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
Efficient Pre-Processing of Hard Problems: New Approaches, Basic Theory and Applications. Computers store even larger amounts of data about all aspects of human and industrial activity. However, they have not become significantly better at solving common problems in optimization and search. Traditional complexity theory indicates many of these problems require algorithms that are very unlikely to exist. The Parameterized Complexity approach allows us to obtain very efficient algorithms for a lar ....Efficient Pre-Processing of Hard Problems: New Approaches, Basic Theory and Applications. Computers store even larger amounts of data about all aspects of human and industrial activity. However, they have not become significantly better at solving common problems in optimization and search. Traditional complexity theory indicates many of these problems require algorithms that are very unlikely to exist. The Parameterized Complexity approach allows us to obtain very efficient algorithms for a large variety of problems, but the machinery required was diverse and complicated. This research will organize the machinery into a new approach that systematically finds good algorithms by applying simplifications around a parameter of the domain of the problem. As a result, efficient algorithms are obtained for many diverse areas.Read moreRead less
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
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
Coarse Grained Parallel Algorithms. Various fields of research face barriers created by problems that are computationally hard and/or require processing of large amounts of data. For example, some computational biochemistry methods on protein or gene sequences can not be scaled up to data sets required for human health research because of performance problems. Parallel computing enables new research by increasing the size of solvable problems. In addition to fundamental parallel computing resear ....Coarse Grained Parallel Algorithms. Various fields of research face barriers created by problems that are computationally hard and/or require processing of large amounts of data. For example, some computational biochemistry methods on protein or gene sequences can not be scaled up to data sets required for human health research because of performance problems. Parallel computing enables new research by increasing the size of solvable problems. In addition to fundamental parallel computing research, this project studies parallel algorithms for structure-based drug design and protein-protein interaction prediction that will enable new biochemistry research, as well as parallel algorithms for data cubes that will help enable the next generation of very large data warehouses.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