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Function, Mechanism and Dynamics in Fluorescent Proteins: a Computational Investigation. The rich reservoir of chromoproteins and fluorescent proteins in the ecosystem of the Great Barrier Reef offers Australia a unique natural advantage for the development of a niche biotechnology industry based on fluorescent markers for cellular biology and biomedical imaging. This project provides a crucial component of the science that is necessary for developing such an industry: a molecular-level knowledg ....Function, Mechanism and Dynamics in Fluorescent Proteins: a Computational Investigation. The rich reservoir of chromoproteins and fluorescent proteins in the ecosystem of the Great Barrier Reef offers Australia a unique natural advantage for the development of a niche biotechnology industry based on fluorescent markers for cellular biology and biomedical imaging. This project provides a crucial component of the science that is necessary for developing such an industry: a molecular-level knowledge of how these proteins function and how we can manipulate and enhance their properties as imaging agents. It will achieve fundamental advances in biomolecular modelling techniques, train graduates with exceedingly valuable skill sets as well as deriving knowledge that aids the development of Australia's biotech industries.Read moreRead less
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0668520
Funder
Australian Research Council
Funding Amount
$560,000.00
Summary
South Australian Supercluster Facility. This project will maintain and build on existing excellence and strength in areas ranging from computational chemistry, bioinformatics, and plant functional genomics through to water resources management, fluid dynamics and novel fibres and materials for photonics. It will enable the development of cutting edge computational tools and techniques and will maintain and grow strong international links. It will produce graduates of the highest quality able t ....South Australian Supercluster Facility. This project will maintain and build on existing excellence and strength in areas ranging from computational chemistry, bioinformatics, and plant functional genomics through to water resources management, fluid dynamics and novel fibres and materials for photonics. It will enable the development of cutting edge computational tools and techniques and will maintain and grow strong international links. It will produce graduates of the highest quality able to use advanced computing to solve real-world problems. The training provided and the tools and techniques developed will bring major economic benefits and provide excellent links to Australian industry.Read moreRead less
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0347582
Funder
Australian Research Council
Funding Amount
$500,000.00
Summary
South Australian Supercomputing Facility. This grant will fund the construction and installation of a state-of-the-art, heterogeneous supercomputing facility to be named the "South Australian Supercomputing Facility". The facility will be available to all of the State's academic and industrial researchers with advanced high-performance computing needs in a transparent and equitable way. Areas of research excellence to be supported by the facility include but are not limited to: research in comp ....South Australian Supercomputing Facility. This grant will fund the construction and installation of a state-of-the-art, heterogeneous supercomputing facility to be named the "South Australian Supercomputing Facility". The facility will be available to all of the State's academic and industrial researchers with advanced high-performance computing needs in a transparent and equitable way. Areas of research excellence to be supported by the facility include but are not limited to: research in computational physics, computational chemistry, geophysics, computational fluid dynamics, oil and water resource modelling, plant science, bio-informatics, space-environment research, and high-performance, parallel, and grid-based computing.Read moreRead less
Transformation of organics in the unpolluted atmosphere. This project will develop the chemistry needed to model the removal of methane and other organic compounds from the unpolluted atmosphere. While the chemistry of urban environments is now understood, there are major shortcomings when describing remote environments, limiting our ability to model the lifetimes of key greenhouse gases and toxins.
How do biomolecules control excited-state dynamics? This project will use a combined theoretical and experimental approach to find out why non-fluorescent dyes become fluorescent when they bind certain biomolecules. This project's science will help guide the development of smart, biomimetic energy technologies and increase our understanding of how light powers living things.
The First Chemically Accurate Tools in Theoretical Materials Research. Non-metallic materials are widely used in catalytic, separation and sensing applications. This project will create a new, accurate, general and systematic approach to the computational study of non-metallic materials and will provide an enormous step forward in our ability to design these materials for specific applications. With ever increasing demand, growing world population and shrinking natural resources, the benefits of ....The First Chemically Accurate Tools in Theoretical Materials Research. Non-metallic materials are widely used in catalytic, separation and sensing applications. This project will create a new, accurate, general and systematic approach to the computational study of non-metallic materials and will provide an enormous step forward in our ability to design these materials for specific applications. With ever increasing demand, growing world population and shrinking natural resources, the benefits of such rational materials design impact on the development of new, safer, more efficient, reusable materials in chemical, engineering, electronic and biological applications. 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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Quantum chemical methods: From wavefunction to density functional theory. This project aims to address a major challenge in quantum chemistry - how to extend the applicability of high-level quantum chemical methods to larger molecules. High-level quantum chemical methods can consistently obtain reliable thermochemical and kinetic data, but due to their steep computational cost, they are only applicable to relatively small molecules. The project expects to introduce new concepts and methodologies ....Quantum chemical methods: From wavefunction to density functional theory. This project aims to address a major challenge in quantum chemistry - how to extend the applicability of high-level quantum chemical methods to larger molecules. High-level quantum chemical methods can consistently obtain reliable thermochemical and kinetic data, but due to their steep computational cost, they are only applicable to relatively small molecules. The project expects to introduce new concepts and methodologies that build on recent breakthrough research in the field of ab initio computational chemistry. The new methods should be capable of energetic predictions of unprecedented accuracy for relatively large systems across the Periodic Table and will be used for the development of better density functional theory procedures.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
Computer simulation of DNA biochips. The DNA biochip technology has been a major breakthrough in cell biology and clinical analysis. Companies in Australia and in the rest of the world are now developing biochips for genome sequencing and point-of-care diagnosis. DNA biochips have the potential to provide simple, fast and accurate clinical analysis, thus enhancing the efficiency of medical treatments and reducing the costs of health care.
The structural properties of the immobilized DNA are cri ....Computer simulation of DNA biochips. The DNA biochip technology has been a major breakthrough in cell biology and clinical analysis. Companies in Australia and in the rest of the world are now developing biochips for genome sequencing and point-of-care diagnosis. DNA biochips have the potential to provide simple, fast and accurate clinical analysis, thus enhancing the efficiency of medical treatments and reducing the costs of health care.
The structural properties of the immobilized DNA are critical for determining the DNA chip sensitivity and efficiency. A fundamental understanding of the molecular interactions at the surface of a biochip is therefore not only relevant for the scientific community, but can have direct implications for the design of improved DNA chips.Read moreRead less