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.
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
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