First Principles Design of Second-Generation Protein Stains. Proteomics is an emerging technology which has the potential to revolutionize modern biology and medicine. Extremely sensitive protein stains are a key proteomics technology, and in conjunction with gel electrophoresis, they facilitate the rapid and quantitative detection of all polypeptides in a cell. However, the tools of proteomics must rapidly advance (cheaper, greater sensitivity, more reliable, safer to handle) before the techn ....First Principles Design of Second-Generation Protein Stains. Proteomics is an emerging technology which has the potential to revolutionize modern biology and medicine. Extremely sensitive protein stains are a key proteomics technology, and in conjunction with gel electrophoresis, they facilitate the rapid and quantitative detection of all polypeptides in a cell. However, the tools of proteomics must rapidly advance (cheaper, greater sensitivity, more reliable, safer to handle) before the technology can mature to the stage where its full potential is realized. We will enable the evolution of proteomics by devising second generation fluorescent protein stains, using the environmentally-friendly natural product, epicocconone, as our design platform.Read moreRead less
Persistent Triplet Carbenes. Viable or Not? Triplet carbenes have significant potential real world applications, such as in modern electronics. However, they are highly reactive (lifetimes typically < 1 day), and this has stymied their development. Can I design so called persistent triplet-carbenes, which have significant lifetimes? I will try to using computer chemistry. In doing so, I will provide synthetic chemists with 'high-value' targets for preparation, hence saving tax dollars and minimi ....Persistent Triplet Carbenes. Viable or Not? Triplet carbenes have significant potential real world applications, such as in modern electronics. However, they are highly reactive (lifetimes typically < 1 day), and this has stymied their development. Can I design so called persistent triplet-carbenes, which have significant lifetimes? I will try to using computer chemistry. In doing so, I will provide synthetic chemists with 'high-value' targets for preparation, hence saving tax dollars and minimizing creation of environmentally damaging waste. Read moreRead less
Voids in molecular crystals: Novel computational approaches to their characterization, physicochemical nature, and influence on bulk properties. Key to the research objectives is further development of our own innovative software and techniques, now used by hundreds of researchers worldwide for the visualization and exploration of the structure and properties of molecular crystals. Through involvement of postdoctoral fellows and PhD students in an international collaborative research program inv ....Voids in molecular crystals: Novel computational approaches to their characterization, physicochemical nature, and influence on bulk properties. Key to the research objectives is further development of our own innovative software and techniques, now used by hundreds of researchers worldwide for the visualization and exploration of the structure and properties of molecular crystals. Through involvement of postdoctoral fellows and PhD students in an international collaborative research program involving a synergy between software development and visualization, and sophisticated modelling of the detailed nature of molecular crystals, the project contributes directly to producing researchers familiar with state-of-the-art theoretical and computational techniques, and well equipped to match the needs of one of the nation's articulated research priorities.Read moreRead less
Computational Nanofluidics. This project will generate an increased level of skill and expertise in Australia in the emerging science of nanotechnology. To realise the promise of nanotechnology, a means of controlled propulsion on the nano scale is vital. A deeper understanding of nanofluidics that allows greater predictive capacities can greatly aid this realisation. It is highly likely that computational nanofluidics will play as important a role in nanotechnology based industries as computat ....Computational Nanofluidics. This project will generate an increased level of skill and expertise in Australia in the emerging science of nanotechnology. To realise the promise of nanotechnology, a means of controlled propulsion on the nano scale is vital. A deeper understanding of nanofluidics that allows greater predictive capacities can greatly aid this realisation. It is highly likely that computational nanofluidics will play as important a role in nanotechnology based industries as computational fluid dynamics (CFD) currently plays in today's manufacturing, automotive and aerospace industries. The skills and knowledge gained from this project will enhance our international competitiveness in this area. Read moreRead less
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.
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
Accurate quantum modeling of the van der Waals interaction and its application to molecular physisorption onto surfaces. Developing zero emission clean fuel technology for transportation and developing sensitive diagnostic markers for medical diagnosis will clearly benefit Australia. In both cases large technological challenges need to be overcome. This investigation will provide theoretical insight and understanding into the molecular processes which underpin these highly desirable technologies ....Accurate quantum modeling of the van der Waals interaction and its application to molecular physisorption onto surfaces. Developing zero emission clean fuel technology for transportation and developing sensitive diagnostic markers for medical diagnosis will clearly benefit Australia. In both cases large technological challenges need to be overcome. This investigation will provide theoretical insight and understanding into the molecular processes which underpin these highly desirable technologies and aid scientists and engineers in their development. A further, more general, outcome will be an accurate and predictive methodology for investigating nanotechnology problems in any material where molecular physisorption is an important process.Read moreRead less
Fundamental Theoretical Study of Hydrogen Interactions with Novel Nanostructures. While governments around the world are planning to implement a hydrogen-based energy economy in the next several decades, the delivery of practical hydrogen energy technology has proven elusive to date, with major developments required in the production, storage and transport of hydrogen. This research will undertake to provide one key step in the development of safe and efficient hydrogen storage, namely a fundam ....Fundamental Theoretical Study of Hydrogen Interactions with Novel Nanostructures. While governments around the world are planning to implement a hydrogen-based energy economy in the next several decades, the delivery of practical hydrogen energy technology has proven elusive to date, with major developments required in the production, storage and transport of hydrogen. This research will undertake to provide one key step in the development of safe and efficient hydrogen storage, namely a fundamental study delivering basic knowledge of hydrogen interactions with nano-structured materials constructed from inexpensive light metals such as Aluminium.Read moreRead less
Understanding and controlling the processes underlying self assembly of nanostructures on surfaces. Efficient clean fuel technology, new classes of nano- and bio-materials, bio specific drug delivery systems, efficient environmental remediation technologies, advanced catalytic applications, namely every area of technology would benefit from the ability to control self-assembly of matter at the atomic level during fabrication of nanodevices. This proposal seeks to understand the processes driving ....Understanding and controlling the processes underlying self assembly of nanostructures on surfaces. Efficient clean fuel technology, new classes of nano- and bio-materials, bio specific drug delivery systems, efficient environmental remediation technologies, advanced catalytic applications, namely every area of technology would benefit from the ability to control self-assembly of matter at the atomic level during fabrication of nanodevices. This proposal seeks to understand the processes driving self-assembly of nanomaterials and how to control these processes.Read moreRead less