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
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
Molecular Energies and Non-Bonded Interactions. The development of new techniques that allow non-bonded chemical interactions to be modelled and predicted reliably and accurately will allow researchers in the chemical, and pharmaceutical sciences to predict the physical and chemical behaviour of moderately large molecular systems with an accuracy and efficiency that has not previously been possible. The software that will result will enable cost and time savings in molecular design within the m ....Molecular Energies and Non-Bonded Interactions. The development of new techniques that allow non-bonded chemical interactions to be modelled and predicted reliably and accurately will allow researchers in the chemical, and pharmaceutical sciences to predict the physical and chemical behaviour of moderately large molecular systems with an accuracy and efficiency that has not previously been possible. The software that will result will enable cost and time savings in molecular design within the medical and agricultural contexts.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
Multivariate Algorithmics: Meeting the Challenge of Real World computational complexity. This Project will result in better methods for designing the algorithms that all computer applications depend on. Algorithms are the instruction sets that tell computers how to process information. Some information processing tasks are intrinsically difficult, even for computers working at enormous speeds. This Project will deliver new mathematical approaches to overcome these difficulties. More efficient al ....Multivariate Algorithmics: Meeting the Challenge of Real World computational complexity. This Project will result in better methods for designing the algorithms that all computer applications depend on. Algorithms are the instruction sets that tell computers how to process information. Some information processing tasks are intrinsically difficult, even for computers working at enormous speeds. This Project will deliver new mathematical approaches to overcome these difficulties. More efficient algorithmic approaches for difficult problems enable advances in all areas of computer applications such as medical diagnosis and health prediction, national security, communications efficiency, industrial productivity and all fields of science and engineering.Read moreRead less
Algorithms and computation in four-dimensional topology. This project will establish Australia as a world leader in computational topology, particularly in the all-important areas of topology in three and four dimensions. In four dimensions this work will be truly groundbreaking; until now the field has seen little development due to the complexity of the algorithms and computations required, and the applicant is in the unique position of having the necessary tools to make significant progress ....Algorithms and computation in four-dimensional topology. This project will establish Australia as a world leader in computational topology, particularly in the all-important areas of topology in three and four dimensions. In four dimensions this work will be truly groundbreaking; until now the field has seen little development due to the complexity of the algorithms and computations required, and the applicant is in the unique position of having the necessary tools to make significant progress in a feasible time frame. In three dimensions this project will strengthen the distinguished computational topology community in Melbourne, led by pioneers such as Rubinstein, Goodman, Hodgson as well as the applicant himself.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
Algebraic Methods in Design and Analysis of Stream Ciphers. The project investigates the problem of communication security in the mobile environment where both confidentiality and authenticity are of prime concern. Stream ciphers are a very natural choice in mobile environment as they provide an efficient cryptographic protection using a limited computing resources. We model stream cipher as a system of multivariate equations. In this approach, security of stream ciphers can be measured as the c ....Algebraic Methods in Design and Analysis of Stream Ciphers. The project investigates the problem of communication security in the mobile environment where both confidentiality and authenticity are of prime concern. Stream ciphers are a very natural choice in mobile environment as they provide an efficient cryptographic protection using a limited computing resources. We model stream cipher as a system of multivariate equations. In this approach, security of stream ciphers can be measured as the complexity of an algorithm that solves the appropriate system of equations. This project leads to new techniques for the design and analysis of stream ciphers.Read moreRead less
Algebraic Models of Stream Ciphers. The project investigates communication security in the mobile environment where both confidentiality and authenticity are of a prime concern. Stream ciphers are a natural choice in mobile environments as they provide an efficient cryptographic protection using a limited computing resources. We treat stream ciphers as algebraic objects whose properties fully determine their cryptographic strength. We first analyse existing stream ciphers showing their algebraic ....Algebraic Models of Stream Ciphers. The project investigates communication security in the mobile environment where both confidentiality and authenticity are of a prime concern. Stream ciphers are a natural choice in mobile environments as they provide an efficient cryptographic protection using a limited computing resources. We treat stream ciphers as algebraic objects whose properties fully determine their cryptographic strength. We first analyse existing stream ciphers showing their algebraic properties and later we derive a design methodology for provably secure stream ciphers. The project leads to new secure and efficient designs for stream ciphers that are the preferred cryptographic tools used in Australian industry.Read moreRead less