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
How Large Earthquakes Change Our Dynamically Deforming Planet. The project aims to understand the multiscale dynamics of interacting faults on a global scale using novel computer simulations with unprecedented spatial and temporal resolution. The focus of the research is to investigate the two-way coupling that exists between cycles of great earthquakes on plate boundaries, the global stress field, deformation within the crust, and changes to the Earth's dynamic topography. This is an important, ....How Large Earthquakes Change Our Dynamically Deforming Planet. The project aims to understand the multiscale dynamics of interacting faults on a global scale using novel computer simulations with unprecedented spatial and temporal resolution. The focus of the research is to investigate the two-way coupling that exists between cycles of great earthquakes on plate boundaries, the global stress field, deformation within the crust, and changes to the Earth's dynamic topography. This is an important, foundational question in the emerging field of decadal scale global geodynamics. The tools are intended to improve reference models used to study sea-level changes in response to global ice loss. They support better climate models and improved forward planning tools for at-risk coastal communities.Read moreRead less
Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying c ....Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying cutting edge genome biology tools and algorithms. The economically significant study system is the devastating wheat stripe rust fungus. This pathogen costs Australian farmers over $100 million a year. New understanding is expected to lead to better disease management, reduced fungicide applications, and increased yields.Read moreRead less
A theoretical hierachy to investigate the electronic behaviour of graphene nanostructures under realistic conditions. One of the most exciting new nano-materials is graphene which promises to be the basis of a new industry producing nano-electronics and nano-devices such as chemical sensors. This project aims to provide sound scientific knowledge on the effects of environmental conditions on the properties of graphene which are vital for its industrial use.
Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of new metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of industrial and synthetic importance. These outcomes will have a significant impact on the development of both novel transition metal systems for synthetic chemistry and new industrial procedures for the activation and cleavage of multiply-bonded molecules su ....Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of new metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of industrial and synthetic importance. These outcomes will have a significant impact on the development of both novel transition metal systems for synthetic chemistry and new industrial procedures for the activation and cleavage of multiply-bonded molecules such as molecular nitrogen and carbon dioxide. They will lead to new consumer products, better methods of production, and potential downstream applications such as nitric oxide/nitrogen dioxide converters and carbon dioxide emission controls.Read moreRead less
Activation and Scission of Small Molecules using Three-Coordinate Metal Complexes. Chemists have long admired the ease with which such fundamental molecules as nitrogen, oxygen and carbon dioxide are processed in biological systems under mild conditions in contrast to existing industrial processes such as nitrogen 'fixation' which require drastic temperatures and pressures. Our project addresses this inbalance by using powerful computational methods to design highly-tuned chemical systems based ....Activation and Scission of Small Molecules using Three-Coordinate Metal Complexes. Chemists have long admired the ease with which such fundamental molecules as nitrogen, oxygen and carbon dioxide are processed in biological systems under mild conditions in contrast to existing industrial processes such as nitrogen 'fixation' which require drastic temperatures and pressures. Our project addresses this inbalance by using powerful computational methods to design highly-tuned chemical systems based on three-coordinate metal complexes which are specific for the activation and scission of important small molecules possessing multiple bonds.Read moreRead less
Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of chemical importance. This will have a significant impact on industry by providing cheaper and safer alternatives to currently expensive and hazardous processes for producing nitrogen and phosphorus containing compounds esential to the chemical and agricultural i ....Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of chemical importance. This will have a significant impact on industry by providing cheaper and safer alternatives to currently expensive and hazardous processes for producing nitrogen and phosphorus containing compounds esential to the chemical and agricultural industries. It will also greatly benefit the chemical community by providing novel routes to constructing metal complexes with unusual and exotic ligands. These outcomes will lead to new consumer products and potential downstream applications such as nitric oxide/nitrogen dioxide converters and carbon dioxide emission controls.Read moreRead less
Generalised density functional theory for accurate chemistry. The project aims to construct two new methods for predicting chemical structure, bonding and reactivity. The first of these (gLDA2) would be useful for modelling molecules whose electrons are constrained to a two-dimensional plane. The second (gLDA3) would be useful for modelling molecules with unconstrained electrons. The project plans to implement the two methods in user-friendly software packages and made available to researchers i ....Generalised density functional theory for accurate chemistry. The project aims to construct two new methods for predicting chemical structure, bonding and reactivity. The first of these (gLDA2) would be useful for modelling molecules whose electrons are constrained to a two-dimensional plane. The second (gLDA3) would be useful for modelling molecules with unconstrained electrons. The project plans to implement the two methods in user-friendly software packages and made available to researchers in Australia and around the world improve manufacturing efficiency in the chemical, biological, medicinal and agricultural contexts. Unlike the semi-empirical approaches that they seek to replace, these two new methods will be derived from the properties of electrons on spheres or hyperspheres and thereby have a solid foundation in quantum mechanics.Read moreRead less
The energetics and dynamics of chemical reactions of polyatomic molecules involving multiple electronic states. This project will produce, from first principles, the first quantitatively accurate computer simulations of chemical reactions which involve several atoms and multiple electronic states. Many of the most important chemical reactions in the atmosphere (and elsewhere) involve changing both the shape of the molecules and their electronic structure. Many of these reactions are difficult to ....The energetics and dynamics of chemical reactions of polyatomic molecules involving multiple electronic states. This project will produce, from first principles, the first quantitatively accurate computer simulations of chemical reactions which involve several atoms and multiple electronic states. Many of the most important chemical reactions in the atmosphere (and elsewhere) involve changing both the shape of the molecules and their electronic structure. Many of these reactions are difficult to study in the laboratory, and consequently computer simulation is an essential component of the study of such reactions. U nderstanding how these reactions occur, and how fast they proceed, are important to our understanding of the dynamics of the atmosphere and other large scale reactors.Read moreRead less