Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0775562
Funder
Australian Research Council
Funding Amount
$500,000.00
Summary
The Melbourne Nanofabrication Facility. Australia is desperately short of facilities for actual fabrication, prototyping and construction of advanced micromechanical and nanoscale systems. This is impeding both academic researchers and industrial developers in the materials, optics and biotechnological industries. The proposed instrument would complete the development of Australia's newest high resolution microscopy centre and enable a wide range of users to image, measure, build and design comp ....The Melbourne Nanofabrication Facility. Australia is desperately short of facilities for actual fabrication, prototyping and construction of advanced micromechanical and nanoscale systems. This is impeding both academic researchers and industrial developers in the materials, optics and biotechnological industries. The proposed instrument would complete the development of Australia's newest high resolution microscopy centre and enable a wide range of users to image, measure, build and design complex nanostructures at the atomic level and upwards. Read moreRead less
Realistic models of permeation in ion channels. Ion channels are formed by proteins in cell membranes and provide pathways for fast and controlled flow of selected ions. This activity generates action potentials in nerves and muscles that forms the basis of all movement, sensation and thought processes. Recent determination of the crystal structure of channel proteins has enabled construction of models that can relate channel function to its structure--necessary for understanding their operati ....Realistic models of permeation in ion channels. Ion channels are formed by proteins in cell membranes and provide pathways for fast and controlled flow of selected ions. This activity generates action potentials in nerves and muscles that forms the basis of all movement, sensation and thought processes. Recent determination of the crystal structure of channel proteins has enabled construction of models that can relate channel function to its structure--necessary for understanding their operation and seeking cures for diseases caused by their malfunction. This project aims to develop accurate ion-protein-water interactions for permeation models based on stochastic and molecular dynamics simulations using both classical and quantum mechanical methods.Read moreRead less
TOWARDS A COMPLETE DESCRIPTION OF HOW ENZYMES WORK: development of simulation methods and protocols, blind test predictions, and experimental validation. Enzymes catalyze quite fantastic chemistry under mild physiological conditions. Many special chemical concepts (such as "transition-state stabilization" and "entropy-enthalpy compensation") proposed to explain these powers are unnecessary. Uniquely for a catalyst, these powers are integral to the structure, properties and dynamics of the protei ....TOWARDS A COMPLETE DESCRIPTION OF HOW ENZYMES WORK: development of simulation methods and protocols, blind test predictions, and experimental validation. Enzymes catalyze quite fantastic chemistry under mild physiological conditions. Many special chemical concepts (such as "transition-state stabilization" and "entropy-enthalpy compensation") proposed to explain these powers are unnecessary. Uniquely for a catalyst, these powers are integral to the structure, properties and dynamics of the protein, as constrained and selected by evolution. The question is how do they work? Answering this requires energetic and thermodynamic analysis beyond current experimental techniques, but accessible by computer simulation. We aim to develop a robust toolkit of simulation methods and protocols, blind test them by predicting the mechanism of a new enzyme, with followup experimental validation.
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Importance of conformational and electrostatic contributions in simulations of enzyme reaction mechanisms. The research will contribute to the development of biomolecular simulation in Australia by demonstrating its potential to complement experiment, and also promote the effective use of APAC (Australian national supercomputer facilities) resources by providing advanced programs and computational protocols for other researchers. It will assist the diffusion of computational biology technology i ....Importance of conformational and electrostatic contributions in simulations of enzyme reaction mechanisms. The research will contribute to the development of biomolecular simulation in Australia by demonstrating its potential to complement experiment, and also promote the effective use of APAC (Australian national supercomputer facilities) resources by providing advanced programs and computational protocols for other researchers. It will assist the diffusion of computational biology technology into industrial applications such as rational drug design and protein engineering, as, for example, in our associated Linkage project grant, and provide novel insights into protein engineering and other sorts of design, which transcend concepts currently used in biomimetic chemistry.Read moreRead less
Hydrogen Abstraction in Chemical, Biochemical and Polymerization Processes. Hydrogen-abstraction reactions are of vital importance in the chemical, biochemical and polymerization processes that occur in everyday life. The objective of the proposed research is to improve our understanding of such reactions. State-of-the-art quantum chemistry calculations will be used to examine a broad range of hydrogen-abstraction reactions, and to obtain accurate information about the factors that influence suc ....Hydrogen Abstraction in Chemical, Biochemical and Polymerization Processes. Hydrogen-abstraction reactions are of vital importance in the chemical, biochemical and polymerization processes that occur in everyday life. The objective of the proposed research is to improve our understanding of such reactions. State-of-the-art quantum chemistry calculations will be used to examine a broad range of hydrogen-abstraction reactions, and to obtain accurate information about the factors that influence such reactions. Building on this work, more detailed case studies will be performed in two important areas: the hydrogen-abstraction steps in biochemical reactions mediated by coenzyme B12, and chain-transfer processes in conventional and controlled free-radical polymerization.Read moreRead less
Diversity out of a hybrid zone: the interplay of reinforcement and sexual selection in the formation of new species. How are there so many different species? Understanding how new species arise is a fundamental question because it explains current biodiversity and reveals the processes that will continue to give rise to new species in the future. An integral part of any animal species is who they choose to mate with, but how mate choice evolves to create new species remains poorly understood. He ....Diversity out of a hybrid zone: the interplay of reinforcement and sexual selection in the formation of new species. How are there so many different species? Understanding how new species arise is a fundamental question because it explains current biodiversity and reveals the processes that will continue to give rise to new species in the future. An integral part of any animal species is who they choose to mate with, but how mate choice evolves to create new species remains poorly understood. Here I will be studying the processes that affect the evolution of mate choice in an Australian rainforest frog hybrid zone. This system is uniquely suitable for providing internationally important insights into the evolutionary processes that form new species.Read moreRead less
Escalation of a coevolutionary arms race between cuckoos and their hosts: cognitive causes and evolutionary consequences. Cuckoos lay their eggs in the nests of other species, provoking an evolutionary arms race in which hosts evolve defences against parasitism and cuckoos evolve ever more cunning tricks to gain reproductive success. In principle, the degree of specialization required to defeat host defences could cause cuckoo speciation. Our previous research has revealed that the arms race bet ....Escalation of a coevolutionary arms race between cuckoos and their hosts: cognitive causes and evolutionary consequences. Cuckoos lay their eggs in the nests of other species, provoking an evolutionary arms race in which hosts evolve defences against parasitism and cuckoos evolve ever more cunning tricks to gain reproductive success. In principle, the degree of specialization required to defeat host defences could cause cuckoo speciation. Our previous research has revealed that the arms race between the Horsfield's bronze-cuckoo and its superb fairy-wren host has reached a uniquely advanced stage, hitherto undescribed, and previously thought imposssible to attain. We aim to investigate the mechanisms underlying this specialization and investigate whether it is driving speciation of the Chrysococcyx cuckoos.Read moreRead less
A multidisciplinary research program to assess limiting factors and predict impacts of climate change for endangered Australian orchids. Climate change poses a significant threat to biodiversity. Australian sexually deceptive orchids are dependent on obligate and specialised interactions with pollinators and fungi. Consequently, they may face a high risk of extinction if climate change uncouples these interactions. Thus orchids provide an important bio-indicator of change. The tools and expertis ....A multidisciplinary research program to assess limiting factors and predict impacts of climate change for endangered Australian orchids. Climate change poses a significant threat to biodiversity. Australian sexually deceptive orchids are dependent on obligate and specialised interactions with pollinators and fungi. Consequently, they may face a high risk of extinction if climate change uncouples these interactions. Thus orchids provide an important bio-indicator of change. The tools and expertise developed will contribute directly to the conservation of endangered Australian orchids, and will take into account the risks of climate change. The project will contribute to the priority research goals of sustainable use of Australia's biodiversity as well as responding to climate change and variability. The project will also provide high quality, cross-disciplinary training.Read moreRead less
Understanding “reinforcement”, an evolutionary process that can lead to the origin of new species and generate species diversity. Understanding how species are formed is of broad significance. National benefit will come from internationally competitive research and collaborations with leading international researchers. Benefits will also come under the ARC Priority Goals of 'An Environmentally Sustainable Australia' as I will (i) provide genetic data that will be invaluable for the conservation ....Understanding “reinforcement”, an evolutionary process that can lead to the origin of new species and generate species diversity. Understanding how species are formed is of broad significance. National benefit will come from internationally competitive research and collaborations with leading international researchers. Benefits will also come under the ARC Priority Goals of 'An Environmentally Sustainable Australia' as I will (i) provide genetic data that will be invaluable for the conservation of a highly threatened species, (ii) determine the importance of contact zones for generating new species and maintaining the evolutionary potential of regions, and (iii) address the role of climate change in shaping diversity over recent evolutionary time, an understanding of which is essential for predicting the impact of future change. Read moreRead less
Molecular Phylogenetics of Australian Myobatrachid Frogs and the Evolution of Reproductive Strategies. The Family Myobatrachidae (22 genera, 120+ species) is wholly endemic to the Australo-Papuan region, represents 57% of the Australian frog fauna and displays more diversity in reproductive strategies than any other group of frogs. We will recover a robust molecular phylogeny for all species in this family and use it to exploit existing ecological and behavioural data sets to provide powerful te ....Molecular Phylogenetics of Australian Myobatrachid Frogs and the Evolution of Reproductive Strategies. The Family Myobatrachidae (22 genera, 120+ species) is wholly endemic to the Australo-Papuan region, represents 57% of the Australian frog fauna and displays more diversity in reproductive strategies than any other group of frogs. We will recover a robust molecular phylogeny for all species in this family and use it to exploit existing ecological and behavioural data sets to provide powerful tests of alternative hypotheses concerning the evolution of diverse reproductive strategies. This multi-disciplinary research project will provide detailed phylogenetic information for one of the most diverse vertebrate radiations in Australia and address important questions in historical ecology.Read moreRead less