Dr Soroush Safaei

BE Sharif, PhD

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Research Fellow

Biography

Soroush is a post-doctoral research fellow in Auckland Bioengineering Institute at the University of Auckland and has been a member of Physiome project group since 2010. He completed his PhD at the University of Auckland in 2015 around modelling the cardiovascular system and his undergraduate studies in Mechanical Engineering at Sharif University of Technology in Iran. In 2019, he received a prestigious post-doctoral fellowship award funded by Aotearoa Foundation to establish a new research group around modelling the brain haemodynamics and various tissue exchange processes related to neurodegenerative disease such as Alzheimer’s Disease. He took a leadership role in the Virtual Brain Project to complement the ABI’s central research themes by working with researchers in the ABI, the Centre for Brain Research (CBR) and the Liggins Institute.

His research interests in bioengineering lie in the areas of computational modelling, cerebral circulation, biomechanics of the brain and neurodegenerative disease. He has collaborated actively with researchers in several other disciplines of physiology, neuroscience and pharmacology for understanding human physiology, from proteins and cells to tissues and organs, with multi-scale models that use computational techniques derived from engineering and software approaches from computer science.

The Virtual Brain Group is specialised in advanced image processing driven by AI, multi-scale modelling of neurovascular coupling and in-silico modelling of the cardiovascular system. The group consists of PhD students, research scientists and software developers, developing technologies to generate subject-specific cardiovascular and brain tissue models from medical images to study the link between the cardiovascular system, brain perfusion and clearance.

Research | Current

Lists of publications are available directly from these links: Google Scholar.

The human brain is the most complex and the least well understood organ of the human body. Bioengineering contributions to brain research have been relatively few so far and we would like to address this by developing a comprehensive framework for modelling the brain using computational methods built on bioengineering principles.

Computational physiology often relies on multi-scale models of coupled physical processes that can both accurately represent anatomical organ/tissue structure and link to molecular mechanisms. Soroush is developing a mathematical framework based on the transfer, storage and dissipation of energy that addresses these molecule-to-organ scales. The organ level models are typically based on finite element descriptions of organ anatomy upon which biophysical field equations can be solved, using material constitutive laws that are described in relation to underlying tissue structure. These models then invoke cellular mechanisms that are described by a bond graph framework to ensure both conservation of mass or charge and conservation of energy.

 

Research group

Virtual Brain Project
Physiome Project
 

Postgraduate supervision

PhD students 

  1. Jiantao Shen (Mar 2020-present): Computational haemodynamic assessment in the brain using MRI and its association with Alzheimer’s Disease (Jointly with Gonzalo Maso Talou)
  2. Robyn May (May 2020-present): In the search of vascular culprits: a computational model of the cardiovascular system for newborns and their developmental prognosis (Jointly with Gonzalo Maso Talou, Frank Bloomfield)
  3. Harshil Magan (Aug 2020-present): Physics-aware integrated networks and their application to 3D brain haemodynamics (Jointly with Gonzalo Maso Talou, Peter Hunter)
  4. Cameron Apeldoorn (Jul 2021-present): Sprouting life or rooting hypertension? Understanding vascular remodelling contributions to hypertension via computational models (Jointly with Gonzalo Maso Talou)
  5. Reza Kalbasi (Oct 2015-present): Towards enhanced computational physiology through semantically linked health data (Jointly with David Nickerson)
  6. Finbar Argus (Mar 2017-Aug 2021): Multisystem computational modelling and control for physiology (Jointly with Chris Bradley, Peter Hunter)
  7. Elias Ghadam Soltani (Jun 2015-May 2020): Modelling thermoregulation of the human body (Jointly with Chris Bradley, Kumar Mithraratne)
  8. Nima Afshar Ghotli (Jun 2015-Mar 2020): Computational modelling of glucose uptake mechanism in the small intestine (Jointly with Vinod Suresh, Peter Hunter)
  9. Renfei Ma (Nov 2015-Apr 2020): An anatomically accurate modelling of hepatic perfusion and biliary fluid dynamics in the human liver for clinical applications (Jointly with Harvey Ho, Peter Hunter)

ME students

  1. Cameron Apeldoorn (2020): Latent vasculature in MRI sequences: A generative adversarial approach for recovering vasculature from standard MRI sequences (Jointly with Gonzalo Maso Talou)
  2. Zohreh Ekhlasi (2018): Modelling of cerebral aneurysms with fluid-structure interaction (Jointly with Chris Bradley)

Distinctions/Honours

  • 2020 Marsden Fund Award, Royal Society of NZ.
  • 2019 Aotearoa Fellowship Award, Aotearoa Foundation.
  • 2016 Science for Technological Innovation Post-doctoral Award, NZ.

Areas of expertise

  • Cerebral Haemodynamics
  • Cardiovascular System
  • Computational Physiology
  • Neurovascular Coupling
  • Medical Imaging

Committees/Professional groups/Services

University of Auckland service (present) 

  • 2018-2021 Chair of the Early Career Researchers (ECR) Committee

University of Auckland service (past) 

  • 2018-2020 Teaching Doctoral Training Program (DTP) - Computational Physiology
  • 2017 Auckland Bioengineering Institute FRDF/PBRF Funding Allocation Committee
  • 2016 UoA Representative in the Ministerial Trade Mission to Iran

Selected publications and creative works (Research Outputs)

As of 29 October 2020 there will be no automatic updating of 'selected publications and creative works' from Research Outputs. Please continue to keep your Research Outputs profile up to date.
  • Ma, R., Hunter, P., Cousins, W., Ho, H., Bartlett, A., & Safaei, S. (2019). Modeling the hepatic arterial flow in living liver donor after left hepatectomy and postoperative boundary condition exploration. International journal for numerical methods in biomedical engineering10.1002/cnm.3268
    Other University of Auckland co-authors: Harvey Ho, Peter Hunter
  • Brown, P., Tan, A.-C., El-Esawi, M. A., Liehr, T., Blanck, O., Gladue, D. P., ... Yeung, A. W. K. (2019). Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database : the Journal of Biological Databases and Curation, 201910.1093/database/baz085
    Other University of Auckland co-authors: Andrew Chen
  • Ma, R., Hunter, P., Cousins, W., Ho, H., Bartlett, A., & Safaei, S. (2019). Anatomically based simulation of hepatic perfusion in the human liver. International journal for numerical methods in biomedical engineering, 35 (9)10.1002/cnm.3229
    Other University of Auckland co-authors: Harvey Ho, Peter Hunter, Adam Bartlett
  • Afshar, N., Safaei, S., Nickerson, D. P., Hunter, P. J., & Suresh, V. (2019). Computational Modeling of Glucose Uptake in the Enterocyte. FRONTIERS IN PHYSIOLOGY, 1010.3389/fphys.2019.00380
    Other University of Auckland co-authors: David Nickerson, Peter Hunter, Vinod Suresh
  • Afshar, N., Safaei, S., Nickerson, D., Hunter, P., & Suresh, V. (2018). Computational Modelling of the Role of GLUT2 in Glucose Uptake by Intestinal Epithelial Cells. Paper presented at 2018 Virtual Physiological Human Conference, Zaragoza, Spain. 5 September - 7 September 2018. Related URL.
    URL: http://hdl.handle.net/2292/46716
    Other University of Auckland co-authors: Vinod Suresh, David Nickerson, Peter Hunter
  • Safaei, S., Blanco, P. J., Muller, L. O., Hellevik, L. R., & Hunter, P. J. (2018). Bond Graph Model of Cerebral Circulation: Toward Clinically Feasible Systemic Blood Flow Simulations. FRONTIERS IN PHYSIOLOGY, 910.3389/fphys.2018.00148
    Other University of Auckland co-authors: Peter Hunter
  • Chase, J. G., Preiser, J.-C., Dickson, J. L., Pironet, A., Chiew, Y. S., Pretty, C. G., ... Safaei, S. (2018). Next-generation, personalised, model-based critical care medicine: a state-of-the art review of in silico virtual patient models, methods, and cohorts, and how to validation them. Biomedical engineering online, 17 (1)10.1186/s12938-018-0455-y
    Other University of Auckland co-authors: Peter Hunter, Merryn Tawhai
  • de Bono, B., Safaei, S., Grenon, P., & Hunter, P. (2018). Meeting the multiscale challenge: Representing physiology processes over ApiNATOMY circuits using bond graphs. Interface Focus, 8 (1)10.1098/rsfs.2017.0026
    Other University of Auckland co-authors: Peter Hunter

Identifiers

Contact details

Primary office location

UNISERVICES HOUSE - Bldg 439
Level 6, Room 601
70 SYMONDS ST
AUCKLAND 1010
New Zealand

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