Biotechnology sector

Biotechnology is a strategic area for South Australia, which hosts many world-class bioscience research groups in medical, agricultural and environmental bioscience with a wide range of applications including diagnosis and treatment of disease, wine chemistry, plant and livestock breeding, aquaculture, pest management, and water quality.

One of the crucial requirements for biotechnology is access to leading-edge bioinformatics capability enabling storage, querying and processing of biological data sets. This includes support for computationally intensive tasks such as searching and analysis of gene and protein data, protein modelling studies, drug design, and molecular dynamics simulations.

Biological data is increasing rapidly in size and complexity, which is driving the uptake of advanced high performance computing and grid computing technologies in bioscience. The Department of Plant Science at the Waite Institute and the recently established Australian Centre for Plant Functional Genomics study the physiology, molecular biology and genetic makeup of plants, with particular focus on the improvement of commercially important food crops such as wheat and barley.

The Centre has made signficiant contributions to support eResearch SA's high performance computing facilities, which are used for a variety of applications including gene and protein sequence analysis.

Bioinformatics

In the field of bioinformatics, the combination of computer science, information technology and the life sciences has been producing extraordinary results. Complex biological systems have begun to yield their secrets to the superior analytical and processing power of eResearch methods and technologies.

At eResearch SA, we’re working with bioinformatics researchers to develop new approaches for analysing patterns of ‘repeats’ in genetic code. Our bioinformatics specialists work closely with academic researchers to discover patterns in repeated code, annotate them, and classify them into groups.

We’re working with local scientists to scrutinise the bovine and equine genomes (among others) and learn more about which patterns occur together and which don’t. From this process, researchers are uncovering previously unknown repeat patterns in a variety of genomes.

The meaning and implications of repeated fragments has long been a subject of debate for genetic researchers. Strings of ‘repeated’ DNA comprise the bulk of the human genome but we know very little about what they do and how the segments relate to each other.

Understanding how and why these repeats function might one day help uncover some of the mysteries of evolution, explain different traits in populations of the same species, or reveal the workings of ‘repeat disorders’ in humans, such as Huntington’s Disease and Fragile X Syndrome.

Chemistry

The use of high performance computing in chemistry plays an important role in determining molecular structure and function, and the energetics and rates of chemical reactions. eResearch SA has a variety of computational tools available to enable chemists to apply the most appropriate theoretical modelling approach to the molecular systems of interest.

The design of advanced materials and molecular assemblies with novel physical and chemical properties represents a critical component in the development of emerging technologies. Molecular recognition is a specific non-covalent molecular attraction. Researchers are using eResearch SA's resources to explore a range of molecular recognition phenomena, including the molecular topologies of metal ion activated molecular receptors and light or pH controlled molecular devices. The figure shown here illustrates the structures of two aromatic anion receptors.

Another project concerns the oxidation chemistry of silylene (SiH₂), which is important in semiconductor manufacture and the photonics and aerospace industries.

Computer science

Researchers in the Distributed and High Performance Computing (DHPC) group work closely with eResearch SA in the procurement, installation, benchmarking and testing of supercomputing facilities. The DHPC group also uses eResearch SA facilities for research projects in parallel and grid computing.

Recent work has developed improved tools that allow highly accurate measurements of the communications performance of parallel computers. This has many applications, including the testing and optimisation of communications networks, protocols and algorithms. Results from these tools are also used in related work that has developed more accurate techniques for modelling and analysing the performance of parallel programs.

The DHPC group has been working on grid computing for several years. This research addresses the problem of effectively utilising multiple distributed computing resources for complex applications, particularly those involving the access and processing of data from large distributed data archives, such as image data from satellites or aerial surveys.

Fluid dynamics

Research mathematicians and engineers have a major impact on a wide variety of fundamental industrial, geophysical and engineering problems, encompassing applications such as:

• fluid flow through permeable media (petroleum engineering and water resource and salinity management)
• clean combustion technologies (reducing greenhouse emissions)
• drag reduction and noise control (automobile, ship and submarine design)

All these applications require techniques from computational fluid dynamics combined with very powerful computers to produce reliably accurate solutions to the nonlinear equations governing fluid flow.

Access to eResearch SA facilities allows Australian researchers in computational fluid dynamics to remain competitive with US, European and Japanese researchers at the forefront of these fields. It also provides an attraction to international collaborators. eResearch SA facilities also support new initiatives in modelling the dynamics of plasmas in the space environment.

Numerical modelling of ocean waves

A scientist at the US National Weather Service/NOAA studying the contribution of ocean swell to the global wave climate began his research in Adelaide on eResearch SA computers. Dr Jose Henrique Alva is using numerical modelling to study ocean wave heights, which is important in areas such as oceanographic and meteorological studies, ship routing, engineering design and recreational activities.

Figure 1 (below left) shows the yearly average significant height of waves generated at high latitudes of the South Atlantic Ocean for 2001. Figure 2 (below right) shows the monthly mean significant height of waves generated at high latitudes of the South Indian Ocean during December 2001. Both figures show how far waves generated with-in a given ocean basin can penetrate into other oceans as swell, carrying significant amounts of energy over very long distances over the Earth. This information will be used to generate the first study of how global swell affects ocean wave conditions.

Dr Alves has collaborated on this project with Professor Ian Young (University of Adelaide), Dr Hendrik Tolman (NWS/NOAA) and Mr Fabricio Branco (University of Sao Paulo, Brazil).

Computation of flow over a long circular cylinder

Flow over long circular cylinders occurs commonly in engineering projects. A prime example is towed array sonar, where a cylindrical tube containing a series of hydrophones is towed behind a ship or submarine. The sounds detected by the hydrophobes can be processed to obtain information such as the bearing of neighbouring vessels or the possible locations of oil reserves. The turbulent flow of water over the surface of the sonar interferes with the detection of weak acoustic signals. Detailed study of such flows will be expected to lead to improved sonar designs and processing techniques. The figure shows a snapshot of the time varying flow speed near a stationary cylinder in axial flow, computed using a parallel program developed by Milton Woods, a doctoral student in mechanical engineering.

Physics

The Standard Model of the universe is founded on quantum field theories in which the forces between the constituents of matter are mediated by the exchange of particles. Of particular interest is quantum chromodynamics (QCD), the theory proposed to describe the strong nuclear force, one of four fundamental forces of nature. The only way to reveal the properties of this fundamental theory is to numerically simulate the theory on a space-time lattice with millions of sites, which requires the use of high performance parallel supercomputers.

It was once thought that the vacuum of space was empty, however we now understand it to be permeated with quark and gluon field fluctuations described by QCD. In fact, scientists believe it requires an enormous amount of energy to clear these fields from the vacuum. Flux tubes of QCD fields form between quarks and confine them within particles such as protons and neutrons, making it impossible to isolate a single quark.

Recent breakthroughs in simulation techniques combined with eResearch SA's world-class supercomputing resources will enable South Australian physicists to determine the predictions of QCD and reveal the manner in which the fundamental forces  of nature give rise to the world around us.