24 Aug 2017: Chang-Joon Lee

Thu 24 Aug 2017 3:30pm (Murdoch University, Senate Room 121.1.002)

Dude, where’s my oxygen? – A computational study of factors that predispose the kidney to hypoxia

Chang-Joon Lee

School of Engineering and IT, Murdoch University & Faculty of Engineering and Mathematical Sciences, The University of Western Australia

great interest due to the perplexing fact that the kidney is highly susceptible to hypoxia despite being well-supplied with oxygenated blood and having the lowest oxygen extraction ratio of the major organs. One leading hypothesis for this paradox is that a fraction of the oxygen delivered to the kidney never reaches renal tissue, but instead diffuses from arterial to venous segments of the cortical vasculature. However the biological significance of arterial-to-venous (AV) oxygen shunting in the renal cortex remains a matter of controversy.

To assess the physiological significance of AV oxygen shunting and identify other potential factors that may play a major role in renal hypoxia, we generated a new pseudo-three-dimensional computational model of renal cortex based on the cortical vasculature in the rat kidney. The model provides estimates of oxygen tension (PO2) in the renal tissue and how it changes for given combinations of renal oxygen delivery and/or consumption, as well as the magnitude of oxygen shunted from the arterial to venous segments.

While a number of lines of evidence suggest AV shunting is significant, most importantly our computational model predicts AV shunting is small under normal physiological conditions (~0.9% of total renal oxygen delivery), but increases under pathologic states (up to ~3.0% of total renal oxygen delivery). We conclude that AV oxygen shunting normally has only a small impact on renal oxygenation, but may exacerbate renal hypoxia during certain pathologic states. We further conclude that, among other factors that may predispose the kidney to renal hypoxia, renal hypoxia is most likely to be initiated by drastic reduction in the surface area of peritubular capillaries.

25 May 2017: Rob Atkins

Thu 25 May 2017 3:30pm (Murdoch University, ECL Postgraduate Suite, 460.2.031)

Structure, Solutes and Surfaces in Ionic Liquids

Rob Atkin

School of Molecular Sciences, The University of Western Australia, WA 6009, Australia

Ionic Liquids (ILs) are a subset of molten salts, distinguished by having melting points below 100 °C. Their low melting points are brought about by weakening electrostatic interactions between the ions and hindering their packing into a crystal lattice. Electrostatic forces are reduced by engineering their molecular structure so that at least one of the ions is large and organic, which increases the distance between neighbouring charged centres, and by delocalising the ionic charge over a large molecular volume. Ionic liquids have some unusual and remarkable properties, including pronounced nanostructures, which is one of their unique, yet unifying, characteristicss.

Neutron diffraction measurements modelled with reverse Monte Carlo simulations will be used to show that ILs have a sponge-like (bicontinuous) nanostructure; IL cation alkyl chains and ionic groups are segregated into domains that percolate throughout the bulk liquid.1-3 A snapshot of the simulation box for ethylammonium nitrate (EAN, a protic IL) is shown in Figure 1 (left). Varying the structure of the ions changes way inter-ionic forces are expressed, which leads to changes in nanostructure. The effect of dissolved water, glycerol and octanol on bulk IL nanostructure will be examined.4,5

High resolution amplitude modulated atomic force microscope images (c.f. Figure 1) will be used to demonstrate how IL nanostructure changes at a solid surface with the ion structure, and the effect of dissolved solutes.6-8 A 20 nm × 20 nm topographic AM-AFM images of the 1-Ethyl-3-methylimidazolium bis(trifluoromethyl- sulfonyl) imide – graphite Stern layer is shown in Figure 1 (middle), with the position of the ions shown in the magnified area in Figure 1 (right). The effect of applying a potential to a conducting solid surface on the IL interfacial nanostructure will also be discussed, and recent results for the spontaneous exfoliation of graphene into an ionic liquid will be described.9

Figure 1. (left) Snap shot of simulation box used to fit neutron diffraction data for EAN. (middle and right) AM-AFM image of the 1-Ethyl-3-methylimidazolium bis(trifluoromethyl- sulfonyl) imide – graphite Stern layer.


(1) Atkin, R.; Warr, G. G. J. Phys. Chem. B 2008, 112, 4164.

(2) Hayes, R.; Imberti, S.; Warr, G. G.; Atkin, R. Physical Chemistry Chemical Physics 2011, 13, 3237.

(3) Hayes, R.; Imberti, S.; Warr, G. G.; Atkin, R. Angewandte Chemie International Edition 2013, 52, 4623.

(4) Hayes, R.; Imberti, S.; Warr, G. G.; Atkin, R. Angewandte Chemie International Edition 2012, 51, 7468.

(5) Murphy, T.; Hayes, R.; Imberti, S.; Warr, G. G.; Atkin, R. Physical Chemistry Chemical Physics 2014, 16, 13182.

(6) Elbourne, A.; Voitchovsky, K.; Warr, G. G.; Atkin, R. Chemical Science 2015, 6, 527.

(7) Page, A. J.; Elbourne, A.; Stefanovic, R.; Addicoat, M. A.; Warr, G. G.; Voitchovsky, K.; Atkin, R. Nanoscale 2014, 6, 8100.

(8) Elbourne, A.; McDonald, S.; Voïchovsky, K.; Endres, F.; Warr, G. G.; Atkin, R. ACS Nano 2015, 9, 7608.

(9) Elnourne, A.; Mclean, B. D.; Voïchovsky, K.; Warr, G. G.; Atkin, R J. Phys. Chem. Lett., 2016, 7, 3118


Rob Atkin is a Professor of Chemistry at the University of Western Australia. Rob obtained his PhD from the University of Newcastle (Australia) in 2003 under the supervision of Prof Simon Biggs, then joined the group of Prof. Brian Vincent at Bristol University as a postdoctoral fellow, working on polymer microencapsulation. In 2005 he was awarded an Australian Research Council (ARC) Postdoctoral Fellowship to study surfactant self-assembly in ionic liquids at the University of Sydney in collaboration with Prof Greg Warr. He returned to Newcastle in 2007 as a University of Newcastle Research Fellow, was awarded an ARC Future Fellowship in 2012, and promoted to Professor in 2015. In March 2017 Rob moved to his current position at the University of Western Australia. Rob has published 6 book chapters and 130 journal articles and collaborates with groups in Australia and in the UK, Sweden, Germany, the USA, Japan and France.

7 Apr 2017 : Jitendra Mata

Fri 7 Apr 2017 – 3:30pm (Murdoch University, Senate Room)

Nanoscale Characterisation Techniques at ANSTO

Dr Jitendra P. Mata — ANSTO

ACNS, Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia.

E-mail: jitendra.mata@ansto.gov.au

SANS instruments at ACNS

S mall angle X-ray and neutron scattering (SAXS, SANS) are versatile techniques for investigating the nanoscale structure of soft materials such as food, surfactants, polymers, colloids, minerals processing fluids, and emulsions. These techniques have been exceptionally useful for studying complex materials of industrial importance in recent years. The use of small angle scattering (SAS) in combination with traditional techniques offers a unique insight into the structure, size, shape and morphology of the materials. Different processes like aggregation, structural transitions, crystallization and phase separation can be studied using SAS techniques in various conditions. SAS are well-established characterisation techniques for the nano and microstructure (from 1 nm to >1000 nm) investigations in various materials. These techniques are mostly nondestructive, and particularly useful to study systems in complex sample environment, in-situ, and at different kinetic stages. The use of deuterated molecules and partial deuteration has enhanced the applicability of these methods for soft materials (particularly for SANS technique). We discuss the advantages and limitations of these techniques, and provide examples of recent applications in mineral processing, food technology and colloid science in this talk.

Australia is the home of state of the art reactor based SANS instrument known as Quokka (at the ACNS, ANSTO). Combining Quokka with onsite lab based SAXS instrument or with the Australian Synchrotron based SAXS-WAXS instrument provide versatile techniques to study complex soft matter systems. ANSTO is known for its high class neutron scattering based science, outstanding deuteration facility, and exceptional sample environment options to couple with various neutron scattering techniques. A general overview of the institute and techniques available will also be provided.

16 Feb 2017 : Philipp Schönhöfer

Thu 16 Feb 2017 – 3:30 pm (Murdoch University, Senate Conference Room)

Entropic self-assembly of bicontinuous structures : the gyroid … and more?

Mr Philipp Schönhöfer – Murdoch University

Note: Philipp is a PhD candidate in the School of Engineering and IT, and this talk is part of his confirmation of candidature process.

Many biological and synthetical systems  (like lipid/water mixtures [1] and di-block copolymers [2]) form highly complex and symmetric triply-periodic, bicontinous structures by enthalpic self-assembly. Studies by Barmes et al. [3] and Ellison et al. [4] showed that one of these structures, the so called Ia(-3)d double gyroid, can also be generated in equilibrium systems of hard pear-shaped particles with suitable tapering and aspect ratio and consequently systems where entropy is the key factor and no attractive forces are needed.

Performing MD and MC simulations, we  have reproduced the spontaneous formation of the gyroid by hard tapered particles and generated a density-tapering phase diagram. To compare the differences between the enthalpically and entropically driven processes further, we studied the geometrical and morphological properties of the gyroid phase, using scattering functions and Voronoi tessellations. Through this, we show that the formation mechanisms prevalent in this entropy-driven system differ from those found in systems which form Gyroid structures in nature.

Subsequently, hard spheres which shall take up the role of solvent to model mixtures with a solvent are introduced into the simulations. With an explicit solvent the system should be complex enough to model most common phenomena in cubic phases. In this particular case we especially examine a potential stabilizing influence of spheres on the gyroid structure. From a biological point of view this will give information on the formation of other bicontinous structures like the Pn3m double diamond or unbalanced membranes (eg. if the generation of the I4(1)32 gyroid structure is solez entropy driven). Hence, systems with different concentrations and sphere sizes are analysed.

[1] J. M. Seddon and R. H. Tepler, Phil. Trans. R. Soc. A 344(1672), 377–401 (1993).

[2] M. W. Matsen and M. Schick, PRL 72(16), 2660 (1994).

[3] F. Barmes, M. Ricci, C. Zannoni, and D. J. Cleaver, Phys. Rev. E 68, 021708 (2003).

[4] L. J. Ellison, D. J. Michel, F. Barmes, and D. J. Cleaver, Phys. Rev. Lett. 97, 237801 (2006).

24 Nov 2016 : Peter Metaxas

Thu 24 Nov 2016 – 3:30 pm (Murdoch University, Postgrad Suite ECL2.031)

Towards frequency-based electronic bio-detection at the nano-scale

Dr Peter Metaxas — School of Physics, University of Western Australia

Magnetic biosensing exploits chemically functionalised magnetic nanoparticles for labelling and subsequent detection of analytes of interest in biological samples, opening routes to new technologies for point-of-care medical diagnostics [1]. Many solid state nanoparticle detection techniques are voltage-level based. For example, in conventional magnetoresistive sensors, the magnetic configuration within the device is modified by the nanoparticles’ stray magnetic fields, generating a change in the device resistance (and thus the voltage across the device). In contrast, electrically probed, field-dependent magnetisation dynamics in magnetic nanostructures offer a route towards intrinsically frequency-based electronic biosensing. This resonance-based approach potentially offers high speed sensing with nano-scale devices [2] which can operate under very large magnetic field ranges [3]. We demonstrate the potential of this approach first using large area, periodically nanostructured ferromagnets (“magnonic crystals”) [3,4]. These systems enable us to probe the effect of nanoparticles on ferromagnetic resonances that are confined to regions in the crystal with lateral dimensions on the order of 100 nm. Secondly we look at nanoparticle sensing exploiting the “gyrotropic” resonance of ferromagnetic vortices. We show how the localized field of a nanoparticle can stiffen the vortex, leading to field sensitivities exceeding those conventionally measured in uniform fields [5]. Finally, we experimentally demonstrate spintronic, frequency-based detection of superparamagnetic beads and discuss future directions of this work (e.g. [5]).

This work would not have been possible without contributions from collaborators at the the Unité Mixte de Physique CNRS/Thales (France), University of Southampton (UK), the National University of Singapore and AIST (Japan).

[1] Gaster et al., Nat. Med., 15, 1327 (2009). [2] Braganca et al., Nanotechnol., 21, 235202 (2010). [3] Sushruth et al., Phys. Rev Appl., 6, 044005 (2016).  [4] Metaxas et al., Appl. Phys. Lett. 106, 232406 (2015).  [4] Fried and Metaxas, Phys. Rev. B, 93, 064422 (2016). [5] Albert et al., Nanotechnol. 27, 455502 (2016).


9 Nov 2016: Peter Harrowell

Wed 9 Nov 2016 – 2:30*pm (Murdoch University, Senate Room)

Rethinking Structure in Amorphous Materials: From Geometry to Statistics

Peter Harrowell — School of Chemistry, University of Sydney

Despite a long history, there remain many important open questions about, not just the best description of structure in liquids and glasses, but what use these structures provide in terms of understanding the properties of amorphous materials. This talk will introduce the basic questions concerning the role of structure in materials science, how that structure is characterised and then present recent results on how the geometry of the locally stable structures in an amorphous materials influence the stability of the material with respect to crystallization.2016_11_10_peterharrowell_imageA central conclusion of this research is that advances in the study of amorphous structure will involve abandoning the traditional descriptive geometrical approach to structure in favour of regarding structure in terms of the statistical correlations between local structural elements. It is hoped that the description of this exciting open problem will be both accessible to and of interest for mathematicians.

(* Peter’s talk will be at 4pm, but is part of a mini-workshop that starts at 2:30 *)

9 Nov 2016: Julian Gale

Wed 9 Nov 2016 – 2:30pm (Murdoch University, Senate Room)

Exploring the Nucleation of Biominerals: When Hard Rocks Meet Soft Matter

Paolo Raiteri, Raffaella Demichelis, Wen Zhao, Kasia Koziara, Alicia Schuitemaker and Julian D. Gale

Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), Department of Chemistry, Curtin University, PO Box U1987, Perth, WA 6845

2016_11_10_juliangale_imageThe nucleation of minerals from ions in aqueous solution underpins important processes from biomineralisation to scale formation and carbon sequestration. All this begins with ion pairing, but what happens next is still a matter that is hotly debated for systems such as calcium carbonate, where the classical nature of nucleation has been called into question [1,2,3]. Therefore it is vital to use both experiment and simulation to fill in the missing details as to how crystalline minerals form. In this presentation we will examine the possible pathways by which two common biominerals, calcium carbonate and calcium oxalate, nucleate in order to try to explain how proteins may influence and control this process. Based on simulation results it will be demonstrated that hard rocks and soft matter are perhaps not as different as they might seem during their earlier stages of formation.


[1] D. Gebauer, A. Völkel, H. Cölfen, Science, 322, 1819 (2008).

[2] R. Demichelis, P. Raiteri, J.D. Gale, D. Quigley, D. Gebauer, Nature Comm., 2, 590 (2011).

[3] A.F. Wallace, L.O. Hedges, A. Fernandez-Martinez, P. Raiteri, J.D. Gale, G.A. Waychunas, S. Whitelam, J.F. Banfield and J.J. De Yoreo, Science, 341, 885-889 (2013)

6 Oct 2016 : Sandy Peterhaensel

Detection of nanometer size differences through human color vision

Speaker : Sandy Peterhänsel, Stuttgart University

Venue    : Thu 6 Oct 2016, 3pm (Murdoch University, Senate Room)

We study how accurately a naked human eye can determine the thickness of thin films and the geometric parameters (height and width) of optical gratings from the observed color. Our approach is based on color-matching experiments, where a sample with unknown parameters is observed next to a reference field of same size. The study of the limits of color discrimination and their dependence
on surrounding conditions for human eyes are one of the major trends in color science [1]. For thin lms this is done by placing the  sample in direct contact to a LCD display, see Fig. 1. For matching of gratings the setup is more complex, as shown in gure 2. This is due to the fact, that only the zeroth order should be observed, as higher orders will lead to an angular dispersion of the wavelengths present in the spectrum of the light source.

In both cases, the color of the reference field is matched by several test persons. From their selection the geometric properties of the thin films, as well as of the gratings are reconstructed via rigorous simulation. We found that the human color observation provides an extremely accurate evaluation of the lm thickness and is comparable to sophisticated instrumental methods in this case. Even for the more complex reconstruction of the grating parameters an accuracy in the range of much more sophisticated methods like scanning  electron microscopy could be observed. Our results suggest that for a wide range of structures, the  color observation may help to get quick, but still accurate, results, without any sophisticated instrumentation.
[1] R.G. Kuehni, Color Res. Appl. 33(324), (2008).
[2] S. Peterhänsel, H. Laamanen, J. Letholahti, M. Kuittinen, W. Osten and J. Tervo, Optica 2(7), (2015)
[3] S. Peterhänsel, H. Laamanen, M. Kuittinen, J. Turunen, C. Pruss, W. Osten and J. Tervo, Opt. Lett. 39(3547), (2014)

13 Oct 2016 : Karol Miller

Paradigm shift in biomechanics: no more research on mechanical properties of tissues

Speaker : Winthrop Professor Karol Miller – University of Western Australia

Venue    : Thu 13 Oct 2016, 4pm (Murdoch University, Senate Conference Room)

It is now recognised that the most urgent task of biomechanists is to devise methods for clinically-relevant patient-specific modelling. A large proportion of the biomechanics community believes that the main obstacle in creating patient-specific models is the difficulty (or impossibility?) of measuring patient-specific properties of tissues to be used in biomechanical models.

For about ten years Intelligent Systems for Medicine Laboratory has advocated a complete refocus of biomechanical research away from describing mechanical properties of tissues. We postulate that instead we need to reformulate computational mechanics problems in such a way that the results are weakly sensitive to the variation in mechanical properties of simulated continua. This suggestion constitutes a paradigm shift in the field and has encountered strong resistance of the more traditionally inclined members of the biomechanics community.

In this seminar I will describe briefly how ISML members’ thinking on this completely new approach to biomechanics has evolved over the years. I will also demonstrate the success of our new approach using examples from the fields of image-guided neurosurgery and vascular biomechanics.

(This talk was previously given as the Hamlyn Distinguished lecture at Imperial and recently at Harvard School of Engineering)