Electron and Positron Interactions with Bio-Molecules. This program of research will quantify reaction rates and elucidate reaction pathways for a range of important processes in our bodies involving ionising radiation. It will lead to a greatly improved understanding of positron and electron interactions with biological systems, including DNA and its constituent molecules and, through a better understanding of the underlying fundamental interactions, will lay foundations for improvements in te ....Electron and Positron Interactions with Bio-Molecules. This program of research will quantify reaction rates and elucidate reaction pathways for a range of important processes in our bodies involving ionising radiation. It will lead to a greatly improved understanding of positron and electron interactions with biological systems, including DNA and its constituent molecules and, through a better understanding of the underlying fundamental interactions, will lay foundations for improvements in technologies such as PET imaging. 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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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
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
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
Special Research Initiatives - Grant ID: SR0354716
Funder
Australian Research Council
Funding Amount
$10,000.00
Summary
Energetically Open Systems Research Network Study. Conceptual frameworks arising in the physical sciences, such as non-equilibrium statistical mechanics and thermodynamics, synergetics, chaos and dynamical systems theory, are seminal in the emerging science of complexity. This study will lay the groundwork for a network to link Australian and overseas research on these fundamental concepts, and their application within the context of entropy-producing systems vital to the long-term sustainabilit ....Energetically Open Systems Research Network Study. Conceptual frameworks arising in the physical sciences, such as non-equilibrium statistical mechanics and thermodynamics, synergetics, chaos and dynamical systems theory, are seminal in the emerging science of complexity. This study will lay the groundwork for a network to link Australian and overseas research on these fundamental concepts, and their application within the context of entropy-producing systems vital to the long-term sustainability of the earth - oceans, atmosphere, biosphere, CO2-free energy production, space and solar environment. The network would facilitate the development of young investigators and be linked into wider complex systems networks such as the CSIRO Centre for Complex Systems Science.Read moreRead less
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989915
Funder
Australian Research Council
Funding Amount
$127,000.00
Summary
X-ray Nano-scale Coherence Facility. Australia is rapidly developing into a world leader for x-ray imaging. This position has been supported by leading research groups and more recently by the development of the Australian Synchrotron. This project will fill a vital missing link in the experimental capability of Australian researchers - a flexible facility that can provide a nanoscale x-ray source. This enhanced capability will lead to new developments in coherent imaging methods. These new meth ....X-ray Nano-scale Coherence Facility. Australia is rapidly developing into a world leader for x-ray imaging. This position has been supported by leading research groups and more recently by the development of the Australian Synchrotron. This project will fill a vital missing link in the experimental capability of Australian researchers - a flexible facility that can provide a nanoscale x-ray source. This enhanced capability will lead to new developments in coherent imaging methods. These new methods will be used in the study of biological systems, leading to better drug design as well as in the study of materials, leading to stronger and lighter components. Read moreRead less
Intermolecular interactions revisited-Flaws in the fabric and applications to lower-dimensional structures. This project aims to capitalise on recent developments, that have shown that previously accepted theories are deeply flawed, in various applications in fundamental physics and in unsolved problems in biology that involve electromagnetic fields. Interactions driven
by electromagnetic fluctuation forces, and real photon exchange, between molecules will be investigated. The project will inv ....Intermolecular interactions revisited-Flaws in the fabric and applications to lower-dimensional structures. This project aims to capitalise on recent developments, that have shown that previously accepted theories are deeply flawed, in various applications in fundamental physics and in unsolved problems in biology that involve electromagnetic fields. Interactions driven
by electromagnetic fluctuation forces, and real photon exchange, between molecules will be investigated. The project will investigate how dispersion interactions change in mesoscopic pores, in electrolytes, and at finite temperatures. Applications involve
catalysis, molecular formation, and quantum logic. The project also aims to develop a unified theory for energy and charge transfer, relevant for photosynthesis and the way biological molecules transfer information.Read moreRead less
Polymer Globules: Beyond the Homopolymer Model. Polymers are long chainlike molecules which play a crucial role in many aspects of our lives. As plastics they represent the most versatile and ubiquitous of man-made materials. Moreover, all living things depend on polymers for the structure of their cells and for the inheritance and function through DNA and proteins. Despite their importance our understanding of polymers is rather limited. The research funded by this proposal will enable us to ....Polymer Globules: Beyond the Homopolymer Model. Polymers are long chainlike molecules which play a crucial role in many aspects of our lives. As plastics they represent the most versatile and ubiquitous of man-made materials. Moreover, all living things depend on polymers for the structure of their cells and for the inheritance and function through DNA and proteins. Despite their importance our understanding of polymers is rather limited. The research funded by this proposal will enable us to understand more complicated kinds of polymers. This will help uncover some fascinating physics and in the long term develop new materials and promote new advances in biology. Read moreRead less