Development Of Microscope-in-a-needle Devices For Improved Clinical Diagnostics
Funder
National Health and Medical Research Council
Funding Amount
$327,746.00
Summary
We have developed a new high-resolution optical imaging technology. The unique aspect of our research has been to redesign the imaging probe, miniaturising it to a few hundred microns in diameter, and encase it in a hypodermic needle – a ‘microscope-in-a-needle’. We are developing specific imaging probes to aid in the assessment of lung disease; the diagnosis of liver disease; and integrated into a brain biopsy needle to enable safer brain biopsies.
Imaging defects at atomic resolution via state-of-the-art atomic force microscopy and petascale simulations. Atomic force microscopy (AFM) promises to deliver resolution of individual atoms on surfaces and therefore, in principle, is capable of observing surface defects. However, the image obtained is a convolution of many complex interactions. Thus the key questions are what is being actually observed when we see something with “atomic resolution” in AFM and can point defects be really detected ....Imaging defects at atomic resolution via state-of-the-art atomic force microscopy and petascale simulations. Atomic force microscopy (AFM) promises to deliver resolution of individual atoms on surfaces and therefore, in principle, is capable of observing surface defects. However, the image obtained is a convolution of many complex interactions. Thus the key questions are what is being actually observed when we see something with “atomic resolution” in AFM and can point defects be really detected? The aim of this proposal is to combine state-of-the-art experimental AFM techniques with computer simulations that are capable of generating AFM images to answer these questions. Our ability to harness the potential of AFM for many applications in areas such as nanoscience and crystal engineering hinges on being able to correctly interpret AFM images.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
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
Developing Interpretable Machine Learning Models For Clinical Imaging And Single-cell Genomics
Funder
National Health and Medical Research Council
Funding Amount
$1,312,250.00
Summary
Machine learning methods will be vital to make best use of the deluge of data generated by high-throughput technologies in biomedical science. To get the most out of these models, however, we need to be able to unpack the 'black box'. I will use curated clinical and public research data to benchmark and develop interpretable deep learning models and software tools. These models will be used for breast cancer screening programs and for analysis of complex, large-scale single-cell genomics data.
Simulation of ligand binding-induced conformational changes in biological systems. This project is focused on the development of a methodology that will allow using molecular dynamics simulations to study fundamental biochemical reactions. The benefits to the Australian community are two fold: i) the software developed will be made available to the whole scientific community through peer-reviewed publication. Australian researchers will have the possibility to exploit the software in advance thr ....Simulation of ligand binding-induced conformational changes in biological systems. This project is focused on the development of a methodology that will allow using molecular dynamics simulations to study fundamental biochemical reactions. The benefits to the Australian community are two fold: i) the software developed will be made available to the whole scientific community through peer-reviewed publication. Australian researchers will have the possibility to exploit the software in advance through collaborations with our research group. ii) During this collaboration Australian PhD students will have the opportunity to spend a few months overseas to learn about the most advanced computational techniques and interact with top researchers in the computational chemistry field.Read moreRead less
Modelling the structure of Australian wool auction prices. Australian wool auction ($3.5-4 billions per year) is an on-going process. The prices paid in this auction market are used by the Australian production and service sectors to identify the quality preferences the international retail markets and the intermediate processors. The proposed research will optimise the information that can be extracted and used by these sectors in the production and distribution of the raw wool clip. A two- ....Modelling the structure of Australian wool auction prices. Australian wool auction ($3.5-4 billions per year) is an on-going process. The prices paid in this auction market are used by the Australian production and service sectors to identify the quality preferences the international retail markets and the intermediate processors. The proposed research will optimise the information that can be extracted and used by these sectors in the production and distribution of the raw wool clip. A two-stages algorithm in tree-based regression will be developed. The project will provide a challenge environment to train a Ph.D. student in agriculture modelling and optimisation.Read moreRead less
Learning to predict polymorphism through simulation of nucleation and nanoparticle evolution. Many substances are capable of exhibiting a myriad of different structures despite having the same composition. This behaviour can have a significant impact on the production of new pharmaceuticals, since the sudden appearance of a new form can lead to instant withdrawal of the drug. By understanding how different forms grow, rather than focusing on just the stability of the product, this research will ....Learning to predict polymorphism through simulation of nucleation and nanoparticle evolution. Many substances are capable of exhibiting a myriad of different structures despite having the same composition. This behaviour can have a significant impact on the production of new pharmaceuticals, since the sudden appearance of a new form can lead to instant withdrawal of the drug. By understanding how different forms grow, rather than focusing on just the stability of the product, this research will lead to more reliable prediction of how pharmaceutical molecules might assemble. The same technology will potentially have impacts in many areas of nanoscience through improvements in efficiency, including the production of minerals, desalination and undersea gas recovery.Read moreRead less
Unique Chemistry from Radioactive Decay in the Solid-State. Australia is an important member of the international nuclear fuel cycle. It holds one-third of the world's uranium reserves and is a major player in the development of technology for immobilizing radioactive waste. We will use computer simulation to answer a very important question which is extremely difficult to study experimentally: How does radioactive decay inside a solid change the chemistry of the material over time? Not only wil ....Unique Chemistry from Radioactive Decay in the Solid-State. Australia is an important member of the international nuclear fuel cycle. It holds one-third of the world's uranium reserves and is a major player in the development of technology for immobilizing radioactive waste. We will use computer simulation to answer a very important question which is extremely difficult to study experimentally: How does radioactive decay inside a solid change the chemistry of the material over time? Not only will our study improve nuclear waste storage, it will also reveal how in-situ chemical change creates new kinds of solids which cannot be made by conventional means. These solids can exhibit unusual and useful behaviour; this project provides the first investigation of this unexplored technological niche.Read moreRead less