Dr Alys Rachel Clark

BA(Hons) Oxf., MSc PhD Adel.

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Senior Research Fellow


Alys Clark obtained her Bachelor of Arts (Honours) in Mathematical Sciences from the University of Oxford and her Masters and PhD degrees in Applied Mathematics at the University of Adelaide. She joined the ABI in 2008 as a Postdoctoral Research Fellow in the Lung Research Group and now is one of the lead researchers in that group, as well as leading an active research group in reproductive health and development. Alys is a current awardee of a RSNZ Rutherford Discovery Fellowship (2014), and the JH Michell Medal for Applied Mathematics (2017).


Research | Current

Alys’ research interests focus on understanding how we get oxygen from our environment, before and after birth, and using this new knowledge to improve diagnosis and treatment strategies when things go wrong. Alys develops computational models of lungs, placenta and ovaries, which account for complexities in their structure and can predict the impact of disease on organ function. Her expertise lies in developing efficient and reliable methods for modelling physical processes that occur simultaneously in complex networks of tissue and blood vessels.

Placental health 

Abnormal vascular stucture in the uterus and placenta have been implicated in serious complications of pregnancy, such as intra-uterine growth restriction and pre-eclampsia. We aim to construct structural and functional models of the placenta uterus throughout pregnancy that can help to detect problems earlier and more reliably.

Lung health

The impact of lung disease on daily life is considerable, with sufferers often unable to go about activities without becoming short of breath. Lung disease often starts small, via tiny changes in lung tissue structure, and is often undectable in conventional CT imaging until significant damage is done. We aim to develop new models predicting the impact of lung disease on an individual, and new image analysis tools to improve detection of disease before it becomes severe. Importantly, we consider how age (young and old) modifies disease impact, and so should be considered in treatment planning. 

Project linkages

Postgraduate supervision



  • Wendy Kang A computational model of integrative lung physiology for studying nasal high flow therapy.
  • Hamed Minaeizaeim Computing abnormalities in chest x-ray.
  • Rojan Saghian Modelling the uterine circulation to understand the causes and consequences of inadequate spiral artery remodelling.
  • Yuwen Zhang Integration of dynamic lung imaging with structure-based models of lung function
  • Michael Gravatt Modelling the collective behaviour of swimming microorganisms
  • Win Min Tun Oxygen and shear stress in placental vascular development
  • Nurul Izza Ismail Cellular and molecular mechanisms of maternal immune response in early pregnancy
  • Luca Parisi Developing and validating a novel integrated computational model of the human lung to understand the pathophysiology of Acute Respiratory Distress Syndrome
  • Zay Yar Win Patient-specific computational models of lung mechanics and gas exchange to optimise invasive mechanical ventilation




  • Fung Chan Multimodal lung image registration.
  • Arthur Postles Arterial wall shear stress in acute and chronic pulmonary embolism.



2012 - Aotearoa Foundation Postdoctoral Fellowship

2014 - Rutherford Discovery Fellowship

2017 - ANZIAM JH Michell Medal

Areas of expertise

Alys' areas of expertise include

  • Multi-scale modelling of blood flow, air flow and nutrient transport mechanisms.
  • Image analysis, including functional interpretation of images with computational models.
  • Modelling structure-function relationships in complex vascular networks through life.

Selected publications and creative works (Research Outputs)

  • Clark, A. R., Kumar, H., & Burrowes, K. S. (2017). Capturing complexity in lung system modelling. Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine, 231 (5), 355-368. 10.1177/0954411916683221
    Other University of Auckland co-authors: Haribalan Kumar, Kelly Burrowes
  • James, J. L., Chamley, L. W., & Clark, A. R. (2017). Feeding Your Baby In Utero: How the Uteroplacental Circulation Impacts Pregnancy. Physiology (Bethesda, Md.), 32 (3), 234-245. 10.1152/physiol.00033.2016
    Other University of Auckland co-authors: Jo James, Larry Chamley
  • Saghian, R., James, J. L., Tawhai, M. H., Collins, S. L., & Clark, A. R. (2017). Association of Placental Jets and Mega-Jets With Reduced Villous Density. Journal of biomechanical engineering, 139 (5).10.1115/1.4036145
    Other University of Auckland co-authors: Jo James, Merryn Tawhai, Rojan Saghian
  • Osanlouy, M., Zhang, Y., Kumar, H., Clark, A., Malcolm, D., Hoffman, E. A., & Tawhai, M. (2017). Age-Associated Changes In Thoracic Structure And The Impact On Lung Function: A Quantitative Study. Paper presented at International Conference of the American-Thoracic-Society (ATS), Washington, AFGHANISTAN. 19 May - 24 May 2017. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. (pp. 1).
    Other University of Auckland co-authors: Haribalan Kumar, Merryn Tawhai
  • Clark, A. R., & Kruger, J. A. (2017). Mathematical modeling of the female reproductive system: from oocyte to delivery. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 9 (1).10.1002/wsbm.1353
    URL: http://hdl.handle.net/2292/32044
    Other University of Auckland co-authors: Jennifer Kruger
  • Lin, M., Mauroy, B., James, J. L., Tawhai, M. H., & Clark, A. R. (2016). A multiscale model of placental oxygen exchange: The effect of villous tree structure on exchange efficiency. Journal of theoretical biology, 408, 1-12. 10.1016/j.jtbi.2016.06.037
    URL: http://hdl.handle.net/2292/30031
    Other University of Auckland co-authors: Jo James, Merryn Tawhai, Mabelle Yuling Lin
  • Saghian, R., James, J., Tawhai, M., & Clark, A. R. (2016). THE INFLUENCE OF TROPHOBLAST PLUGS ON SPIRAL ARTERY HEMODYNAMICS. Paper presented at Meeting of the International-Federation-of-Placenta-Associations (IFPA) - Placenta-Back to the Basics, Portland, OR. 13 September - 16 September 2016. PLACENTA. (pp. 1).
    Other University of Auckland co-authors: Merryn Tawhai
  • Saghian, R., James, J., Collins, S. L., Tawhai, M., & Clark, A. R. (2015). Modelling the relationship between maternal blood flow and villus tree density in normal human pregnancy. Placenta. 10.1016/j.placenta.2015.07.224
    Other University of Auckland co-authors: Jo James, Rojan Saghian, Merryn Tawhai


Contact details

Primary location

Level 7, Room 717
New Zealand

Social links

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