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
Multiscale stochastic modelling of genetic regulatory mechanisms. 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 ex ....Multiscale stochastic modelling of genetic regulatory mechanisms. 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 for exploring and validating genetic regulatory models in general. This will be used on an exemplar application for understanding the induction process in lambda phage.Read moreRead less
Use of Interval Arithmetic and GRID Computing in Computational Molecular Science: Bounding Errors and Locating Global Minima. Catastrophic failure of the Ariane 5 rocket in 1996 and the inability of Patriot missile systems to reach their targets during the 1991 Gulf war were both attributed to numerical computing errors. Less dramatic, but in a similar vein, this project aims to study the numerical stability of contemporary computational molecular science applications. The focus will be on linea ....Use of Interval Arithmetic and GRID Computing in Computational Molecular Science: Bounding Errors and Locating Global Minima. Catastrophic failure of the Ariane 5 rocket in 1996 and the inability of Patriot missile systems to reach their targets during the 1991 Gulf war were both attributed to numerical computing errors. Less dramatic, but in a similar vein, this project aims to study the numerical stability of contemporary computational molecular science applications. The focus will be on linear scaling electronic structure codes, methods that are critical to the study of nano- and bio-materials, and are therefore of great importance to our economic future and medical well being. The project will build expertise within Australia in the area of interval arithmetic, an area that is currently poorly represented.Read moreRead less
Advanced computational techniques for micro/nano multiscale systems of NEMS/BioMEMS. The outcome of this project will have the following benefits to Australia.
1) It will improve the research level in the area of multiscale simulation of NEMS/BioMEMS;
2) The project will be beneficial to possibly establish new industries in the areas of nanotechnology as well as to make good use of today's microelectronics, mircofabrication and computer technology that have already established in Australia;
....Advanced computational techniques for micro/nano multiscale systems of NEMS/BioMEMS. The outcome of this project will have the following benefits to Australia.
1) It will improve the research level in the area of multiscale simulation of NEMS/BioMEMS;
2) The project will be beneficial to possibly establish new industries in the areas of nanotechnology as well as to make good use of today's microelectronics, mircofabrication and computer technology that have already established in Australia;
3) The manpower trained by this project in the areas of multi-scale simulation of MEMS/NEMS/BioMEMS will provide a crucial support for the future industry of Australia.
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Computer Assisted Research Mathematics and its Applications. The mathematics community will benefit from infusion of new computer-assisted techniques and modalities for research and training post-graduate students, both from my pure research project and through development of an associated research centre. Ultimately, this should also help more school students learn mathematics well and so play a part in addressing Australia's skill shortage. Also, the work on optimization algorithms promises to ....Computer Assisted Research Mathematics and its Applications. The mathematics community will benefit from infusion of new computer-assisted techniques and modalities for research and training post-graduate students, both from my pure research project and through development of an associated research centre. Ultimately, this should also help more school students learn mathematics well and so play a part in addressing Australia's skill shortage. Also, the work on optimization algorithms promises to improve the performance and quality of many practical signal reconstruction methods. These are used by varied Australian industries from telecommunication to mining and by researchers in the digital arts and fields such as astronomy, physics, chemistry, bioscience, geoscience, engineering and medicine.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
Black Hole Accretion: The Effects of Magnetic Fields and Radiation. This project represents a significant contribution by Australian researchers to one of Science's Big Questions: How do Black Holes channel gravitational energy into radiation at many different energies and into high speed outflows. It offers Australian Astronomy an opportunity to expand its endeavours into the rapidly growing and high profile areas of high-energy and computational astrophysics, injecting new expertise into the i ....Black Hole Accretion: The Effects of Magnetic Fields and Radiation. This project represents a significant contribution by Australian researchers to one of Science's Big Questions: How do Black Holes channel gravitational energy into radiation at many different energies and into high speed outflows. It offers Australian Astronomy an opportunity to expand its endeavours into the rapidly growing and high profile areas of high-energy and computational astrophysics, injecting new expertise into the interpretation of multi-wavelength data on accreting black holes. We will train a new cohort of internationally competitive students and early career researchers, equipping them with the advanced computational and modelling skills that are in increasingly higher demand in many technology-based industries.Read moreRead less
Modelling soft filled viscoelastic solids. Wheat flour doughs are made in vast quantities daily, and improvements in processing, especially in sheeting (rolling) and extrusion are needed. To enable this we will create a novel mathematical description of the material which will be useful for predicting the shapes of processed products. Wheat breeding cycles can be shortened by using the model rheological parameters, since baking quality is closely linked to dough rheology. A number of Australian ....Modelling soft filled viscoelastic solids. Wheat flour doughs are made in vast quantities daily, and improvements in processing, especially in sheeting (rolling) and extrusion are needed. To enable this we will create a novel mathematical description of the material which will be useful for predicting the shapes of processed products. Wheat breeding cycles can be shortened by using the model rheological parameters, since baking quality is closely linked to dough rheology. A number of Australian wheats will be considered and their rheologies will be compared.Read moreRead less
Optimal Transforms of Random Vectors. This proposal focusses on development of optimal transforms to describe and model nonlinear phenomena when only statistical information is known. An optimal transform is a mathematical procedure that enables us to process information in a way that is most suited to the task in hand. These transforms have been successfully used in approximation, information theory, communications, control theory and signal and image processing. Applications include modelli ....Optimal Transforms of Random Vectors. This proposal focusses on development of optimal transforms to describe and model nonlinear phenomena when only statistical information is known. An optimal transform is a mathematical procedure that enables us to process information in a way that is most suited to the task in hand. These transforms have been successfully used in approximation, information theory, communications, control theory and signal and image processing. Applications include modelling of physical, chemical and biological systems, filtering and compression of signals and data classification and clustering. We propose two new hybrid models for realistic transforms in a general structural framework.
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HYBRID METHODS FOR SOLVING LARGE-SCALE OPTIMISATION PROBLEMS. Mathematical modelling and optimisation plays a crucial role in the advancement of modern business, science and technology. A significant benefit of this project is the development of a range of powerful computational tools for improving the productivity of Australian industry, including: agriculture; communications; defence; manufacturing; mining and petroleum; transport and logistics. These tools will be built upon advances in the f ....HYBRID METHODS FOR SOLVING LARGE-SCALE OPTIMISATION PROBLEMS. Mathematical modelling and optimisation plays a crucial role in the advancement of modern business, science and technology. A significant benefit of this project is the development of a range of powerful computational tools for improving the productivity of Australian industry, including: agriculture; communications; defence; manufacturing; mining and petroleum; transport and logistics. These tools will be built upon advances in the fundamental theory developed by the research team. The resulting high quality publications and associated algorithms will greatly enhance Australia's international scientific reputation and provide Australian industry with new cutting-edge optimisation technology.Read moreRead less