Discovery Early Career Researcher Award - Grant ID: DE230100178
Funder
Australian Research Council
Funding Amount
$453,913.00
Summary
Fast, lightweight and live nanopore sequencing analysis. This project aims to address limitations in nanopore sequencing (latest emerging technology in genomics) by applying advanced computational methods. This project expects to create new knowledge in bioinformatics and computer science through innovative approaches that leverage the live data streaming capability of nanopore devices to deliver results rapidly, or in real-time. Expected outcomes include improved, highly efficient analysis meth ....Fast, lightweight and live nanopore sequencing analysis. This project aims to address limitations in nanopore sequencing (latest emerging technology in genomics) by applying advanced computational methods. This project expects to create new knowledge in bioinformatics and computer science through innovative approaches that leverage the live data streaming capability of nanopore devices to deliver results rapidly, or in real-time. Expected outcomes include improved, highly efficient analysis methods and designs for future creation of custom computer hardware for nanopore analysis. This will facilitate widespread adoption of nanopore technology in bioscience research and applied domains (health, agriculture, ecology, biosecurity and forensics), including for portable in-the-field applications. Read moreRead less
Next generation high throughput lipidomics using adaptive modelling. This project aims to develop a unique high-throughput method to capture the lipidomic profile of human plasma suitable for large human population screening. Lipids are fundamental to every biological system, but our understanding of their regulation in humans have been largely superficial. By incorporating a new lipidomics approach, with genomic data, this project aims to expand our understanding of human biology by identifying ....Next generation high throughput lipidomics using adaptive modelling. This project aims to develop a unique high-throughput method to capture the lipidomic profile of human plasma suitable for large human population screening. Lipids are fundamental to every biological system, but our understanding of their regulation in humans have been largely superficial. By incorporating a new lipidomics approach, with genomic data, this project aims to expand our understanding of human biology by identifying regulators of lipid metabolism. The large diversity in humans necessitate sufficient sample sizes to identify true genetic regulators, but to date techniques capturing phenotypic data (lipids) have been largely limited. It is anticipated that this study will identify new regulators of lipid metabolism in humans.Read moreRead less
3D Structure determination of biomacromolecular assemblies from sparse data. This project has direct impact on pharmaceutical research: Biomacromolecular interactions are key points for pharmaceutical intervention and detailed structural knowledge of dynamic protein interactions can significantly accelerate drug development. Australia has invested in expensive instrumentation that can be used with new laboratory methods to obtain information on delicately balanced biomacromolecular interactions, ....3D Structure determination of biomacromolecular assemblies from sparse data. This project has direct impact on pharmaceutical research: Biomacromolecular interactions are key points for pharmaceutical intervention and detailed structural knowledge of dynamic protein interactions can significantly accelerate drug development. Australia has invested in expensive instrumentation that can be used with new laboratory methods to obtain information on delicately balanced biomacromolecular interactions, and how they malfunction in disease. This project will provide a computational framework to increase the impact of this investment by integrating measurements from a range of novel technologies and developing understanding of changes in structure of large protein complexes in different functional states.Read moreRead less
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
Gravity Current Driven Smoke Dispersion In a Stratified Ambient. Smoke from bushfires transported by gravity currents, and known to occur nationwide, caused the shutdown of businesses, education and events in Canberra in 2019. Recent scientific investigations have shown that the speed of propagation and concentration of smoke in these three-dimensional gravity currents have a long term ‘memory’ of their initial configuration. In this project, high-fidelity computational and experimental techniq ....Gravity Current Driven Smoke Dispersion In a Stratified Ambient. Smoke from bushfires transported by gravity currents, and known to occur nationwide, caused the shutdown of businesses, education and events in Canberra in 2019. Recent scientific investigations have shown that the speed of propagation and concentration of smoke in these three-dimensional gravity currents have a long term ‘memory’ of their initial configuration. In this project, high-fidelity computational and experimental techniques will be used to elucidate the fundamental mechanisms of gravity current entrainment and propagation. This knowledge will set a strong foundation to improve operational forecasts of smoke transport that will allow government agencies to better respond to the negative impact of these complicated flows.Read moreRead less
On the mechanism of boiling instability in microchannels. This project will enable designers to create highly efficient miniaturised devices based on the boiling of fluids such as water or organics. These devices include micro-power generation systems, coolers for computer chips and solar collectors, and micro-chemical process systems. Such devices provide environmental, safety and economic benefits.
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
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
Robust Reformulation Methods. Many decision problems in engineering, business and economics are modeled as nonlinear continuous optimization problems. Often these are made difficult by the existence of constraints. In this project, we reformulate such problems as constrained nonsmooth equations, rather than optimization problems, and develop generalized Newton and quasi-Newton methods for solving them. The expected outcomes of this project include a systematic theory of reformulation methods, ....Robust Reformulation Methods. Many decision problems in engineering, business and economics are modeled as nonlinear continuous optimization problems. Often these are made difficult by the existence of constraints. In this project, we reformulate such problems as constrained nonsmooth equations, rather than optimization problems, and develop generalized Newton and quasi-Newton methods for solving them. The expected outcomes of this project include a systematic theory of reformulation methods, and robust and efficient algorithms for solving some important nonlinear continuous optimization problems. There is high potential for applications in engineering, business and finance.Read moreRead less