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New Supercomputer To Power Leading Research

New Supercomputer To Power Leading University Research

The University of Auckland has taken delivery of a supercomputer from IBM that is the most powerful in New Zealand and gives its researchers the computing muscle necessary to stay at the forefront of global research efforts.

Users will include the bioengineering team led by Professor Peter Hunter working to create a 'virtual body', the bioinformatics initiative led by Prof John Fraser of the Department of Molecular Medicine, and the theoretical chemistry research of Prof Peter Schwerdtfeger of the Department of Chemistry.

The purchase has come about through a strategic alliance in the United States between IBM Global Services and Physiome Sciences, a New York based firm that collaborates with The University of Auckland's bioengineering team.

IBM and Physiome Sciences have entered into a broad strategic collaboration to develop and deploy software and hardware to enhance biological modelling for drug discovery, and The University of Auckland purchased one of IBM's new eServer* POWER4-based supercomputers. The supercomputer is the Regatta H, 32 Processor with 32 Gigabytes of operating memory.

Professor Peter Hunter, leader of the bioengineering research group in The University of Auckland's School of Engineering, said he looked forward to working with the supercomputer. "This is the most powerful computer in New Zealand and a real asset for The University of Auckland's research community.

"Biomedical engineering industries are making a major contribution to the economies of most industrialised nations. We have a centre of excellence here in Auckland. This investment by the university and IBM will allow us to build on that strength for the benefit of all New Zealanders."

The bioengineering team has developed the world's first accurate computer model of a human heart that behaves like a human heart when subjected to chemical or electrical changes, drugs or other influences.

"The potential applications of this research are enormous," Professor Hunter said. "Our collaboration with Physiome Sciences has helped bring this technology into use to streamline the process by which new drugs are developed. A model for human lungs is also being developed.

"With the assistance of a New Economy Research Fund grant from the Foundation for Research, Science and Technology, the bioengineering team will build a database of every muscle, bone and ligament in the body, with a particular emphasis on understanding and modelling the function of the knee."

The financial terms of the deal will not be disclosed.


Background Material

Professor John Fraser (Molecular Medicine Dept, The University of Auckland)

Professor Fraser is leading the development of bioinformatics at the University of Auckland, an area in which the supercomputer will play a key role. Bioinformatics is the science of using computers to solve complex biological problems and has come about because of three things, the Internet, faster computers, and high throughput technologies that can generate massive amounts of information - the decoding of the human genome being one perfect example that would not have happened without bioinformatics.

"Bioinformatics is changing the world of biology forever," says Professor Fraser. "Already over 80 genomes have been completely sequenced including most of our most dangerous disease causing pathogens."

One of the first applications of The University of Auckland supercomputer will be to provide for the first time, real-time access to the many massive gene and protein databases that are currently only accessible in other global locations such as the US, UK or Japan via the internet. The machine will allow researchers here to do far more intensive operations than were possible before. One example would be to compare every single gene in an entire genome of one organism against the genomes of several other organisms to find similar matches that might be important as generic drug targets. The function of many of the genes in the genome databases are currently unknown, and one important step is to develop computational methods that assign function using multiple similarity methods to other distantly related genes from other organisms. Professor Fraser's group along with a group led by Prof. Ted Baker of the School of Biological Sciences are particularly interested in comparative genome searching of microbial genomes for the purpose of identifying new antibiotic drug targets.

"As more information is added, bioinformatics becomes more powerful. Already vast, the pool of data grows exponentially every year. And it is important to the New Zealand science community that at least one central database repository and bioinformatics facility exists. The Regatta 32 will take our research at Auckland to a new level of capability," Professor Fraser concluded.

Professor Peter Schwerdtfeger

Prof. Peter Schwerdtfeger's research at Auckland University is concerned with fundamental aspects of interactions between atoms and molecules by using computational quantum methods. Computational quantum chemistry and physics is quantum theory applied to chemistry, condensed matter physics, fluid dynamics, particle physics and molecular biology. Early efforts in the late 60s of the last century were concentrated on solving the so-called "Schrödinger equation" and its extension to solid systems by using either ab-initio or density functional methods.

In the last 30 years we saw great progress in design of algorithms and increase in computer power and computational results now reach the level of experimental accuracy. In molecular quantum chemistry and condensed matter physics one faces fundamental problems that the computer time scales exponentially with increasing number of interacting particles involved.

Professor Schwerdtfeger says the underlying physical laws are so complicated that sophisticated algorithms implemented on a supercomputer are required to obtain any useful information at the microscopic level. "A typical calculation solving the so-called "Dirac-equation" for small molecules can run for months on a supercomputer and would need many years on a PC. With the new IBM larger molecules can now be tackled and studied in detail."

"Thus access to fast- and parallel processor machines with large memory and disk space requirements are essential for the computational treatment of such systems. This allows predictions to be made for properties of yet unknown atoms and molecules. For example, out of the four fundamental forces in nature the weak force leads to a breakdown of mirror image symmetry in molecules. Nature also reflects Amino acids are left-handed and sugars are right-handed in nature. Their mirror image (right-handed amino acids and left-handed sugars) are (with a few exceptions) not used in living organisms. Weak interactions could be responsible for this inherent asymmetry in nature. Despite many efforts, weak interactions in handed molecules have not been discovered yet. Peter's research group has made accurate predictions for such weak effects, and the laser group in Paris headed by Prof. Christian Chardonnet is now preparing for experiments to detect such tiny differences between handed molecules."

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