off the northwest coast. Excitingly, 3 emerging companies (Carnegie, Bombora and Protean) are making waves by harnessing the power of the ocean to generate energy.

This high-tech, innovative environment is complemented by a rapidly burgeoning start-up ecosystem. In this vibrant sector, Unearthed runs events, competitions and accelerators to create opportunities for entrepreneurs in the resources space. Spacecubed provides fabulous co-working space for young entrepreneurs, including the recently launched FLUX for innovators in the resource sector. The online graphic design business Canva, established by two youthful Western Australians epitomises what entrepreneurial spirit and can-do attitude can achieve. In this amazingly interconnected world, the sky’s the limit.

Professor Peter Klinken

Chief Scientist of Western Australia

Read next: Professor Barney Glover, Vice-Chancellor and President of Western Sydney University and Dr Andy Marks, Assistant Vice-Chancellor (Strategy and Policy) of Western Sydney University on Making innovation work.

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