Industry and Research

ARC Linkage Grants 

Resolving the impact of the warming East Australian Current on a coastal marine food web (2016-2019) (led out of Macquarie University)

Industry Partner: Zoological Parks Board of NSW; Australian Antarctic Division; Office of Environment and Heritage.

A/Prof Moninya Roughan
 (with Dr Ian Jonsen; Professor Robert Harcourt; Professor Iain Suthers; Associate Professor Martina Doblin; Dr David Slip; Dr Martin Cox)

This project aims to understand the effects of climate change on marine food webs, from plankton production to predation by iconic marine fauna, by integrating data on oceanographic conditions and fish distribution with the foraging patterns and breeding success of seabirds. Warming waters due to strengthening western boundary currents have unknown consequences for coastal marine food webs. Innovative prey capture signatures from accelerometers, and advanced movement models from satellite locations will show how predators locate and prey upon fish schools. Anticipated outcomes are insight into how changing resource availability in the oceans affects ecosystem resilience; improved viability for coastal industries; and ecosystem-based conservation management strategies.


Industry Partner: Department of Primary Industries; NSW Rock Lobster Association.

A/Prof Moninya Roughan (with Prof Andrew Jeffs, University of Auckland;  Dr Geoffrey Liggins and Dr Melinda Coleman, Dept. Primary Industries).   

This projects plans to explore the causes of the worldwide decline in the highly lucrative spiny lobster fisheries that has occurred in recent decades. This decline has been attributed to ocean warming, however, the exact mechanism contributing to the demise of lobsters is not known. This project will use a hierarchy of oceanic models of increasing complexity combined with a unique spiny lobster data set to investigate the relationship between larval health, physiology and environmental variables and how this affects survival and successful recruitment into the fishery. An understanding of these complex relationships is expected to enable the first predictions of larval survival and settlement in a region of accelerated ocean warming, and provide critical information for sustainable fisheries management.       

Advancing vegetation classification and mapping to meet conservation needs (2015-2018)

Industry Partner: NSW Office of Environment and Heritage/National Parks and Wildlife Service

Prof David Warton (with Prof David Keith, UNSW; Prof Stuart Phinn, UQ; Dr Jane Elith, Melbourne; Mr Daniel Connolly, OEH).

Classifications and maps of vegetation are part of the fundamental information infrastructure needed for planning, management and regulatory decisions for biodiversity conservation in Australia, and worldwide. A key requirement for such applications is for classifications and maps to accurately represent the distribution of biota.  In this project we will develop modern, advanced statistical and modelling techniques to classify and map vegetation over very large areas, using the most extensive and detailed vegetation data set in Australia, and new methods to evaluate these classifications.

Innovative mathematical modelling to determine incorporation of gene therapy in different cell lineages; Human Immunodeficiency Virus (HIV) as a model setting (2013-2016)

Industry Partner: Calimmune

Gene therapy is a promising therapeutic that is being developed to address genetic diseases and viral infections such as Human Immunodeficiency Virus (HIV). This project, involving collaboration between Prof John Murray from the School and Dr Geoff Symonds of Calimmune, will produce mathematical models of how gene therapy delivered to one type of cell can differentiate into the desired end target and impact disease.


The trophic ecosystem of a purpose-built, offshore artificial reef: do coastal currents supply sufficient nutrients for the local production of fish? (2012-2015)

Industry Partner: NSW Department of Primary Industries (Fisheries NSW).

A/Prof Moninya Roughan (with Prof Iain Suthers and Prof Emma Johnston, UNSW, and Michael Lowry, Matthew Taylor and Charles Gray, Dept. Primary Industries).   

Artificial reefs are increasingly used for the growing tourism and recreational fishing sectors, but do these reefs simply attract fish or do they support an ecosystem that sustainably produces fish? We will determine if the recreational catch of fish around artificial reefs is based on the flow of nutrients and plankton through the complex structure, compared to the boundary layer flow over natural reef. Reef surface area, flow disturbance and residence time of fish may be the key ecosystem parameters. The deployment of such reefs in video range of the Sydney cliffs, in the midst of an existing ocean observing system, will provide a scientific basis for the 12 reefs proposed off our coast and elsewhere around Australia.  


Innovative approaches to identifying regional responses of biodiversity to climate change (2010-2013)

Industry Partner: The Australian Museum

Prof David Warton (with Dr Daniel Ramp, Dr Kim Jenkins, Dr Mick Ashcroft, Dr John Gollan, Dr Patrick Driver). Prof Warton and Australian Museum collaborators are developing innovative methods of mapping biodiversity and how biodiversity may respond to climate change at the regional scale. This project will produce climate models that are more detailed and which better reflect the climate experienced in species habitats than was previously possible, using new field measurements and novel modelling approaches. Novel biodiversity modelling approaches will then be used to study the potential threats of climate change to biodiversity in unique World Heritage Areas in the Sydney region.

Can an anti-HIV gene in blood stem cells protect from immune depletion by HIV? (2010-2012)

Industry Partner: Calimmune

Calimmune is developing a gene therapy that suppresses the expression of the HIV co-receptor CCR5, so that when administered to a person with HIV infection their immune cells will be protected. Prof John Murray from the School and Dr Geoff Symonds of Calimmune obtained a Linkage Grant to investigate the effectiveness of this therapy in the laboratory, and to estimate the impact such a gene therapy could have in an HIV-infected individual. This collaboration between Prof Murray and Dr Symonds follows on from previous joint work related to another anti-HIV gene therapy developed and tested in a clinical trial by Johnson & Johnson Research Australia. Mathematical modeling will play an important role in this project, as it has done in their previous work.

Optimisation Projects with Industry

Prof Gary Froyland has led several optimisation projects with industry and government.

BHP Billiton: Two ARC Linkage Projects (with Prof. Natashia Boland, Prof. Peter Taylor, Mr Peter Stone, Dr Merab Menabde, and Dr Mark Zuckerberg) and an externally funded project developed a suite of novel optimisation methodologies to improve BHP Billiton's strategic planning of open pit mining projects. These improvements included the development of long-term plans to maximise project Net Present Value (NPV), the development of optimisation methods to optimise NPV when presented with uncertain geological information, and improved algorithms to optimise long-term plans using huge geological models of very high resolution over several decades.  

Patrick Corporation: Development of new scheduling algorithms for Patrick Corporation’s new container exchange facility at Port Botany (with Dr Thorsten Koch, Dr Nicole Megow, and Mr Howard Wren). The optimisation algorithms produced a gantry crane schedules that completely eliminated wasteful rehandling moves of containers, and were incorporated into the Port Botany operations. 

Defence Science and Technology Agency (DSTO): Research project (with Dr Jez Gray and Dr Therese Keane) to optimally schedule landing operations of amphibious vehicles deployed from navy ships, and to most efficiently pack vehicles and other supplies on multi-decked ships with multiple unloading modes.

NSW Bureau of Crime Statistics: Undertook collaborative research (with Dr Don Weatherburn) to model the dynamics of prison populations and the effects of government policy decisions. We showed that significant reductions in prison populations could be achieved by lowering recidivism, particularly when the recidivism rate is very high.

Hunter Valley Coal Chain Logistics Team: Studied the coal supply chain at the Port of Newcastle to better understand the supply chain dynamics and reduce inefficiencies and ship queue lengths off Newcastle (with Dr Peter Pudney and Dr Palitha Welgama).

Biomedical Applications of Mathematical Modelling

Dr Adelle CosterProf Bruce Henry and Prof John Murray work in the area of mathematical biology. John Murray has a joint appointment with the National Centre in HIV Epidemiology and Clinical Research, holds NHMRC grants and grants with pharmaceutical companies, and provides consulting to the pharmaceutical industry on mathematical modelling. Bruce Henry works on a number of projects funded by NIH and ARC grants with the Computational Neurobiology and Imaging Center, Mount Sinai School of Medicine, New York. Adelle Coster has a joint appointment with the Garvan Institute for Medical Research and works on the link between insulin receptor signalling and glucose uptake into muscle and fat cells.

There are considerable opportunities for PhD and honours projects with a number of these in collaboration with biomedical research institutes. Scholarships for PhD study may be available. For details please contact Adelle, Bruce, or John.