— 2018 School of science HDR Research Projects Applied Physics DR230/ MR230 Contents Click on the project links for more information Professor Toby Allen • Computational Biophysics and Pharmacology of Ion Channels • Computational Molecular Neuroscience and Understanding General Anaesthetics • Computational Biophysics of Membranes, Ion Pumps and Cholesterol Professor Gary Bryant • Rapid measurement of the effects of antimicrobial drug candidates on bacterial motility • Effects of vitrification (glass formation) on biological membranes Professor Andrew Greentree • Information-based approaches to imaging • Laser Threshold Magnetometry • Waveguide Adiabatic Passage for Quantum Gates and Boson Sampling Professor James Macnae • Characterising the shallow sub-surface with a hybrid Ground Penetrating Radar and Electromagnetic system • PRBS waveforms from multi-transmitters for geophysical borehole exploration Associate Professor Jared Cole • Exciton transport and open-quantum systems theory • The quantum mechanics of superconducting electronics • Dissipationless charge transport in topological insulators and two- dimensional materials Professor Peter Daivis • Phase-field modelling of cryoprotectant performance • Modelling shear banding and stick-slip behavior in complex lubricant systems • Thermodynamics of shearing viscoelastic materials Professor Yonggang Zhu • AlveoliChip Associate Professor Brant Gibson • Next generation endoscopic imaging probes using new computational microscopy techniques • Mobile phone microscopy using integrated and ambient light for point-of-care diagnostics • Near-infrared fluorescent carbon-based nanomaterials for bioimaging and sensing Professor Salvy Russo • Understanding Energy Transfer Mechanisms in Light Harvesting complexes Associate Professor Lan Wang • Spin transport and spin transfer torque in heterostructures of two-dimensional materials • Realizing high temperature quantum anomalous Hall effect in two dimensional topological insulators Dr Tamar Greaves • Enzyme Biocatalysis in Ionic Liquids • Interaction of novel cryoprotectants and model membranes Dr Asma Khalid • Bioinspired silk nanovehicles: A new-generation platform for cell imaging and drug release Dr Nicolas Menicucci • Quantum information theory of observers in analogue gravity • Theoretical Quantum Computing with Continuous Variables DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics) School of Science HDR Project 2018 Computational Biophysics and Pharmacology of Ion Channels Physics Discipline/Computational Biophysics Group – RMIT City Project Description This PhD project, to be carried out within the Computational Biophysics Group headed by Prof. Toby Allen, provides an opportunity for a talented student to undertake their Ph.D. on a National Institutes of Health (USA)-funded computational biophysics project of medical significance. The Computational Biophysics Group develops advanced physical and chemical simulation approaches to explore problems associated with membrane charge transport. In particular, ion channels are proteins that control the movements of ions across cell membranes, enabling critical electrical activity such as heartbeat and brain activity, and are chief targets for drugs that control neuronal function. Our studies require the development and application of advanced computer simulation methods to explore the mechanisms of ion channel function. Investigations extend to describe how these channels are modulated by drugs, as therapeutics for a range of neurological and cardiac diseases. This project has established experimental collaborators in the USA and Australia, and uses state of the art supercomputing resources, including NCI, IVEC, CSIRO, Melbourne Bioinformatics, local clusters and the new DE Shaw Anton 2 supercomputer in the USA. New high-resolution X-ray and cryo-EM structures of voltage-activated sodium and potassium channels have created an opportunity to see how these molecular devices operate at the atomic level. This project will develop computational methodologies to solve for the pathways and energetics underlying channel conduction, activation and inactivation using advanced statistical and quantum mechanical methods on supercomputers. These methods will then explore the mechanisms of drug molecules, ensuring quantitative accuracy for the binding of anti-epileptics, anti-arrhythmics and local anaesthetics. This will expose the mechanisms of channel modulation, leading to improved predictive capabilities for future drug development. To be eligible for this scholarship you must: • have a first class Honours Degree (or equivalent Masters by Research) in physics, chemistry, biophysics, biology, biomolecular engineering or related discipline. • preferably have research experience involving theory and/or computation in condensed matter physics, physical chemistry, computational biology or related techniques. • possess a strong desire to study biological and medical problems using physical and chemical methods, and passion for molecular science and modern supercomputing. References: [1]. C. Boiteux, et al. & T. W. Allen. 2014. Proceedings of the National Academy of Sciences (PNAS), USA. 111:13057-13062. With editorial in PNAS, 111:12955-12956. [2]. C. Boiteux, I. Vorobyov & T. W. Allen. 2014. PNAS. 111:3454–3459. [3]. B. Lev et al. & T.W. Allen. 2017. PNAS. 114:E4158–E4167. (News: www.rmit.edu.au/news/all-news/2017/may/supercomputer-study-unlocks-secrets-of-brain-and-safer- anaesthetics). [4]. V. Yarov-Yarovoy, T.W. Allen & C.E. Clancy. 2015. Drug Discovery Today. 14:3–10. (Review) [5]. J.I. Vandenberg, E. Perozo & T.W. Allen. 2017. Trends in Pharmacological Sciences. 12th July 2017. DOI: 10.1016/j.tips.2017.06.004. (Review) Contact Details: To discuss this project further please contact: Prof. Toby W. Allen – Office 50439. Email [email protected] DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics) School of Science HDR Project 2018 Computational Molecular Neuroscience and Understanding General Anaesthetics Physics Discipline/Computational Biophysics Group – RMIT City Project Description This PhD project, to be carried out within the Computational Biophysics Group headed by Prof. Toby Allen, provides an opportunity for a talented student to undertake their Ph.D. on an NHMRC-funded molecular biophysics project of much medical significance. The Computational Biophysics Group develops advanced physical and chemical simulation approaches to explore problems associated with membrane charge transport. In particular, ion channels are proteins that control the movements of ions across cell membranes, enabling critical electrical activity such as heartbeat and brain activity, and are chief targets for drugs and anaesthetics. Our studies require the development and application of advanced computer simulation methods to explore the mechanisms of ion channel function and modulation by therapeutics for a range of neurological and cardiac diseases. This project has established experimental collaborators in Australia and France, and uses state of the art supercomputing resources at NCI, IVEC, Melbourne Bioinformatics, local clusters and the new DE Shaw Anton 2 supercomputer in the USA. Understanding the actions of general anaesthetics has been the goal of over 150 years of scientific and medical studies. We now have atomic structures of the proteins responsible and are on the cusp of understanding their actions to aid the discovery of more effective and safer anaesthetics. In this project the student will model how protein switches are activated by binding molecules to generate electrical signals in the brain. These switches, called ligand-gated ion channels, are primary electrical components of our nervous systems. General anaesthetics work by blocking “on” switches and enhancing “off” switches, leading to loss of sensation and the ability to feel pain. We will explain how these channels are activated, and how the binding of anaesthetics controls that activation. This project will develop computational methodologies to solve for the pathways and energetics underlying ligand-gated ion channel activation and modulation using advanced statistical mechanical methods on supercomputers. These methods will lead to improved predictive capabilities for future anaesthetic development. To be eligible for this scholarship you must: • have a first class Honours Degree (or equivalent Masters by Research) in physics, chemistry, biophysics, biology, biomolecular engineering or related discipline. • preferably have research experience involving theory and/or computation in condensed matter physics, physical chemistry, computational biology or related techniques. • possess a strong desire to study biological and medical problems using physical and chemical methods, and passion for molecular science and modern supercomputing. References: [1]. B Lev et al & TW Allen. 2017. Proceedings of the National Academy of Sciences (PNAS). 114:E4158–67. (News story: www.rmit.edu.au/news/all-news/2017/may/supercomputer-study-unlocks-secrets-of-brain-and-safer- anaesthetics). [2]. C Boiteux, et al & TW Allen. 2014. PNAS. 111:13057-62. With editorial PNAS 111:12955-12956. [3]. C Boiteux, I Vorobyov & TW Allen. 2014. PNAS USA. 111:3454–9. [4]. V Yarov-Yarovoy, TW Allen & CE Clancy. 2015. Drug Discovery Today. 14:3–10. (Review) Contact Details: To discuss this project further please contact: Prof. Toby W. Allen – Office 50439. Email [email protected] DR230 – PhD (Applied Physics) MR230 – Master