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Marsden success for Sciences

Monday, 20 November 2017

Congratulations to all recipients in the latest Marsden Fund annual round – our most successful round since 2013.

Division of Sciences researchers have gained over $7.2m for 12 world-class research projects as Principal Investigators and a further $6m as Assistant Investigators working in collaboration with researchers both across Otago and in external organisations.

2017 heralds Otago as the most successful university in terms of the number of awards and total funding awarded at just short of $24m, the highest amount ever secured by Otago.

The funding secured by Principal Investigators in Sciences includes eight standard projects and four ‘Fast-Start’ projects designed to support outstanding researchers early in their careers.

Pro-Vice-Chancellor Professor Richard Barker says that he is “delighted at the success of researchers in the Division in gaining funding from the extremely competitive Marsden Fund. The strength of fundamental research in the Sciences at Otago combined with highly innovative approaches to solving complex problems underpins our success. The breadth of Departments represented in this funding is an aspect of this success that is also highly pleasing”.

2017 Marsden recipients

(Please note. Only those studies involving Sciences researchers have been listed. Names include the study’s Principal Investigator(s) and Sciences Assistant Investigators where relevant.)

Single photon control of optical phase using ultracold Rydberg atoms
$300,000 (Fast Start)

Principal Investigator: Dr Amita Deb, Physics

Light beams interact with each other extremely weakly in conventional materials. This makes light a fantastic carrier of information, but severely limits its use in information processors. In this proposal, we will create an artificial medium, consisting of atoms at ultralow temperatures, where the interaction is so strong that a single quantum of light (photon) will control the transmission and the delay of an entire beam of light. A key ingredient for photon-based information processing in such a medium is the ability to catch photons and store them for long enough. This has proved a challenging task due to detrimental collisions between randomly moving atoms. By employing a variant of atoms that has a tendency to anti-bunch for fundamental reasons, we will make atoms stay away from each other. This keeps lossy atomic collisions at bay and achieves long-lived storage and an efficient retrieval of photons on-demand. Enabled by this, we will build - piece by piece - a photonic logic module where two light beams act strongly upon each other in a highly controlled way. Our novel and scalable approach addresses a fundamental, long-standing goal of quantum optics and extends the frontiers of photon-based quantum technologies.

Searching for a human sensory ‘fingerprint’ – a personalised index of hedonic eating
$300,000 (Fast Start)

Principal Investigator: Dr Mei Peng, Food Science
Assistant Investigator: Dr Elizabeth Franz, Psychology

Fighting against our human desire to over-eat is challenging in a world where food is becoming increasingly accessible, varied, and palatable. Recent data indicate that some people are particularly susceptible to ‘hedonic’ eating for pleasure. While this behaviour is thought to be related to brain networks responding to reward, it is unclear why food holds greater rewards for some people than for others. Because eating is a multi-sensory experience, we predict that the key to understanding this paradox may rest in looking at data across multiple senses. Indeed, tantalising new findings suggest the possibility that we each have a unique sensory ‘fingerprint’ that controls reward-related brain networks and determines individual susceptibility to over-eating. In this project, we will search for this fingerprint and unravel its relationship to hedonic eating using neuroimaging techniques and sensory analyses. This new interdisciplinary research approach promises to revolutionise our understanding of human eating behaviour.

The small scales call the shots: the effect of microinstabilities on collisionless cosmic fluids
$300,000 (Fast Start)

Principal Investigator: Dr Jonathan Squire, Physics

Virtually all of the ordinary matter in the universe is plasma: a fluid that is so diffuse that its ions and electrons cannot recombine into atoms. Very hot and diffuse plasmas, which have weak magnetic fields and infrequent interparticle collisions, are hypersensitive: with any tiny change in the magnetic field, microinstabilities abruptly grow and violently mix the plasma. Despite being enormously smaller in scale than the motions that caused them in the first place, these microinstabilities strongly influence the plasma's macroscale dynamics. We will quantify these effects by developing a new theory for the fluid dynamics (large-scale behaviour) of plasmas under these conditions. This theory will quantify the evolution of microinstabilities, and how they affect the macroscale plasma motions and magnetic fields. Our work will critically improve our fundamental knowledge of this exotic (but widespread) form of matter, will lay the foundation for understanding its turbulent dynamics, and will yield the first practical techniques for simulating such plasmas. These in turn will be crucial for unravelling key astrophysical processes such as galaxy formation, the interaction of the Earth with the sun, and the magnetisation of the universe itself.

Interactive 3D computational videography
$300,000 (Fast Start)

Principal Investigator: Dr Stefanie Zollmann, Computer Science

An emerging paradigm called 3D computational videography uses recently developed image-processing techniques to extract 3D data from videos. However, existing techniques in this area require multiple cameras, or intensive computer processing, or time-consuming human annotation. The aim of the current project is to construct a 3D scene from a single unconstrained video file, with minimal human annotation, in close to real time. After the 3D scene is reconstructed, a user will be able to explore the scene freely, selecting new viewpoints and perspectives. To illustrate, imagine being able to experience a family gathering, captured on a single video, as a fully explorable 3D scene, so that your choices about how to move and where to look can be different from those of the camera operator.
The goal of this project is to advance 3D computational videography with techniques drawn from two existing areas, that have not so far been combined. We will draw on the one hand on well-known computational photography techniques going beyond the boundaries of traditional photography and allowing to extract 3D structure from a single photography and on the other hand on techniques recently developed in augmented reality, that emphasise real-time computer vision and computer graphics.

Making, probing, and understanding two-dimensional quantum turbulence

Principal Investigator: Dr Ashton Bradley, Physics

Fluid turbulence subtly shapes our daily existence — we are living in it. It also plays a dominant role in many applied settings including the design of air and water craft, and the prediction of extreme weather events. Yet fluid turbulence remains poorly understood, even though many of its features are universal, appearing in similar forms for a wide range of fluids, and on very different length scales.

In a flattened quantum fluid made of atomic Bose-Einstein condensate, turbulence is stripped down to its bare essentials: the chaotic interaction of tiny quantum whirlpools moving in only two dimensions. Bose-Einstein condensates also offer a promising pathways for studying turbulence due to their precise experimental control and clear theoretical description. While recent advances in manipulation and imaging enable new routes to creating and understanding turbulence in quantum fluids, fully-developed planar quantum turbulence has yet to be observed in nature. We will develop theoretical tools for making, probing, and understanding fully developed two-dimensional quantum turbulence, with close ties to experiments designed to realise these chaotic quantum states. The outcomes of this work will reveal generic features of fluid turbulence, and exotic behaviour unique to fluids obeying the principles of quantum mechanics.

Polymer-immobilized carbon monoxided donors: Agents for tissue protection

Principal Investigators: Professor David Larsen, Chemistry
Professor Ivan Sammut, Pharmacology & Toxicology

Once viewed as a “silent killer” through its binding to haemoglobin, carbon monoxide (CO) is now accepted as a cyto-protective molecule with multiple important physiological signalling roles. However, the complexity of controlling low dose CO gas delivery in a clinical setting, combined with the hazardous consequences of any gas leak, have been acknowledged as significant impediments for its use in gaseous form. CO-releasing molecules (CORMs) provide a much safer alternative as administration of the therapeutic dose can be closely controlled. Most CORMs are small molecule transition-metal carbonyl complexes that have shown beneficial effects but have inherent toxicities prohibiting human applications. We have recently developed a novel small molecule, metal-free, organic class of CORMs that shows valuable promise as an additive in organ/tissue transplant solutions, and as a prophylactic in heart bypass surgical applications. Using our technology we will develop these compounds further for human applications by immobilising them onto polymer supports to overcome problems with cellular toxicity and aqueous solubility. Our polymers are designed for ease of use by improving solubility in biological media, and by delivering clinically relevant CO-release profiles. Additionally, synthesising polymers with trackable markers will help answer fundamental controversies surrounding the mechanism of action of CORMs.

Microbes at the helm: are microbiomes shaping parasite phenotypes?

Principal Investigator: Professor Robert Poulin, Zoology

The microbiome revolution is rapidly changing how we study ecology and evolution, as researchers increasingly realise that much of an organism’s phenotype can be attributed to its metagenome (combined DNA of its resident microorganisms). Parasitic organisms also have their own microbiomes. Can these shape parasite biology and host-parasite interactions? This could have far-reaching implications for our understanding of parasitism and the development of new anti-parasite therapies. Using two flatworms which parasitise native aquatic animals, we will address this question, testing for ontogenetic, inter-individual and geographic variation in parasite microbiomes and experimentally quantifying their impact on parasite development and, ultimately, their phenotype. Our research will use a set of powerful tools ranging from metagenomic sequencing to experimental manipulation of microbiomes, to explore how bacteria shape what parasitic worms actually do.

Stretching ice to the limit: New flow laws for ice sheets

Principal Investigator: Professor David Prior, Geology
Assistant Investigator: Professor Christina Hulbe, Surveying

Ice deformation and ice-sheet flow control future sea level. Although strain in glacial ice is high, laboratory studies of ice deformation that yield mechanical data have only been conducted to low strains (<30%). Rock deformation experiments suggest that microstructural change and mechanical weakening in ice should continue to strains of >500%. Therefore, it is very likely that existing models underestimate the contribution of deformation to ice-sheet flow. We propose new torsion experiments (twisting a cylindrical sample) to quantify microstructural and mechanical evolution of ice to high strain (>500%). We will derive a new high strain ice flow law, from experiments at temperatures between -5°C and -30°C and across two orders of magnitude in strain-rate. We plan to test the extrapolation of the new flow law to natural (slow) strain rates in two ways; firstly by measuring the stresses needed to deform glacial samples at natural strain-rates and temperatures and secondly through a field experiment to constrain the deformation conditions in the shear margin of an Antarctic glacier. Micromechanical models will be used to explore how rates of different grain-scale processes contribute to microstructural and mechanical evolution and to provide simple strain-dependent parameters to use in large-scale ice sheet models.

Microresonator frequency combs through second-order nonlinearities

Principal Investigator: Dr Harald Schwefel, Physics

Frequency combs are light sources whose spectrum consists of numerous equally-spaced lines. They were first invented in 2000, triggering a string of breakthroughs; the Nobel Prize followed in 2005. In 2007, a revolutionary new way of frequency comb generation emerged: a laser beam launched into a microscopic resonator spontaneously transformed into a comb! Unfortunately, the third-order nonlinear light-matter interactions that underpin the transformation gives rise to complex instabilities, and do not permit straightforward access to the visible and mid-infrared spectral regions.

In this project, we will experimentally demonstrate an entirely new paradigm of microresonator frequency combs based on second-order light-matter interactions, whose unique and unexplored advantages have full potential to enable stable frequency combs and access to new spectral regions. Through synergetic combination of theory and experiment, we will leverage distinct second-order processes to demonstrate novel microresonator comb sources satisfying critical needs at three distinct spectral regions: (i) the near-infrared, (ii) the visible, and (iii) the mid-infrared. The developed second-order microresonator frequency comb sources will represent an entirely new technology that has full potential to offer unprecedented performance for a myriad of applications, including multi-wavelength telecommunications (near-infrared), imaging (visible), and molecular spectroscopy (mid-infrared).

Whakaarahia anō te rā kaihau! Raise up again the billowing sail! Revitalising cultural knowledge through analysis of Te Rā

Principal Investigator: Dr Catherine Smith, Centre for Materials Science and Technology

Despite the centrality of sailing in New Zealand history, only one customary Māori sail survives. The sail (Te Rā), probably collected by Cook (c.1768-79), is in closed storage at the British Museum, London. Te Rā has been exhibited once, but has not been experienced in New Zealand since collection. Little information exists about customary Māori sails, despite revitalisation of ocean-voyaging waka and related knowledge systems which have had demonstrated benefits for Māori cultural health. This collaborative and interdisciplinary project, connecting Mātauranga Māori and science, brings experienced weavers and scientists together to unlock the cultural knowledge only available through study of Te Rā. Enquiry into Te Rā provides a vehicle for all New Zealanders to engage with the story of an unparalleled journey that brought people to the last unexplored landmass, and the birth of Aotearoa. As the physical embodiment of cultural knowledge of voyaging, Te Rā also shows evidence of the emergence of a distinctively Māori response to new plants, animals and sailing. This project is at the nexus of Mātauranga Māori and Western science, providing a model for robust knowledge development beneficial to iwi, practitioners and academics through comprehensive research on the sole remaining Māori sail, Te Rā.

How does the Earth stop global warming? Testing climate stabilisation during ‘hyperthermal’ events

Principal Investigator: Associate Professor Claudine Stirling, Chemistry

The Earth is in the midst of a climate crisis, with a carbon cycle disturbance comparable to those that drove biological turnover and even mass-extinction events in geological history. The side-effects of warmer global temperatures are already occurring, including ocean acidification, toxic phytoplankton blooms, and expansions of oxygen deprived conditions in the oceans. It is less well known that these threats are also negative feedback mechanisms that remove carbon from the atmosphere, and eventually re-stabilise the climate on geological timescales. The climate recovery process, however, is poorly constrained, and it is not known exactly when or how the natural climate system will return to ‘normal’. Anthropogenic activity might have even delayed the next natural glaciation cycle. We will use novel geochemical proxies and biogeochemical modelling to trace the action of negative feedback mechanisms during past global warming events. These will be applied to a series of events that represent a range of CO2 emission scenarios, analogous to those we face in the future. We will constrain the feedback mechanisms of the climate system to better understand the lifespan of human-induced climate change, providing crucial boundary conditions for modelling future climate scenarios.

The secret life of traumatic memories

Co-Principal Investigator: Associate Professor Rachel Zajac, Psychology

Traumatic memories seem to have a secret life. Influential, but pseudoscientific, clinical theories would have us believe that memories for traumatic experiences are jumbled, and recalled in bits and pieces with parts missing. That is, the memories are said to be fragmented, lacking coherence. In this pseudoscientific view, fragmentation is harmful—caused by the allegedly special mechanism by which the brain encodes only "shallow" aspects of trauma, forgoing deeper conceptual processing. The idea is that with the right therapy, what's called "traumatic amnesia" fades; the fragmented memories fill out, and coherence increases. This view rests entirely on the 40-year-old presupposition that traumatic memories behave differently from non-traumatic memories. But there is no scientific evidence that the harm of fragmentation, the special encoding mechanism, or the "traumatic amnesia" actually exist. More likely, we propose, is that fragmentation is not unique to trauma; instead, people appraise fragmented traumatic memories in unique ways. In doing so, they set in motion a chain of behaviours that shape their memories, their psychological wellbeing, and sometimes their very willingness to question what they remember. We will connect the links in this chain.

Friends on the forest floor: do facilitative interactions dominate in New Zealand’s unique bryoflora?
$300,000 (Fast Start)

Principal Investigator: Dr AJ Brandt, Landcare Research
Assistant Investigator: Associate Professor David Burritt, Botany

Competitive species interactions underpin modern theory on how plant communities are structured and which species are present. Facilitation, where the presence of a neighbouring species benefits rather than hinders a plant’s growth, is considered important mainly in harsh environments, where the neighbour could ameliorate the impact of stressful conditions. Bryophytes (mosses and liverworts) are the oldest land plants. They lack roots and internal transport vessels, making them fundamentally different from flowering plants. Because bryophytes obtain nutrients and water directly from the atmosphere, they may be more likely to share than compete for resources, and thus may be especially reliant on facilitation between species to acquire and maintain water in their cells. To determine whether facilitative interactions increase in strength under stressful conditions or occur along the entire environmental gradient, we will measure the stress and performance responses of bryophytes grown in monoculture and with other species along experimentally -imposed temperature and moisture gradients. This will allow us to test the generality of current ecological theory derived from studies of flowering plants.

Understanding the cellular and molecular drivers governing a unique whole body regeneration phenomenon in a chordate model.

Principal Investigator: Dr MJ Wilson, Anatomy
Assistant Investigator: Associate Professor Miles Lamare, Marine Science

Regeneration is a basic biological phenomenon that involves a complex temporal and spatial interplay of molecular signalling cascades, cell divisions, chemical and mechanical stimuli.
However, the nature of signals that instigate the process of regeneration and the biology of effector cells remain elusive. A striking example of regeneration is the process of whole body regeneration phenomenon in Botrylloides, where a fully functional adult regenerates in under two weeks from isolated minute fragments of blood vessels. Our research programme will combine cell-tracing, gene editing and genomics methods to determine the molecular and cellular basis of regeneration in this amazing animal.

Betwixt two worlds? Disruptive technology and negotiating identity change

Principal Investigator: Professor Janet Hoek, Department of Marketing
Assistant Investigator: Dr Tamlin Conner, Psychology

Are electronic nicotine delivery systems (ENDS) a disruptive technology that could dramatically reduce smoking or could vaping instead undermine cessation? Despite agreement that ENDS pose fewer health risks than smoked tobacco, many people do not fully replace smoking with vaping. We will explore this apparent paradox by probing how smokers negotiate new identity positions and which practices they retain, create or relinquish as they begin vaping. We will also examine whether and how vapers transition to become vape-free, thus offering new insights into a previously unexplored question.

Our novel mixed-methods approach will elicit data using longitudinal qualitative interviews, videographic analyses, and ecological momentary assessments, and develop contrasting perspectives on why and when transition from smoking to vaping, and beyond, occurs. We will use emerging social practice concepts to propose an over-arching explanation of how smoking and vaping practices intersect and evolve in relation to other practices. The Government’s plans to liberalise ENDS regulation make New Zealand a unique setting in which to analyse perplexing and unresolved questions about ENDS uptake. The new perspective we propose developing will complement dominant biomedical addiction discourse and provide a richer understanding of how ENDs, a disputed and ambiguous innovation, could improve health and well-being.

Lattice polytope samplers: theory, methods and applications

Principal Investigator: Professor ML Hazelton, Massey University
Assistant Investigator: Dr Matthew Schofield, Mathematics and Statistics

Statistical inverse problems occur when we wish to learn about some random process that is observed only indirectly. Inference in such situations typically involves sampling possible values for the latent variables of interest conditional on the indirect observations. This project is concerned with inverse problems for count data, for which the latent variables are constrained to lie on the integer lattice within a convex polytope (a bounded multidimensional polyhedron). An illustrative example arises in transport engineering where we observe vehicle counts entering or leaving each zone of the network, then want to sample possible interzonal patterns of traffic flow consistent with those entry/exit counts.

In principle, such sampling can be conducted using Markov chain Monte Carlo methods through a random walk on the lattice polytope, but it is challenging to design algorithms for doing so that are both computationally efficient and have guaranteed theoretical properties. The overall aim of this project is to combine techniques from algebraic statistics with recent geometric insights in order to develop and study new polytope samplers that address these issues. These methods will be applied to confidentialisation of cross-tabulated official statistics, to capture-recapture modelling in ecology, and to inference for traffic flows in transport engineering.

Improved modelling in evolutionary transcriptomics and proteomics will advance understanding of plant adaptation

Principal Investigator: Professor PJ Lockhart, Massey University
Assistant Investigator: Professor David Bryant, Mathematics and Statistics

Reliably predicting the impacts of climate change on the New Zealand alpine flora requires an understanding of plant adaptation in New Zealand, an area of research that has progressed little over the last 100 years. Whether evolution can keep pace with climate change in part depends upon how fast plant species evolve to occupy the available environmental niches. Our proposal studies this capacity in two ways. First, to better understand current physiological responses we will evaluate how transcriptomes and proteomes respond to environmental stress. Second, we will investigate how and why these physiologies evolved. Together these studies will help us understand both the adaptive capacity of present day plant species and their likely responses to future environmental change. As a model we will investigate the recurrent evolution of drought resistance in New Zealand alpine Ranunculus species. Our novel approach uses high throughput methodologies for transcriptome and proteome analyses, physiological measurements of water use efficiency and metabolite composition, as well as novel approaches for sequencing and analysing whole chloroplast genomes. Our approach will test the hypothesis that hybridization allows for rapid adaptation and thereby improves the resilience of evolutionary lineages facing climate change.

Is individual variation relevant to population dynamics?

Principal Investigator: Professor DP Armstrong, Massey University Manawatu
Assistant Investigator: Professor Richard Barker, Mathematics and Statistics

What is the optimal level of complexity to consider when predicting population dynamics? The conventional wisdom is to keep models as simple as possible. However, the recent explosion of research on individual variation in animal personalities and life history traits is increasing our capacity to generate complex individual-based models of population dynamics. But will this increased complexity significantly improve our capacity to predict population dynamics, justifying the need for detailed individual-based monitoring in threatened species programmes? Our project will answer this question using our multiple long-term data sets for reintroduced robin and hihi populations, combined with new data relating personality traits to demographic rates.

Volcanoes can make waves too: a new understanding of tsunamis generated by volcanic eruptions

Principal Investigator: Dr EM Lane, NIWA
Assistant Investigator: Professor James White, Geology

The tsunamis generated by the 1883 eruption of Krakatau killed more than 36,000 people up to 800 kilometres from the crater. Although neither as common, nor as powerful, as earthquake-generated tsunamis, volcanic tsunamis cause destruction much further away than the actual eruption - tsunamis have causes 25% of all deaths during historical volcanic eruptions. Yet we still only have a basic understanding of the processes involved. Discrete explosions, growth and pulsation of erupting columns and pyroclastic flows can all displace water and cause tsunamis. What factors are most important in determining the size of the tsunami an eruption causes? How do the substances involved (gases, liquids and particles) interact: their rheologies, temperatures and phases? Combining wave flume experiments (submarine eruptions and hot flows entering the water) with state-of-the-art computer modelling of multi-phase and granular flows, we will determine key elements of the fascinating processes involved in volcanoes generating tsunamis. This is much more than an historical curiosity. New Zealand is surrounded by potential volcanic tsunami sources – countless lake-filled calderas such as Lake Taupo, Auckland’s coastal volcanic field and the Kermadec Arc of submarine volcanoes stretching to the north-west. Which of these have the potential to cause dangerous tsunamis?

Blossoming of bioinspired supramolecular architectures: Towards applications in catalysis, drug delivery and materials science

Co-Principal Investigator: Associate Professor James Crowley, Chemistry

Nature exploits stimuli-responsive materials and supramolecular forces to control the assembly of molecules into living organisms, including shaping DNA strands into the double helix structure and building the membrane of every cell. Borrowing this concept from biology, we have designed specific supramolecular containers that can open and close reversibly in a controlled manner – just like the petals of a flower in sunlight. These supramolecular flowering structures will be assembled from two different metal centres that are connected by bridging petal ligands. The petals will be opened and closed reversibly by external stimuli, such as redox processes, pH change or light. The structural changes of the supramolecular flowers will be exploited to turn on (and off) catalytic processes or bind and release selected molecules including drugs targeted to tumour tissue. The development of these new switchable bio-inspired supramolecular architectures will open the way for new applications in catalysis, drug development and materials science.

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