High Resolution EPR Spectroscopy - A Tool for Determining Electronic and Geometric Structure of Metalloenzymes. High resolution orientation selective pulsed EPR and END(T)OR in conjunction with computer simulation (XSophe) and computational chemistry will allow the determination of the electronic and geometric structure (distance and orientation of nuclei surrounding the metal ion(s)) of multiple redox centres in DMSOR, DorC and DMSDH to be determined. In addition pulsed ELDOR in conjunction wi ....High Resolution EPR Spectroscopy - A Tool for Determining Electronic and Geometric Structure of Metalloenzymes. High resolution orientation selective pulsed EPR and END(T)OR in conjunction with computer simulation (XSophe) and computational chemistry will allow the determination of the electronic and geometric structure (distance and orientation of nuclei surrounding the metal ion(s)) of multiple redox centres in DMSOR, DorC and DMSDH to be determined. In addition pulsed ELDOR in conjunction with molecular modelling will enable the mapping (distance and orientation) of redox centres in complex multicentered metalloproteins (DMSDH and DorC) and in protein-protein complexes (DMSOR-DorC) providing information on the pathway of electron transfer and hence the role of the pyranopterins.Read moreRead less
Improving the accuracy of phylogenetic reconstruction by improving models of sequence divergence. Phylogenies describe the relationships among species and provide the essential framework for understanding evolutionary processes. They are an essential tool in the identification of functionally important regions in DNA sequences. An important aspect of identifying phylogenies is measuring how DNA sequences change in time. The proposed research will develop sophisticated, practical models of sequen ....Improving the accuracy of phylogenetic reconstruction by improving models of sequence divergence. Phylogenies describe the relationships among species and provide the essential framework for understanding evolutionary processes. They are an essential tool in the identification of functionally important regions in DNA sequences. An important aspect of identifying phylogenies is measuring how DNA sequences change in time. The proposed research will develop sophisticated, practical models of sequence divergence and make them freely available in open source software. The software and models will positively impact on studies seeking to understand Australian biological diversity. The proposed resolution of the eutherian mammal orders will further significantly impact on utilisation of rodents as a model organism for human biology.Read moreRead less
Cross-Entropy Methods in Complex Biological Systems. The Cross-Entropy method provides a powerful new way to find superior solutions to complicated optimisation problems in biology, ranging from better design and implementation of medical treatments to an increased understanding of complex ecosystems.
A Novel Phosphate Fertiliser Enhanced by Biofertiliser Technology. This project will deliver efficient use of the limited supplies of high quality phosphorus minerals as fertiliser-P, simultaneously acting to reverse and prevent soil acidification. These cost-effective benefits from utilising Australia's microbial biodiversity will have major economic and environmental impacts in rural Australia,increasing the profitability of farming and reducing the potential for contamination of aquatic syste ....A Novel Phosphate Fertiliser Enhanced by Biofertiliser Technology. This project will deliver efficient use of the limited supplies of high quality phosphorus minerals as fertiliser-P, simultaneously acting to reverse and prevent soil acidification. These cost-effective benefits from utilising Australia's microbial biodiversity will have major economic and environmental impacts in rural Australia,increasing the profitability of farming and reducing the potential for contamination of aquatic systems and groundwater with nutrients causing algal blooms. By solving needs for fertiliser-P while preventing acidification of soil, farmers are expected to welcome this novel fertiliser technology.Read moreRead less
Spatio-temporal modelling of Ras dependent MAP kinase activation. This project is at the heart of the national research priority 'Frontier Technologies for Building and Transforming Australian Industries'. Using cutting edge methods and techniques of systems biology, coupled with innovative experimental molecular cell biology we will construct and simulate mathematical models of the EGF-regulated MAP kinase pathway. The project will yield new insights into the fundamental mechanisms of cell sign ....Spatio-temporal modelling of Ras dependent MAP kinase activation. This project is at the heart of the national research priority 'Frontier Technologies for Building and Transforming Australian Industries'. Using cutting edge methods and techniques of systems biology, coupled with innovative experimental molecular cell biology we will construct and simulate mathematical models of the EGF-regulated MAP kinase pathway. The project will yield new insights into the fundamental mechanisms of cell signal transduction that drive cell division, differentiation and transformation and may enable the design of new anticancer therapies. Importantly, the modelling and simulation methods developed in the project will have a general applicability to other complex systems such as sustainable ecological systems.Read moreRead less
Stochastic Modelling of Genetic Regulatory Networks: Subtitle - Genetic Regulation is a Noisy Business. The completion of the human genome marked the culmination of one hundred years of reductionist science in cell biology. Although further bioinformatics analysis will continue, the focus is shifting towards synthesis and understanding how the regulatory genetic components dynamically interact to form functional phenotypes. The key to this is the understanding of the roles of stochasticity in ....Stochastic Modelling of Genetic Regulatory Networks: Subtitle - Genetic Regulation is a Noisy Business. The completion of the human genome marked the culmination of one hundred years of reductionist science in cell biology. Although further bioinformatics analysis will continue, the focus is shifting towards synthesis and understanding how the regulatory genetic components dynamically interact to form functional phenotypes. The key to this is the understanding of the roles of stochasticity in cellular processes. This project will explore these roles and will develop an integrated complex systems modelling, simulation and visualisation framework. This will be used on an exemplar application for lineage commitment in haematopoiesis and for exploring and validating genetic regulatory models in general.Read moreRead less
Topological Approaches for Three Dimensional Graph Drawing. Human analysis of huge quantities of relational data in biotechnology, web engineering, social networks, and computer networks requires visualization. In recent years, three-dimensional visualisation has promised to give new insights into such abstract data. However the past ten years of visualization research has had very little impact on the industry; visualization software providers have not adopted visualization methods developed b ....Topological Approaches for Three Dimensional Graph Drawing. Human analysis of huge quantities of relational data in biotechnology, web engineering, social networks, and computer networks requires visualization. In recent years, three-dimensional visualisation has promised to give new insights into such abstract data. However the past ten years of visualization research has had very little impact on the industry; visualization software providers have not adopted visualization methods developed by academics. We hypothesise that current 3D relational visualization methods fail because they do not pay attention to the human perception of topology. In this project we will leverage mathematical topology to construct new methods for the 3D visualization of relational data.
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New Methods for Interactive Visualization of Large Microarray Data Sets. This project will investigate methods for visualising graphs produced by AI-based analysis of real-world biological data. These new visualisation methods will assist biologists to develop new DNA Microarray experiments, the source of raw data for visualisation. Data from new enhanced experiments, plus background knowledge from integrated public databases will produce richer data for visualisation, thus creating a positive f ....New Methods for Interactive Visualization of Large Microarray Data Sets. This project will investigate methods for visualising graphs produced by AI-based analysis of real-world biological data. These new visualisation methods will assist biologists to develop new DNA Microarray experiments, the source of raw data for visualisation. Data from new enhanced experiments, plus background knowledge from integrated public databases will produce richer data for visualisation, thus creating a positive feedback loop in the course of research into both topics.Read moreRead less
Emergence of robust, stable structures via computation within natural networks. An ever-increasing challenge for modern society is the sheer complexity of vast infrastructures. Unexpected, and sometimes catastrophic, behaviour often emerges from interactions between elements of large systems. As a result, highly complex systems such as the Internet, international finance markets, and power grids are highly susceptible to costly problems such as cascading failures, inefficiency, and critical sens ....Emergence of robust, stable structures via computation within natural networks. An ever-increasing challenge for modern society is the sheer complexity of vast infrastructures. Unexpected, and sometimes catastrophic, behaviour often emerges from interactions between elements of large systems. As a result, highly complex systems such as the Internet, international finance markets, and power grids are highly susceptible to costly problems such as cascading failures, inefficiency, and critical sensitivity. High-tech industries, such as biotechnology and information networking, also face problems in coordinating swarms of interacting agents. This project will contribute to solving such problems by identifying and adapting solutions from nature.Read moreRead less
Dual phase evolution in networks. A grand challenge for modern society is the sheer complexity of vast networks arising from organizations and infrastructures. Unexpected, sometimes catastrophic, behaviour often emerges from interactions within such systems. As a result, the Internet, financial markets, power grids and other vital infrastructures are susceptible to costly problems such as cascading failures, inefficiency, and unpredictability. High-tech industries, such as biotechnology and info ....Dual phase evolution in networks. A grand challenge for modern society is the sheer complexity of vast networks arising from organizations and infrastructures. Unexpected, sometimes catastrophic, behaviour often emerges from interactions within such systems. As a result, the Internet, financial markets, power grids and other vital infrastructures are susceptible to costly problems such as cascading failures, inefficiency, and unpredictability. High-tech industries, such as biotechnology and information networking, face problems in coordinating networks of interacting agents. This project will expand the horizon of complex systems by deriving the design principles underpinning stable and resilient network structures and validate these principles on real world networks.Read moreRead less