— 2018 School of Science

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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)

School of Science HDR Project 2018

Computational Biophysics of Membranes, Ion Pumps and Cholesterol

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 ARC-funded molecular biophysics project. The Computational Biophysics Group develops advanced physical and chemical simulation approaches to explore problems associated with membrane charge transport. In particular, ion pumps and channels are proteins that drive electrochemical gradients and regulate the movement of ions, enabling electrical activity in the body. Our studies require the development and application of advanced computer simulation methods to explore the mechanisms of pump and channel function. This project has established experimental collaborators in Australia and Denmark, and uses state of the art supercomputing resources at NCI, IVEC, Melbourne Bioinformatics, local clusters and the DE Shaw Anton 2 supercomputer, USA. Cholesterol may have evolved in animals to optimise the function of proteins in their cell membranes. A prime candidate is the Na+,K+-ATPase (the sodium pump) that provides the driving force for basic functions such as nerve and muscle activity. Without the sodium pump, multicellular animal life would be viable. Data shows that pump activity is massively enhanced by physiological levels of cholesterol. However, the mechanisms by which cholesterol modulates activity remain unknown. Variation among pumps suggests cholesterol may have more than one mode of action, via direct binding or by altering the physical properties of the lipid membrane. The aim of the project is to determine how cholesterol and cholesterol-altered membrane properties affect pump activity. High-resolution structures of the sodium pump allow us to see how these devices operate at the atomic level. We will develop computational methodologies to solve for the mechanisms of pump function using statistical mechanics and supercomputers. 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]. L.J Mares et al, TW Allen & R Clarke 2014. Biophys J 107:1352–63. Cover+editorial: Biophys J 107:1257–8. [2]. A Garcia et al. TW Allen & R Clarke. 2017. BBA Biomembranes1859:813-23. [3]. 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). [4]. C Boiteux, et al & TW Allen. 2014. PNAS. 111:13057-62. With editorial PNAS 111:12955-12956. [5]. C Boiteux, I Vorobyov & TW Allen. 2014. PNAS. 111:3454–9. [6]. C Boiteux and TW Allen. 2016. Current Topics in Membranes 78:145-182 (Review).

Contact Details: To discuss this project further please contact: Prof. Toby W. Allen – Office 50439. Email [email protected] Sc DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Rapid measurement of the effects of antimicrobial drug candidates on bacterial motility

Physics Discipline – RMIT City

Project Description –

Antimicrobial drug resistance is a global health emergency and there is an urgent need for new clinical antimicrobial agents that work in different ways to current drugs, and are therefore more likely to be effective (1). One mechanism of particular interest is motility, the ability of bacteria to explore their environment and spread, as this is how bacteria spread and grow. Despite their enormous potential, antimicrobial drugs that prevent motility have received little attention because of the limitations of traditional techniques to measure bacterial movement (2)). These measurements are critical for assessing the effectiveness of potential drugs.

This project we will apply the new technique of Differential Dynamic Microscopy (DDM) to assess the effectiveness of potential candidate antimicrobial molecules, and understand how such molecules affect motility. DDM (3) was first used to study bacterial motility by the Soft Matter group at Edinburgh University, in collaboration with CI Bryant at RMIT (4). Since then, the Edinburgh group have proved the utility of the technique using E. Coli (5), the bacteria responsible for maladies such as gastroenteritis, meningitis in newborns, pneumonia and urinary tract infections. Bryant’s group at RMIT has recently applied the technique to understand the role of motility in the effects of carbohydrate-based surfactants on bacterial growth, in collaboration with PIs Bansal and Wilkinson (6).

This project will extend this work to look at motility in a range of organisms, and the effects of both existing and novel antibiotics on bacterial motility.

References 1. Carlet J, Collignon P, Goldmann D, Goossens H, Gyssens IC, Harbarth S, et al. Society's failure to protect a precious resource: antibiotics. The Lancet.378(9788):369-71. 2. Berg HC. The rotary motor of bacterial flagella. Annual Review of Biochemistry. 2003;72:19-54. 3. Cerbino R, Trappe V. Differential dynamic microscopy: Probing wave vector dependent dynamics with a microscope. Physical Review Letters. 2008;100(18). 4. Wilson L, Martinez V, Schwarz-Linek J, Tailleur J, Bryant G, Pusey P, et al. Differential Dynamic Microscopy of Bacterial Motility. Physical Review Letters. 2011;106(1). 5. Schwarz-Linek J, Arlt J, Jepson A, Dawson A, Vissers T, Miroli D, et al. Escherichia coli as a model active colloid: A practical introduction. Colloids and surfaces B, Biointerfaces. 2016;137:2-16. 6. Hu, Y, Zou, W, Julita, V, Ramanathan, R, Tabor, RF, Nixon-Luke, R, Bryant, G, Bansal, V and Wilkinson, BL. Photomodulation of bacterial growth and biofilm formation using carbohydrate-based surfactants. Chemical Science. 2016;7:6579 (Cover Image).

Contact Details: To discuss this project further please contact:

Prof Gary Bryant ([email protected]) Supervisor – Office 14.7.6 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Effects of vitrification (glass formation) on biological membranes

Physics Discipline – RMIT City

Project Description

In nature, many species of plants and animals have evolved to avoid membrane damage during freezing and dehydration by vitrifying – ie forming a glass from the concentrated sugar suspensions1. Early studies of the effects of sugars concentrated on the effects of non-vitrified glasses, though there were attempts to understand and model the effects of vitrified glasses2. These studies examined the effects membrane transition temperatures, but not on the membrane structure, due to limitations in the available technology. Over the past few years we have pioneered the study of the effects of various molecules on membrane structure using advanced scattering techniques3-5.

While initial studies of the effects of glasses on membranes In this project we will study thIn this project we will apply these advanced techniques to the study of the effects of glass formation on membrane structure, as well as studying the effects of ice crystallization.

The primary lab based techniques to be used include Small angle X-ray scattering (SAXS) and Differential Scanning Calorimetry (DSC). We will also investigate the properties of the sugar glasses themselves using Powder X-ray Diffraction, DSC and Dynamic Mechanical Analysis (DMA). In addition, we will conduct synchrotron SAXS studies (at the Australian Synchrotron) and neutron scattering studies (at Lucas Heights in Sydney and at overseas facilities), using molecular deuteration to fine tune the location of molecules within the membrane-glass system. As well as studying traditional glass formers, we will study the effects of novel crystallization inhibitors and vitrification agents.

References 1. Koster, K. L.; Anderson, M., Interactions between vitrified sugars and lipid - mechanism by which the fluit-to-gel phase-transition temperature is lowered. Plant Physiology 1995, 108 (2), 110-110. 2. Koster, K. L.; Lei, Y. P.; Anderson, M.; Martin, S.; Bryant, G., Effects of vitrified and nonvitrified sugars on phosphatidylcholine fluid-to-gel phase transitions. Biophysical Journal 2000, 78 (4), 1932-1946. 3. Garvey, C. J.; Lenne, T.; Koster, K. L.; Kent, B.; Bryant, G., Phospholipid Membrane Protection by Sugar Molecules during Dehydration-Insights into Molecular Mechanisms Using Scattering Techniques. International Journal of Molecular Sciences 2013, 14 (4), 8148-8163. 4. Kent, B.; Hunt, T.; Darwish, T. A.; Hauss, T.; Garvey, C. J.; Bryant, G., Localization of trehalose in partially hydrated DOPC bilayers: insights into cryoprotective mechanisms. Journal of the Royal Society Interface 2014, 11 (95). 5. Kent, B.; Hauss, T.; Deme, B.; Cristiglio, V.; Darwish, T.; Hunt, T.; Bryant, G.; Garvey, C. J., Direct Comparison of Disaccharide Interaction with Lipid Membranes at Reduced Hydrations. Langmuir 2015, 31 (33), 9134-9141.

Contact Details: To discuss this project further please contact: Prof Gary Bryant ([email protected]) Supervisor – Office 14.7.6 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Information-based approaches to imaging

Physics Discipline/Australian Research Council Centre of Excellence for Nanoscale BioPhotonics – RMIT City

Project Description

The task of imaging, especially microscopy and nanoscopy (imaging below the diffraction limit of light), is a vital enabling tool for almost all branches of science. As conventional optics reaches the limits of what is achievable in terms of hardware, attention is turning to what can be achieved with software, i.e. algorithmic approaches to improve resolution or extract more information with lower illumination levels. It is therefore remarkable that many approaches to imaging are based solely on historical approaches and do not take into account the recent advances made in information and quantum theory. One way in which information theory can assist in imaging is in finding limits for optimal imaging, i.e. discovery of the protocol that can find a particle with the least resources. The resource that usually needs to be optimized for is photon budget, as excessive light levels can lead to photo-toxicity in cellular environments.

By applying information theoretic approaches, we have recently shown that the task of confocal microscopy can be greatly accelerated [1]. Similarly, we are exploring the improvements in resolution that are obtained by measuring the correlations between photon arrival times.

This project will develop information theoretic approaches to the practical tasks of identifying and tracking particles in biological systems. You will ideally be a motivated theoretical student, and the project will involve a combination of analytical and computational studies. These approaches will be shared with our partners in the ARC Centre of Excellence for Nanoscale BioPhotonics for experimental verification.

References: [1]. Accelerating microscopy: incorporating half-lies in imaging protocols, D.W. Drumm and A.D. Greentree, arXiv:1704.05980 [2]. Beating the Abbe Diffraction Limit in Confocal Microscopy via Nonclassical Photon Statistics, D. Gatto Monticone et al., Physical Review Letters 113, 143602 (2014)

Contact Details: To discuss this project further please contact: Professor Andrew Greentree ([email protected]) – Office 14.05.04 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Laser Threshold Magnetometry

Physics Discipline – RMIT City

Project Description)

The sensing of small magnetic fields is of paramount importance for a range of tasks. Such tasks include monitoring of brain activity (magnetoencephalography), magnetic anomaly detection, and searching for new mineral resources. We have recently developed a new concept in magnetometry – laser threshold magnetometry – that promises a new era in room-temperature magnetic field sensing [1]. Our design for a laser threshold magnetometer employs diamond containing colour centres as a laser medium, with output that varies as a function of the external magnetic field. Our predictions show that this device could operate with femto-Tesla per root Hertz sensitivity at room temperature, which is greater than any commercially available room-temperature system. With our partners at Macquarie University, we showed the first steps towards realizing this device, by demonstrating stimulated emission from nitrogen-vacancy colour centres in diamond [2].

The preliminary modeling indicates the great opportunity of our laser threshold approach, but questions still remain around the practical sensitivities that are achievable. This project will combine theory and experiments, with detailed quantum mechanical and electromagnetic modeling.

References: [1]. Laser threshold magnetometry, J. Jeske, J.H. Cole and A.D. Greentree, New Journal of Physics 18, 013015 (2016) [2]. Stimulated emission from nitrogen-vacancy centres in diamond, J. Jeske et al. Nature Communications 8, 14000 (2017)

School of Science HDR Project 2018

Waveguide Adiabatic Passage for Quantum Gates and Boson Sampling

Physics Discipline – RMIT City

Project Description

Boson sampling is expected to be one of the first problems to demonstrate quantum supremacy, i.e. it is a task that will be more efficiently solvable on accessible quantum devices than conventional computational simulators [1]. However to prove the supremacy of quantum over classical, especially for photonic devices, requires minimization of photon loss and improvements in precision of device fabrication. Spatial Adiabatic Passage is a quantum mechanical transport protocol that has the advantage of robustness against a range of fabrication imperfections [2]. Recently, we demonstrated that this method can be applied to create robust quantum gates [3]. This project will look at the more challenging task of designing systems of quantum gates using adiabatic design methods for the task of boson sampling.

References: [1]. Quantum sampling problems, BosonSampling and quantum supremacy, A. P. Lund, M. J. Bremner and T. C. Ralph, npj Quantum Information 3, 15 (2017) [2]. Spatial adiabatic passage: a review of recent progress, R Menchon-Enrich, A Benseny, V Ahufinger, A D Greentree, Th Busch and J Mompart, Reports on Progress in Physics 79, 074401 (2016) [3]. Adiabatic two-photon quantum gate operations using a long-range photonic bus, A. P. Hope, T. G. Nguyen, A. Mitchell and A. D. Greentree, Journal of Physics B: Atomic, Molecular and Optical Physics, 48, 055503 (2015)

School of Science HDR Project 2018

Characterising the shallow sub-surface with a hybrid Ground Penetrating Radar and Electromagnetic system

Physics Discipline/Applied Electromagnetic and Radiation Physics Group Geophysics Laboratory – RMIT City

Project Description

This project is part of a larger project that aims to develop novel antennas that extend the use of Ground Penetrating Radar (GPR) into the broadcast band electromagnetic (EM) frequencies. Such a novel system should in theory permit the prediction of material conductivity and magnetic susceptibility as well as dielectric permittivity. With funding from mining company members of AMIRA International, the hardware should be developed and first field data collected in 2018. If the engineering development is successful, the mining companies funding the project have specified that the hybrid system should then be deployed on an unmanned aerial system (UAS). This system will have may applications, for example to repeatedly map the materials beneath the pit floor of mining operations, permitting geologists to better distinguish ore from waste before the next blast. A second likely application is mapping from the UAS nickel rich laterites in areas where unexploded ordnance and landmines from recent conflicts makes conventional exploration very expensive due to dangerous, slow and costly demining procedures.

The student will be involved in data collection in the field at mining and mineral prospecting sites. The research aims of the PhD project will use results of data collection of the hybrid system instrument, who with research group members will develop and test software in MATLAB to model and invert this data, thus predicting in 3D subsurface physical properties and the geometry of boundaries between different materials. The starting point of software development will be high-frequency EM modelling code in MATLAB from a previous AMIRA International project conducted at RMIT, and proprietary FORTRAN code developed by BHPBilliton. These two codes at present provide inconsistent predictions.

Required background includes a good knowledge of both electromagnetic diffusion and waves, preferably their geophysical applications in mineral prospecting and GPR. Computer modelling skills in at least one of MATLAB or FORTRAN is a requirement.

References: [1]. Franke, J. 2016, A review of selected ground penetrating radar applications to mineral resource evaluations: Journal Applied Geophysics 81, 29-37 [2]. Macnae, J., and Hennessy, L., 2017, Magnetic Field Sensors for EM Geophysics, Proceedings of Decennial Mineral Exploration Conference, Toronto, Canada [3]. Jang, H., and Kim, H., 2013, A Scheme for Computing Time-domain Electromagnetic Fields of a Horizontally Layered Earth. Geophysics and Geophysical Exploration 16:3, 139-144. [4]. Macnae, J., 2016, Quantitative estimation of intrinsic induced polarization and superparamagnetic parameters from airborne electromagnetic data, Geophysics 81, E433-E446

Contact Details: To discuss this project further please contact: Professor James Macnae ([email protected]) – (03) 9925-3401 2nd supervisor: Dr. Jan Franke, Groundradar Consultants Inc. (Vancouver, Canada) S DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

PRBS waveforms from multi-transmitters for geophysical borehole exploration

Physics Discipline/Applied Electromagnetic and Radiation Physics Group Geophysics Laboratory – RMIT City

Project Description

This project is part of a larger project to make an order of magnitude improvement in routinely achieved signal/noise of borehole geophysical electromagnetic prospecting systems, more than doubling the effective target detection range from a borehole. Boreholes are the most expensive components of mineral exploration, and geophysics the most useful methodology to detect targets “missed” by the drilling. Doubling the detection range will lower exploration costs for conductive targets, particularly copper, nickel, lead, zinc and other suphide deposits, where electromagnetic methods are the primary exploration tool, and reduce environmental impact though reducing the number of boreholes required for exploration. The project will 1) significantly improve temperature stability of a low-noise borehole B field sensor in the 1 Hz to 20 kHz range and 2) develop methodology to use simultaneous multiple sources with novel waveforms. Other components of the project focus on sensor design and pressure-proofing, sensor to surface communications, and transmitter synchronisation.

This PhD project will focus of some of the alternatives for transmitter waveforms that can be used to energise the earth. The student will investigate methodology for simultaneous, multiple, synchronised transmitters with separable waveforms that in addition increase signal/noise. These include for example pseudo-random- binary-sequences with 50% duty cycles. The student will use samples of typical EM noise from pristine and mining environments to investigate numerically the many alternatives of waveform and signal extraction methodology. Once equipment has been designed and prototyped, the student will participate in field data acquisition and use the results to ground truth the signal/noise predictions of initial work.

This project will provide Physics, Geophysics and to a lesser extent Engineering challenges to the student, broadening their experience. Through the interactions with industry and work in the RMIT research team, opportunities for research employment in either of academia or industry will be greatly enhanced.

References: [1]. Velikin A & A Velikin, 2016, The Results of Field Testing of the Correlation Method of Pulse Electromagnetic Prospecting Systems STEM, Geology & Methodics of Prospect & Exploration of Deposits, (3) 31-38. (In Russian) [2]. Macnae, J., and Hennessy, L., 2017, Magnetic Field Sensors for EM Geophysics, Proceedings of Decennial Mineral Exploration Conference, Toronto, Canada [3]. Macnae J, 2015, Stripping very low frequency communication signals with minimum shift keying encoding from streamed time-domain electromagnetic data: Geophysics 80(6), E343-E353. [4]. Rasmussen, S. et al., 2017 Noise properties of Fourier deconvolution for time-domain electromagnetic soundings. Geophysics 82(5), E257-E266.

Contact Details: To discuss this project further please contact: Professor James Macnae ([email protected]) – (03) 9925-3401 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Exciton transport and open-quantum systems theory

Physics Discipline/Theoretical Chemical and Quantum Physics Research Group and ARC Centre of Excellence in Exciton Science – RMIT City Project Description

The interaction of light and matter is one of the key areas of modern physics research. When a photon interacts with a semiconductor or a molecular, it can create an electron-hole pair that is called an exciton. The creation and movement of excitons in turn is fundamentally important in applications such as solar cells and photosynthesis. Yet there is much we don’t understand about how excitons move, or how they are created and destroyed.

Decoherence theory describes why the macroscopic world rarely displays quantum effects. Although we understand the equation governing closed quantum systems (the Schrödinger equation) the open-quantum system equivalent (the master equation) is far less well understood. Efficient methods to mathematically model spatial correlations and/or non-Markovian effects within the environment of quantum systems are still a very active area of research.

Projects within this topic include studying the role of noise processes in the behaviour of excitons, how excitons move in nanostructures and how they can be controlled. Both the efficiency of exciton transport and the lifetime of an exciton depend on their interaction with vibrations within the nanosctructure or molecule hosting the exciton. The theories developed in this project will be applied to semiconductor and molecular devices, feeding into the wider research aims of the Centre of Excellence in Exciton Science (www.excitonscience.com).

Projects on this topic will be predominantly theoretical and/or computational, so a strong mathematical background and/or programming skills will be advantageous. The TCQP group has strong theoretical and experimental collaborations with other research groups within Australia and overseas, which provides the opportunity for travel to other research groups and conferences.

Recent research on the topic by our group: [1]. J. Jeske and J. H. Cole, Derivation of Markovian master equations for spatially correlated decoherence, Physical Review A, 87(5), 052138 (2013). [2]. J. Lim et al., Signatures of spatially correlated noise and non-secular effects in two- dimensional electronic spectroscopy, Journal of Chemical Physics, 146(2), 024109 (2017). [3]. J. Jeske, N. Vogt & J. H. Cole, Excitation and state transfer through spin chains in the presence of spatially correlated noise, Physical Review A, 88(6), 062333 (2013). [4]. J. Jeske et al., Bloch-Redfield equations for modeling light-harvesting complexes, Journal of Chemical Physics, 142, 064104(2015).

Contact Details: To discuss this project further please contact: Associate Professor Jared Cole ([email protected]) RMIT Office 14.06.12 Our research group webpage is http://tcqp.science DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

The quantum mechanics of superconducting electronics

Physics Discipline/Theoretical Chemical and Quantum Physics - Research Group RMIT City

Project Description

At low enough temperatures (below 1K or lower) some metals enter the superconducting state, in which electrons can flow without resistance. However, what is even more interesting is that when this happens the conventional circuit equations are modified by quantum mechanics. Now not only is charge quantised but so is magnetic flux, resulting in quantum circuits. These circuits can be used for measurement, quantum computing and sensing. This project will focus on understanding the link between material properties and the quantum nature of superconducting circuits.

Projects within this topic include studying the design of quantum circuits, the role of noise processes in the transport of electrons and the influence of the materials used to construct these circuits. Building better circuits, with lower noise characteristics and more flexibility will result in new devices such as quantum computers and high precision magnetic field sensors. Superconducting circuit technology is also used in metrology, the science of measurement, to define and measure the electrical units of the volt and the ampere. Major companies building quantum computers, such as Google and IBM, as well as national standards agencies worldwide use the research done in the TCQP group on this topic.

Recent research on the topic by our group: [1]. J. H. Cole, J. Leppäkangas & M. Marthaler, Correlated transport through junction arrays in the small Josephson energy limit: incoherent Cooper-pairs and hot electrons, New Journal of Physics, 16, 063019, (2014). [2]. J. H. Cole et al., Parity effect in Josephson junction arrays, Physical Review B, 91, 184505, (2015). [3]. K. A. Walker, N. Vogt & J. H. Cole, Charge filling factors in clean and disordered arrays of tunnel junctions, Scientific Reports, 5, 17572, (2015). [4]. J. Lisenfeld et al., Observation of directly interacting coherent two-level systems in an amorphous material. Nature Communications, 6, 6182, (2015).

School of Science HDR Project 2018

Dissipationless charge transport in topological insulators and two- dimensional materials

Physics Discipline/Theoretical Chemical and Quantum Physics Research Group and ARC Centre of Excellence in Future Low-energy Electronics Technologies,

Project Description The topological properties of electron conduction in materials have recently become an important focus of solid-state physics. In particular the idea that electron flow can be dissipationless due to the topological nature of some materials hints at a new generation of low- power electronics. In this project we will develop new computational models to understand how such topologically protected materials and other low-dimensional materials could be used to develop a new generation of electronic devices.

The electrical response of two- and one-dimensional devices is qualitatively different to conventional materials. Only with the development recently of nanotechnology fabrication techniques in the last few decades have we been able to study these devices. The computational and theoretical tools required to model the experiments still lag behind. In the TCQP group we are pushing the boundaries of what can be modelled using existing techniques, as well as developing new mathematical models and computational algorithms. We use non-equilibrium Greens function techniques to model the electrical response of nanoelectronic devices. Projects within this topic are part of the Centre of Excellence in Future Low-energy Electronics technologies (www.fleet.org.au).

Recent research on the topic by our group: [1]. J. S. Smith et al., Electronic transport in Si:P δ-doped wires, Physical Review B, 92, 235420, (2015). [2]. J. S. Smith et al., Electronic properties of delta-doped Si:P and Ge:P layers in the high- density limit using a Thomas-Fermi method, Physical Review B, 89(3), 035306 (2014). [3]. P. Longo et al., Quantum Bocce: Magnon–magnon collisions between propagating and bound states in 1D spin chains, Physics Letters A, 377(18), 1242–1249 (2013). [4]. P.-Q. Jin et al., Lasing and transport in a quantum-dot resonator circuit, Physical Review B, 84(3), 035322 (2011).

School of Science HDR Project 2018

Phase-field modelling of cryoprotectant performance

Physics Discipline/Centre for Molecular and Nanoscale Physics – RMIT City

Project Description

Cryopreservation of biological tissue for long-term storage is widespread in medicine, veterinary science, and medical research, and also in the long-term preservation of the germplasm of endangered species of plants and animals. Cells that can currently be successfully cryopreserved include sperm and egg cells, some blood cell types, and some cancer cells, but the extension of cryopreservation to other cell types including human pluripotent stem cells has proved problematic. Even for cell types that can be cryopreserved, cell viability is usually much less than 100% and purification protocols are required to remove the (toxic) cryoprotectant compounds required to minimise freezing damage. This process is far from ideal for critical applications such as reproductive technologies, preservation of endangered plant and animal species and stem cell therapies. The aim of this project is to use fast and accurate phase-field simulations to guide the design of new carbohydrate-based cryoprotectants that can overcome these limitations. Phase-field methods will be used to model vitrification, ice recrystallisation and the effect of freezing and thawing rates on ice crystal size and shape in the cryoprotectant solution. Phase-field methods model crystallisation with a continuum model for the free energy density expressed in terms of a variable that represents the extent of crystallisation at each point in space and time. Phase-field simulations are orders of magnitude faster than molecular dynamics simulations, making them ideal for studies of slow dynamical processes such as vitrification, ice growth and ice recrystallisation. By including various different terms in the free energy, they have already been used to study the inhibition of crystallisation by vitrification (Berry-2014), ice crystal growth during freezing (van der Sman-2016) and thermal hysteresis due to antifreeze proteins (Kutschan-2014). Typically, the non-isothermal phase-field equations for solidification from a binary solution (van der Sman-2016, Provatas-2010) take the form:

where φ represents the fraction of ice present, τ is an attachment rate constant, f is the free energy density, ψ is the solute concentration, M is a mobility related to the diffusion coefficient, u is the internal energy density, λ is the thermal conductivity and T is the temperature.

References: [1] Berry, J. and Grant, M., Phys. Rev. E 89, 062303 (2014). [2] van der Sman, R.G.M., Int. J. Heat Mass Trans. 95, 153 (2016). [3] Kutschan, B. et al., Phys. Rev. E 90, 022711 (2014). [4] Provatas, N. and Elder, K., "Phase-Field Methods in Materials Science and Engineering" (Wiley-VCH, Weinheim, 2010).

Contact Details: To discuss this project further please contact: Prof Peter Daivis – email: [email protected], Office 14.6.6 Prof Gary Bryant – email: [email protected], Office 14.7.6 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Modelling shear banding and stick-slip behavior in complex lubricant systems

Physics Discipline/Centre for Molecular and Nanoscale Physics – RMIT City

Project Description

Shear banding occurs when an otherwise homogeneous fluid subjected to shear spontaneously forms spatial bands with different velocity gradients corresponding to differing degrees of local order. Shear banding is often associated with a phase or structural transition. It can lead to regions of high and low viscosity being separated by a very small distance, giving rise to localised zones of very high apparent slip. This rapid change in strain rate over a small distance implies that non-local effects may be significant [1]. Shear banding has been observed experimentally and in simulations of both simple [2] and complex [3] fluids under extreme lubrication conditions but to date its implications for lubrication science and tribology remain poorly understood. It seems likely that little progress will be made without explicit consideration of the non-local effects that we aim to include.

Stick/slip behaviour of lubricants at high pressure, recently observed by Dini and colleagues [2, 3], was attributed to the growth and release of elastic strain within the substrate on which one or more of the lubricant components is adsorbed . PhD project supervisors Daivis and Todd have recently developed a new theory [4, 5] that describes the highly non-local coupled response of the density, shear stress and velocity profiles of simple liquids to combined shearing and confining forces. While it was developed in the context of molecular dynamics simulations with periodic boundary conditions, we are currently extending it to confined fluids. By combining this theory with state of the art classical free energy density functional theory for molecular liquids, we will further develop and extend it to predict the complex lubrication behaviour observed by Dini and collaborators. The elements that are needed for this extension already exist. These are statistical associating fluid theory for the equations of state of molecular liquids, fundamental measure theory to account for the effect of confinement on equilibrium liquids [6], and the non-local, nonlinear response functions for hard- sphere-like simple liquids obtained by Daivis and Todd [4, 5]. Using this combination of theoretical tools, it will be possible to account for confinement, phase transitions and the non-local equilibrium and nonequilibrium response of highly confined, sheared fluids.

References: [1] B.D. Todd, J.S. Hansen, P.J. Daivis, Phys. Rev. Lett., 78 (2008) 195901. [2] C. Gattinoni, D.M. Heyes, C.D. Lorenz, D. Dini, Phys. Rev. E, 88 (2013) 052406. [3] S. Maćkowiak, D.M. Heyes, D. Dini, A.C. Brańka, J. Chem. Phys., 145 (2016) 164704. [4] B.A. Dalton, K.S. Glavatskiy, P.J. Daivis, B.D. Todd, Phys. Rev. E, 92 (2015) 012108. [5] K.S. Glavatskiy, B.A. Dalton, P.J. Daivis, B.D. Todd, Phys. Rev. E, 91 (2015) 062132 [6] L.A. Mitchell, B.J. Schindler, G. Das, M. dos Ramos, C. McCabe, P.T. Cummings, M.D. LeVan, J. Phys. Chem. C, 119 (2015) 1457.

Contact Details: To discuss this project further please contact: Prof Peter Daivis – email: [email protected], Office 14.6.6 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Thermodynamics of shearing viscoelastic materials

Physics Discipline/Centre for Molecular and Nanoscale Physics – RMIT City

Project Description

One of the greatest hindrances to the development of theories of non-equilibrium thermodynamics beyond the local equilibrium approximation is the difficulty of formulating definitive experimental tests of the basic concepts. For example, the existence and definition of quantities such as temperature and entropy in far-from- equilibrium systems are extremely difficult questions to address only by experiment [1]. This is partially due to the extraordinary success and great range of validity of non-equilibrium thermodynamics in the local- equilibrium approximation [2]. It is usually necessary to create systems under extreme conditions such as shock waves, if we want to see deviations from the local equilibrium approximation, but non-Newtonian fluids also display strong deviations from local-equilibrium and are therefore an excellent proving ground for extensions of the local equilibrium hypothesis. Non-equilibrium molecular dynamics simulations are an ideal test environment for many concepts in non-equilibrium thermodynamics [3, 4]. Many quantities of interest that are difficult to measure can be directly computed in molecular dynamics simulations.

Recent work indicates that the characterization of nonlinear viscoelasticity is best done within a thermodynamic framework that can precisely separate elastic and viscous components of the response [3, 5]. The aim of this project is to use non-equilibrium molecular dynamics simulations to extract detailed information that can contribute to a deeper understanding of non-equilibrium thermodynamics beyond the local-equilibrium approximation. This work is vital for the modeling of thermodynamic processes occurring in fluids that are far from equilibrium. One example is phase separation of strongly shearing polymer solutions. Another is the development of general constitutive equations describing the nonlinear rheology of deforming (shearing, elongating and squeezed) fluids, which relies strongly on largely untested assumptions about their thermodynamics.

References: [1] D. Jou, J. Casas-Vazquez and G. Lebon, Extended Irreversible Thermodynamics, Springer, Berlin, 2001.

[2] S.R. de Groot and P. Mazur, Non-Equilibrium Thermodynamics, Dover, London, 1984. [3] P.J. Daivis and M.L. Matin, Steady-state thermodynamics of shearing linear viscoelastic fluids, J. Chem. Phys., 118, 11111 (2003); P.J. Daivis, Thermodynamic relationships for shearing linear viscoelastic fluids, J. Non-Newtonian Fluid Mech., 152, 120 (2008). [4] B.D. Todd and P.J. Daivis, Nonequilibrium molecular dynamics - Theory, algorithms and applications, Cambridge University Press (2017). [5] K.S. Cho, K. Hyun, K.H. Ahn and S.J. Lee, A geometrical interpretation of large amplitude oscillatory shear response, J. Rheol., 49, 747 (2005).

School of Science HDR Project 2018

AlveoliChip

Physics Discipline/Flow Physics/Microfluidics – RMIT City

Project Description

This project will develop an alveoli microchip to model the deep lung system and investigate the flow physics of air flow and nano-and micro-particles (PM2.5 particles) in alveoli of the lung. Transport and deposition of micro- and nano-scale particulates in the human lung under respiration has significant implications for human health. Current research on transport and deposition of PM2.5 particles mainly rely on numerical modellings [1,2]. These are based on over-simplified models which can represent neither the true geometry and variations of alveoli nor the true flow dynamics. Due to the complexity of the acini, the experimental studies are limited and the flow behavior could not be properly modelled [3,4]. There have been some recent developments using microfluidics to model the alveolar flows [5]. However, these systems are still over-simplified and do not model well the chaotic flows in varying flow and boundary conditions.

The proposed project would develop an alveolar microfluidic chip (AlveoliChip) to model the 3D alveolar sacs to study the fluid and particulate flows inside. One or more or the last 2-5 levels of the alveolar microflow systems will be developed. The single alveoli sac system will be used to investigate the formation of chaotic flows under the cycling breathing conditions. To quantify the details of 3D flow field, an enlarged single sac model will also be built to measure flow fields and particle trajectories. The multiple sac systems will be developed to investigate the interactions between sacs and the branching effect and the effect on the transport and deposition PM2.5 particles. We will use advanced 3D visualization and flow measurement techniques such as particle imaging velocimetry to study the flow field and flow chaos. The key scientific advancement is to understand the flows in 3D at microscales under these varying flow and boundary conditions. The transport of PM2.5 particles and the subsequent the deposition of such particles in alveoli will be further investigated using experimental methods such as 3D visualization and particle tracking velocimetry. The effect of chaotic flows on the particle movement will be quantified. Such a study could potentially advance significantly the fields of drug delivery, organ-on-a-chip and understanding the impact of air pollution.

References: [1] Sznitman, J. Biomechanics (2013), 46:284–298 (review) [2] Darquenne et al., Phil. Trans. R. Soc. A (2009) 367:2333–2346; [3] Tsuda et al., PNAS (2002) 99(15): 10173–10178; [4] Fishler et al., J. Biomechanics (2017), 50:222–227; [5] Tenenbaum-Katan et al., Biomicrofluidics (2015) 9:014120

Contact Details: To discuss this project further please contact: 1st Supervisor – Prof. Yonggang Zhu, [email protected] 2nd Supervisor – Prof. Gary Rosengarten, [email protected]

DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Next generation endoscopic imaging probes using new computational microscopy techniques

Physics Discipline/ARC Centre of Excellence for Nanoscale BioPhotonics – RMIT City

Project Description

A PhD scholarship is available within the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)1 at the Melbourne city campus of RMIT University in Physics2. At the CNBP, we’re driving the development of new light-based imaging and sensing tools, which can measure in real time, the complex chemical and molecular processes, taking place in and around cells in the living body. Bringing together over 200 researchers in photonics, biochemistry, physics, medicine, engineering and materials science, our innovative work aims to truly understand the ‘machinery of life’ particularly in the key areas of chronic pain (neuroscience), heart disease (cardiology) and reproduction (embryology).

This project will focus on developing the next generation of endoscopic imaging probes using new computational microscopy techniques3,4. There will be an emphasis on computational and imaging optics – a field that is revolutionizing how we understand biology. This project will involve developing new computational microscopy techniques as well as fabricating novel endoscopic imaging probes using state-of- the-art fabrication facilities at RMIT’s Micro Nano Research Facility5. Prospective students should have an interest in optics and/or image processing. A background in physics or engineering is preferred. Programming experience in MATLAB or Python is desirable but not required. It is anticipated that this project will be performed in collaboration with researchers across the CNBP, in particular at The University of Adelaide and Macquarie University, Sydney.

References: [1]. www.cnbp.org.au [2]. www.rmit.edu.au/research/cnbp [3]. E. McLeod and A. Ozcan, Reports on Progress in Physics, 79 (2016) [4]. A. Orth et. al., Scientific Reports 7, 43148 (2017) [5]. RMIT Micro Nano Research Facility

Contact Details: To discuss this project further please contact: Associate Professor Brant Gibson ([email protected]) 1st Supervisor Dr Antony Orth ([email protected]) 2nd Supervisor

DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Mobile phone microscopy using integrated and ambient light for point-of-care diagnostics

Physics Discipline/ARC Centre of Excellence for Nanoscale BioPhotonics – RMIT City

Project Description

Mobile phone microscopes are a natural platform for point-of-care diagnostics, but current solutions require an externally powered illumination source, thereby adding bulk and cost. This project will focus on exploring mobile phone microscopy using integrated light sources or sunlight for illumination, thereby reducing complexity whilst maintaining functionality and performance3. Having a capability of both brightfield and darkfield imaging modes will enable microscopic visualization of samples ranging from plant to mammalian cells. Microscope design principles will be investigated using computer added design software which is a desirable prerequisite skill, but not essential. The assembly process and optical path will also be explored to demonstrate a broad range of imaging capabilities. A background in physics or engineering is preferred. This project will utilize state-of-the-art fabrication facilities at RMIT’s Micro Nano Research Facility4 and the Advanced Manufacturing Precinct at RMIT5. It is anticipated that this project will also be performed in collaboration with researchers across the CNBP, in particular at The University of Adelaide and Macquarie University, Sydney.

References: [1]. www.cnbp.org.au [2]. www.rmit.edu.au/research/cnbp [3]. A. Orth et. al., bioRxiv https://doi.org/10.1101/162008 (2017) [4]. RMIT Micro Nano Research Facility [5]. RMIT Advanced Manufacturing Precinct

Contact Details: To discuss this project further please contact: Associate Professor Brant Gibson ([email protected]) 1st Supervisor Dr Antony Orth ([email protected]) 2nd Supervisor

DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Near-infrared fluorescent carbon-based nanomaterials for bioimaging and sensing

Physics Discipline/ARC Centre of Excellence for Nanoscale BioPhotonics – RMIT City

Project Description

A great challenge in noninvasive biomedical imaging is the acquisition of images inside a biological system at the cellular level. Optical imaging techniques offer resolution on the 100 nanometer scale, but are limited by the strong attenuation of visible light by biological matter and are traditionally used to image on the surface. Near-infrared light in the “biological windows” can penetrate much deeper into biological samples, rendering fluorescence-based imaging a viable option3.

This project will focus on understanding the fundamental physics and the development of carbon-based near- infrared fluorescent nanomaterials for biomedical imaging and sensing applications4. The optical properties of the nanomaterials, such as carbon dots and nanodiamond, will be explored using state-of-the-art confocal fluorescence microscopy facilities within the CNBP laboratories at RMIT. The physical and chemical properties of the nanomaterials will be characterized using atomic force microcopy, X-ray photoelectron spectroscopy, and scanning and transmission electron microscopy using the RMIT Microscopy and Microanalysis Facility5. Prospective students should have an interest in fluorescent nanomaterials and optics. A background in physics or engineering is preferred. It is anticipated that this project will be performed in collaboration with researchers across the CNBP, in particular at The University of Adelaide and Macquarie University, Sydney.

References: [1]. www.cnbp.org.au [2]. www.rmit.edu.au/research/cnbp [3]. P. Reineck, et. al., Adv. Opt. Mat., DOI: 10.1002/adom.201600212 (2016) [4]. P. Reineck and B. C. Gibson, Adv. Opt. Mat., DOI: 10.1002/adom.201600446 (2016) [5]. RMIT Microscopy and Microanalysis Facility

Contact Details: To discuss this project further please contact: Associate Professor Brant Gibson ([email protected]) 1st Supervisor Dr Philipp Reineck ([email protected]) 2nd Supervisor DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Understanding Energy Transfer Mechanisms in Light Harvesting complexes

Physics Discipline/Chemical and Quantum Physics Group/ARC Centre of Excellence in Exciton Science – RMIT City

Project Description

Understanding the transport of Excitons in high harvesting complexes is central to improving the efficiency of conversion of light into current [1]. There exist two main forms of Exciton transport in Organic PhotoVoltaics (OPVs), Förster resonance energy transfer (FRET) [2,3] which is the dominant form of transport for singlet Excitons and Dexter energy transfer [4,5] which is the dominant transport mechanism of triplet excitons. The purpose of this project is to develop an abinitio modeling toolkit to investigate and simulate both FRET and Dexter transfer mechanisms in OPV systems and apply these methods to new light Harvesting complexes being designed within the ARC Centre of Excellence in Exciton Science.

References: [1] G.J. Hedley, A. Ruseckas, and I.D.W. Samuel; Light Harvesting for Organic Photovoltaics, Chem. Rev. 2017, 117, 796−837 [2] D.L. Andrews (1989), A unified theory of radiative and radiationless molecular energy transfer, Chemical Physics, 1989, 135(2): 195-201 [3] K. Feron, X. Zhou, W.J. Belcher, and P.C. Dastoor (2012), Exciton transport in organic semiconductors: Förster resonance energy transfer compared with a simple random walk, J. Appl. Phys: 2012, 111, 044510 [4] D. L. Dexter (1953). A Theory of Sensitized Luminescence in Solids. J. Chem. Phys. 1953, 21: 836–850 [5] G.D. Scholes (2003), Long-range resonance energy transfer in Molecular Systems; Annu. Rev. Phys. Chem; 2003, 54:57–87

Contact Details: To discuss this project further contact: Professor Salvy Russo ([email protected] ) Senior Supervisor (RMIT) Dr Girish Lankwani ( [email protected]) Assoc. Supervisor (USyd)

DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Spin transport and spin transfer torque in heterostructures of two- dimensional materials

Physics Discipline/Quantum Materials and Devices Group (Experiment) – RMIT City

Project Description

This project is supported by ARC Centre of Excellence – Future Low Energy Electronics Technologies from 2017 to 2024 (http://www. fleet.org.au). Associate Professor Lan Wang is the Leader of Theme B (Device Fabrication) in this $35M project.

2D materials: Dimensionality plays a crucial role in determining the fundamental properties of materials, which has already been strikingly high-lighted by the discovery of graphene [1]. Graphene has many attractive properties for electronics and spintronics, such as gate-tunable carrier concentration, exceptional high electric mobility (> 105 cm2V-1s-1 at room temperature) and long spin-diffusion length. Other novel 2D materials offer properties that are complementary to those in graphene. The most attractive material systems include the 2D topological surface states in 3D topological insulators and novel 2D semiconductors, such as monolayer and few-layer black phosphorous, 2D transition metal dichalcogenides (MoS2, WSe2, etc), and ferromagnetic 2D materials [2, 3].

Spintronics: Today we stand on the verge of a new era in microelectronics, where the electron’s spin (which is the origin of magnetism) is utilized in addition to its charge. This concept is termed spin-electronics or spintronics and its technological appeal was aptly demonstrated by the Giant Magnetoresistance phenomenon, which moved from discovery to application (modern disk storage) in under a decade. By manipulating electron charge and spin simultaneously, ultra high speed and low power consumption electronic devices with more functionality can be fabricated. Spintronics has already become one the most important research fields in electronics, materials science and condensed matter physics [4].

This project will involve in making ferromagnetic heterostructures based on atomic layer thick 2D materials, fabricating various spintronic devices based on these heterostructure, and performing electron and spin transport measurements on these devices. Students with strong physics background are preferred.

The aim of this project will be fabricate the next generation low energy spintronic devices, such as spin field effect transistors and spin transfer torque devices for magnetic random access memory (MRAM) application.

References: [1] K. S. Novoselov et al., Science 306, 666 (2004) [2] Q. H. Wang, et al., Nature Nanotech. 7, 699 (2012) [3] M Chhowalla, et al., Nature Chem. 5, 263 (2013) [4] [4] S. Maekawa Concepts in spin electronics, Oxford University Press, 2006

Contact Details: To discuss this project further contact: Associate Professor Lan Wang ([email protected]) 1st Supervisor – Office building 14, Level 6, room 14 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Realizing high temperature quantum anomalous Hall effect in two dimensional topological insulators

Physics Discipline/Quantum Materials and Devices Group (Experiment) – RMIT City

Project Description

Topological insulators are novel quantum materials discovered in recent years [1-6]. The material system has a bulk insulating state and a conducting edge state which has fascinating characteristics. Both three dimensional (3D) and two dimensional (2D) topological insulators have been experimentally realized. Two dimensional (2D) topological insulators are insulating in their interior, but support one-dimensional (1D) conducting modes on their boundaries. These edge modes are protected from backscattering hence can carry currents for macroscopic distances with very low resistance. Furthermore, if the 2D topological insulator can be magnetized, a true zero resistance edge transport can be realized. This is quantum anomalous Hall effect. Realizing high temperature quantum anomalous Hall effect will generate a revolution in modern electronics industry.

This project will involve in making ferromagnet/2D topological insulator heterostructures based on atomic layer thick 2D materials, fabricating various quantum devices based on these heterostructure, and performing electron and spin transport measurements on these devices. The key idea is to use 2D ferromagnetic insulator to magnetize 2D topological insulator by proximity effect. As 2D materials are amenable to manipulation by electrostatic gates (the basis of conventional field-effect transistors), transport measurements with electric field gating will be the most important measurements in this project. Students with strong physics background are preferred.

The aim of this project will be fabricate the next generation low energy electronic devices, such as topological field effect transistors and topological logic devices.

References: [1] M. Z. Hasan and C. L. Kane, Rev. Mod. Phys. 82, 3045 (2010) [2] X. L. Qi and S. C. Zhang, Rev. Mod. Phys. 83, 1057 (2011) [3] D. Pesin and A. H. MacDonald, Nature Mater. 11, 409 (2012) [4] A. A. Taskin, Z. Ren, S. Sasaki, K. Segawa, and Y. Ando, Phy. Rev. Lett. 107, 016801 (2011) [5] B. Xia, P. Ren, A. Sulaev, P. Liu, S.Q. Shen, and L. Wang, Physical Review B 87, 085442 (2013) [6] Y. Xu, I. M. Miotkowski, C. Liu, J. Tian, H. Nam, N. Alidoust, J. Hu, C. K. Shih, M. Z. Hasan, and Y. P. Chen, Nature Phys. 10, 956 (2014)

School of Science HDR Project 2018

Enzyme Biocatalysis in Ionic Liquids

Physics Discipline – RMIT City

Project Description

This project will involve developing new non-aqueous solvents for biocatalysis reactions. Biocatalysts are highly useful in the synthesis of many organic compounds and chemical transformations. However, they are typically limited to use in conditions similar to their natural environment (ie. aqueous conditions, room temperature and at neutral pH). There are potentially new uses for them if we can develop solvents which support enzyme activity across a broader range of solvent conditions.1

The solvents to be used in this project will predominantly be protic ionic liquids (PILs), which are liquid salts below 100 oC. PILs are “designer” solvents due to their high tailorability. They consist of a cation and an anion, and there are thousands of possible combinations, with structural changes leading to changes in their chemical, thermal and solvent properties.2 Previously ionic liquids have been shown to have either a stabilising or destabilising effect on proteins, depending on their ions, concentration and which proteins.3-4

Libraries of PILs will be designed based on the groups previous experience in this field, and these will be synthesised using a Chemspeed robotic platform.5 Commercially available enzymes will be used which are commonly used in organic synthesis. A large range of physical chemistry techniques will be used to characterise the chemical, solvent and thermal properties of the neat PILs. Similarly, a variety of techniques will be used to characterise the enzymes in the PILs, and to monitor the biocatalysis reactions in the PILs. These techniques will include NMR, FTIR, differential scanning calorimetry (DSC), Small and Wide angle X- ray scattering at the Australian Synchrotron (SAXS/WAXS), UV-Vis spectroscopy, as well as measurements of surface tension, density and viscosity.

The aim of this project is to identify which PILs, and PIL solvent features, are beneficial for supporting different types of enzymes for biocatalysis reactions.

The research environment for this project is dynamic, friendly and supportive. It would give the successful candidate great opportunities for development, such as in research, communication, organisation, project management, problem-solving and analysis skills. The supervisors have a high international reputation in this field, and strong publication records.

References: 1.Schmid, A.; Dordick, J. S.; Hauer, B.; Kiener, A.; Wubbolts, M.; Witholt, B., Nature 2001, 409, 258-268. 2.Greaves, T. L.; Drummond, C. J., Chem. Rev. 2015, 115, 11379-11448. 3.Wijaya, E. C.; Separovic, F.; Drummond, C. J.; Greaves, T. L., Phys. Chem. Chem. Phys. 2016, 18, 25926- 25936. 4.Zhao, H., Journal of Chemical Technology and Biotechnology 2010, 85 (7), 891-907. 5.Greaves, T. L.; Ha, K.; Muir, B. W.; Howard, S. C.; Weerawardena, A.; Kirby, N.; Drummond, C. J., Phys. Chem. Chem. Phys. 2015, 17, 2357-2365.

Contact Details: To discuss this project further please contact:

Dr Tam Greaves ([email protected]) 1st Supervisor – Office 3.2.05B Prof Calum Drummond ([email protected]) 2nd Supervisor DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Interaction of novel cryoprotectants and model membranes

Physics Discipline – RMIT City

Project Description Cryopreservation of cells involves storing the cells at very cold temperatures to minimise activity and prevent damage to the cells. However, the freezing process is very risky for cells, and requires cryoprotectants and tailored freezing protocols to enable cells to survive and not dehydrate or burst. Cryoprotectants are additives which allow cells to avoid intra-cellular ice formation, encourage the formation of a glass at low temperatures, and minimize dehydration damage. Thus effective cryoprotectants must have the following properties [1]: i) They must be able to permeate the cell membrane to become internalised ii) They must discourage ice formation iii) They must have minimal toxicity to cells iv) They must be able to vitrify (ie form a glass) at low temperatures

However, there are currently few successful cryoprotectants, and few cells which can be successfully frozen, so there is a strong need for a wider variety of cryoprotectants.

This project will involve developing novel molecules and compounds which are potentially good cryoprotectants. Novel cryoprotectants of ionic liquids [2] and sugars, along with existing cryoprotectants, such as DMSO, glycerol and ethylene glycol will be used. The glass forming properties of each of these additives neat, and in water, will firstly be characterised using differential scanning calorimetry (DSC).

The interactions of these cryoprotectants will be investigated with artificial model cell membranes made from lipid bilayers. The location of cryoprotectants in the membrane, interactions between the cryoprotectants and membrane, and effect on the membrane structure will be explored. The techniques to be used include small angle X-ray scattering (SAXS), small angle neutron scattering (SANS) [3], and infrared spectroscopy. Some of these experiments will be conducted using national or international Synchrotron or Neutron scattering research facilities.

The key aim of this project is to develop fundamental understanding of how cryoprotectants interact with membranes, including their permeability, toxicity, and location within the membrane, and to leads to new, novel cryoprotectants.

References [1] Wolfe, J., Bryant, G. Cryobiology 1999, 39, 103-129. [2] Greaves, T. L.; Drummond, C. J., Chem. Rev. 2015, 115, 11379-11448. [2] Kent, B., Hauß, T., Demé, B., Cristiglio, V., Darwish, T., Hunt, T., Bryant, G., Garvey, C.J. Langmuir 2015, 31, 9134-9141.

Contact Details To discuss this project further please contact:

Dr Tam Greaves ([email protected]) Supervisor – Office 3.2.05B Prof Gary Bryant ([email protected]) Supervisor – Office 14.7.6 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Bioinspired silk nanovehicles: A new-generation platform for cell imaging and drug release

Physics Discipline/ARC Centre of Excellence for Nanoscale BioPhotonics – RMIT City

Project Description

Multifuntional nanomaterials are revolutionizing the ongoing research in the areas of bioimaging, biosensing, disease detection and targeted drug delivery [1]. The development in these fields demands biocompatible hybrid materials that can be employed simultaneously for drug delivery and biomedical imaging [2]. This project will involve the fabrication, characterization and in-vitro study of hybrid nanodiamond-silk spheres for imaging and drug release study. Fluorescent nanodiamonds (NDs) will provide the fluorescence modality for imaging while the degradable silk biopolymer will release the drug in a controlled manner. The current work performs the detailed structural analysis and optical characterization of these spheres and will investigate the methods to efficiently control the release of drug for nano- medicine.

Fluorescent NDs are being widely explored for biomedical imaging applications due to their biocompatibility, bright and photostable optical emission at room temperature and chemical inertness [3]. Regenerated silk fibroin (SF) is biologically derived polymer, which is optically transparent, biodegradable and can be transformed into a range of nanoscale devices for drug delivery and disease diagnosis [4]. The project will focus on combining these two unique optical materials to make powerful tools towards hybrid bio-optics applications.

The aim of this project is to fabricate and perform a study of both the structural and optical properties of these multifunctional spheres to enable better control over drug release dynamics, for improved applications in imaging-monitored drug release. Microfluidics system [5] will be employed to synthesize nano-spheres of SF embedding NDs. The structural properties, ND encapsulation inside the spheres, surface topography and silk’s degradability will be studied through scanning electron and transmission electron microscopy. The optical properties of spheres will be characterized through confocal microscopy. The spheres will be loaded with antibacterial and anticancer drugs and will be employed for imaging and drug tracking in preliminary in-vitro tumor and bacterial models. The live cell imaging will be performed via wide-field commercial microscopy. The SF spheres would enable controlled drug release and NDs would ensure bright and photostable imaging and location tracking of the released drug.

References: [1] A. Khalid et al. ACS Biomater Sci Eng 11 (2015) 1104. [2] A. Khalid et al. Biomed Opt Express 17 (2016) 132. [3] V. Mochalin et al. Nat Nanotech 7 (2012) 11. [4] F. Omenetto & D. Kaplan Adv Mat, 21 (2009) 38.

Contact Details: To discuss this project further contact: st Dr Asma Khalid ([email protected]) 1 Supervisor – Office 14.07.05 Assoc. Professor Brant Gibson ([email protected]) 2nd Supervisor – Office 14.05.03 DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Quantum information theory of observers in analogue gravity

Physics Discipline/ARC Centre of Excellence for Quantum Computation and Communication Technology – RMIT City

Project Description

Do you have outstanding skills in advanced mathematics? Are you interested in quantum physics, general relativity and exploring their interface in the setting of theoretical laboratory physics? If so, you may be right for this project.

RMIT Physics, in conjunction with the ARC Centre of Excellence for Quantum Computation and Communication Technology (CQC2T), is looking for an exceptionally high-performing student to perform advanced theoretical work in relativistic quantum information (RQI). This highly challenging PhD experience will offer you the chance to work on world-class research combining quantum information theory with key aspects of quantum field theory, condensed matter theory and general relativity.

Analogue-gravity models are theoretical models of laboratory systems that display certain aspects of general relativity despite their being perfectly well described by classical (nonrelativistic) physics [1]. These features appear in analogue form, with the speed of sound replacing the speed of light [2]. What is missing from nearly all of the work to date in analogue gravity, however, is any discussion of what an observer inside the model would see. This is crucial to the work because in general relativity, it is only when two objects come together that one claim that an ‘event’ has occurred [3]. Analysing the role of analogue observers is therefore crucial to understanding how far the analogy extends within analogue-gravity models.

This is where you come in.

Your PhD work will include (1) advanced theoretical analysis of various analogue-gravity models where the propagation of sound functionally replaces that of light; (2) theoretical design and analysis of new models of analogue observers who naturally perceive the relativity appearing within these systems; and/or (3) proposal of experiments to be done in an actual laboratory setting to demonstrate the effects under study.

Note: This PhD project is open to candidates who demonstrate an exceptionally high aptitude for advanced mathematics.

References:

[1] S Weinfurtner et al, Phys. Rev. Lett. 106, 021302 (2011). [2] C Barceló, S Liberati, M Visser, Living Rev. Relativity 14, 3 (2011). [3] C Rovelli, Quantum Gravity (Cambridge, 2004), Section 2.2.5.

Contact Details: To discuss this project further please contact: Dr Nicolas Menicucci ([email protected])

DR230 – PhD (Applied Physics) MR230 – Master of Science (Applied Physics)

School of Science HDR Project 2018

Theoretical Quantum Computing with Continuous Variables

Physics Discipline/ARC Centre of Excellence for Quantum Computation and Communication Technology – RMIT City

Project Description

Are you a high-achieving student with an aptitude for advanced mathematics? Are you interested in quantum physics and its use in information technology? If so, you may be right for this project.

The RMIT node of the Centre of Excellence for Quantum Computation and Communication Technology (CQC2T), funded by the Australian Research Council (ARC), is looking for high-performing students to work on advanced theoretical physics for quantum computing and related technologies. This challenging PhD experience will put you at the forefront of an exciting field. As an RMIT PhD student affiliated with CQC2T, you will be part of the flagship organisation for Australian research in quantum computing – comprising 8 Australian universities and more than 30 international partner organisations around the globe.

Quantum technology development is all about harnessing the surprising features of quantum mechanics for practical applications like advanced computing and secure communication. Most of the research to date in this field focusses on qubits (quantum bits), which are two-state quantum systems. Quantum computers can also be designed, however, to use continuous-variable quantum systems instead (e.g., electric-field amplitude) [1]. Recent breakthrough experiments [2,3] show the promise of this technology for creating gigantic resources for quantum computing with relatively small experimental setups. And recent theoretical breakthroughs show that the inevitable imperfections (“noise”) in these systems can be sufficiently tamed [4]. Much more remains to be done, however.

And that’s where you come in.

Your PhD work will include (1) advanced theoretical analysis of the current state of the art in continuous- variable quantum computing; (2) theoretical design and analysis of new and better ways to use continuous- variable quantum systems for high-performance quantum-information processing; and/or (3) theoretical support for our experimental colleagues who are implementing these systems in Australia and at multiple institutions around the world.

Note: Several PhD positions are available, to start as soon as possible.

References: [1] M Gu, C Weedbrook, N C Menicucci, et al, Phys. Rev. A 79, 062318 (2009). [2] J-i Yoshikawa, et al, APL Photonics 1, 060801 (2016). [3] M Chen, N C Menicucci, O Pfister, Phy. Rev. Lett. 112, 120505 (2014). [4] N C Menicucci, Phys. Rev. Lett. 112, 120504 (2014).

Contact Details: To discuss this project further please contact: Dr Nicolas Menicucci ([email protected]) Supervisor