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Dr Mark McDonnell 

Position: Senior Research Fellow Dr Mark McDonnell
Division/Portfolio: Division of Information Technology, Engineering and the Environment
School/Unit: Institute For Telecommunications Research
Campus: Mawson Lakes Campus
Office: W1-19
Telephone: +61 8 830 23341
Fax: +61 8 830 23817
Email: Mark_dot_McDonnell_at_unisa_dot_edu_dot_au
URL for Business Card: http://people.unisa.edu.au/Mark.McDonnell


Other Contacts

 


Dr Mark D. McDonnell is a Senior Research Fellow (Lecturer C) at UniSA's Institute for Telecommunications Research (ITR). He currently holds an Australian Research Fellowship (2010-2014) awarded by the Australian Research Council (ARC) in the Discovery Projects scheme.

Mark McDonnell is Principle Investigator in the Computational and Theoretical Neuroscience Laboratory.

The Laboratory's research is interdisciplinary, and overlaps electronic engineering and the biological sciences. We are motivated to answer fundamental scientific questions about information processing in neurobiology, that may lead to improved health, or inspire new technology.


Recent and past news

7 August 2013: Appointed to Editorial Board of PLoS One.

19 October 2012: John Bekkers and Mark McDonnell awarded a National Health and Medical Research Council (NHMRC) Project Grant: "Persistent firing in cortical interneurons: mechanisms and potential anticonvulsant role" for 2013-2015.

9 July 2012: Mark McDonnell delivered an invited Berstein Lecture at the Bernstein Center for Computational Neuroscience in Munich, Germany.

May 2012: Mark McDonnell is currently a Visiting Professor at University of British Colmbia, Vancouver (Professor Lawrence Ward's Cognitive Neuroscience Laboratory and the Brain Research Centre) until 30 December 2012.

December 2011: Awarded Senior Membership of the IEEE (Institute of Electrical and Electronics Engineers).

December 2011: Mark McDonnell is chair of the Biomimetic Sensors and Neuronal Information Processing Symposium within the IEEE ISSNIP conference in Adelaide.

November 2011: Mark McDonnell awarded an Endeavour Research Fellowship for a research visit to University of British Columbia, Vancouver, Canada, to work with Prof Lawrence Ward and the Brain Research Centre.

June 2011: Paper "The benefits of noise in neural systems: bridging theory and experiment" published in Nature Reviews Neuroscience.

February 2011: UNISA video profiling my work, with a focus on the benefits of holding an ARC funded research fellowship at UNISA: Click here.

August 2010: A generous top-up PhD scholarship (total value $37222 tax free p.a.) is available under Mark McDonnell's supervision, within the Computational and Theoretical Neuroscience Laboratory. Click here for details. Download selection criteria: Selection_Criteria_for_CTNL_Top-up.pdf

May 2010: McDonnell's research group is now known as the Computational and Theoretical Neuroscience Laboratory

October 2009: McDonnell awarded an ARC Australian Research Fellowship (ARF) in the Discovery Project scheme, 2010-2014.

August 2009: Media coverage of the "Two-envelopes" paper:

  • ABC News in Science online: Scientists crack 'two-envelope' problem
  • Physorg.com: New Strategy Solves 'Two-Envelope' Paradox
  • Mebrana.ru: Article in Russian in popular science magazine, Membrana
  • In Top 10 Downloaded Articles from Proceedings of the Royal Society A in 2009.

    March 2009: Mark has been selected as a participant in UNISA's 2009-10 Research Leadership Development program.

    October 2008: McDonnell's book published by Cambridge Univesity Press, "Stochastic Resonance: From Suprathreshold Stochastic Resonance to Stochastic Signal Quantisation."

    May 2008: Article published in popular science magazine: Australasian Science. Noise May Be Music to Bionic Ears, by Mark McDonnell and Robert Morse: "Bionic ear implants could be improved by introducing noise to mimic biological unpredictability."

    August 2007: Mark McDonnell was a 2007 Australian Fresh Scientist:

  • details on my story at the Fresh Science webpage;
  • 2007 UNISA media release on my research;
  • 2007 article in UniSA's The Researcher.

    Academic Awards, Prizes and Fellowships

  • 2012 Endeavour Research Fellowship for a six month visit to University of British Columbia's Brain Research Centre.
  • 2010-2014 Australian Research Council (ARC) Discovery grant and Australian Research Fellowship
  • 2008-09 Young Tall Poppy Science Award News story, Tall Poppy Campaign
  • 2008 ARC Communications Research Network (ACoRN)/ NICTA ECR Award for best presentation at the Australian Communications Theory Workshop, Christchurch, New Zealand
  • 2007-14 UNISA Research SA Fellowship
  • 2007 Fresh Science national finalist
  • 2007-09 Australian Research Council (ARC) Discovery grant and Australian Postdoctoral Fellowship
  • 2006 Postgraduate Alumni University Medallist (awarded for best PhD thesis at The University of Adelaide in 2006)
  • 2006 The Gertrude Rohan Prize (awarded for best PhD on a topic in the area of Information and Communications Technology at The University of Adelaide)
  • 2004 Australian Academy of Science Young Researcher Award

    Dr McDonnell received a PhD in Electrical & Electronic Engineering and Applied Mathematics (2006) (summa cum laude), from The University of Adelaide in Australia.

    Mark commenced at UniSA in June 2007, after being awarded an APD Fellowship from the ARC (2007-2009). He has also been a postdoctoral researcher in the Centre for Biomedical Engineering (CBME) and a lecturer in the School of Electrical and Electronic Engineering at University of Adelaide (2005-2007).


    Professional associations

    Senior Member IEEE (Institute of Electrical and Electronics Engineers)

    Member ANS (Australian Neuroscience Society)

    Accredited Member of the Australian Mathematical Society (MAustMS)

    Member, American Physical Society

    Member ACoRN (ARC Communications Research Network)

    Member COSNET (ARC Complex Open Systems Research Network)

    Member SANI (South Australian Neuroscience Institute)


    Qualifications

    PhD, The University of Adelaide, 2006

    B. Sc. (Hons, Applied Mathematics), The University of Adelaide, 2002

    B. E. (Hons, Electrical and Electronic), The University of Adelaide, 1998

    B. Sc. (Mathematical and Computer Sciences), The University of Adelaide, 1997


    Research interests

    • Computational neuroscience (see Computational and Theoretical Neuroscience Laboratory)
    • Synchronous brain oscillations and their role in intra-brain communication, learning and neurobiological information processing
    • Stochastic facilitation in neurobiology, e.g. suprathreshold stochastic resonance, short term synaptic plasticity.
    • Connectomics: the study of complex network connectivity at multiple-scales in the brain (e.g. whole brain through to neuronal networks), and how functional networks relate to structural networks.
    • Information theory applied in computational neuroscience (e.g. stochastic pooling networks) and biomedical prosthetics (e.g. cochlear implants)
    • Grand challenges for engineering: To reverse-engineer the brain.
    • The world's 23 toughest math questions: Challenge number 1: The Mathematics of the Brain

    Research publications

    BOOKS:

    McDonnell M D, Stocks N G, Pearce C E M and Abbott D (2008) "Stochastic Resonance: From Suprathreshold Stochastic Resonance to Stochastic Signal Quantisation", Cambridge University Press, ISBN 978-0521882620.

    Publisher's webpage for the book

    Amazon.com page

    Book reviews

    1. Professor K. Alan Shore in Contemporary Physics Vol. 50, pp. 428–439, 2009.

    2. Professor Miguel A.F. Sanjuan in Contemporary Physics Vol. 51, pp. 448-449, 2010.

    PUBLISHED FULLY REFEREED JOURNAL PUBLICATIONS (Reverse chronological order):

    31. McDonnell M D and Ward L M. "Small modifications to network topology can induce stochastic bistable spiking dynamics in a balanced cortical model". PLoS One(Accepted, In press), 2014.

    30. Schmerl B A and McDonnell M D (2013). "Channel-noise-induced stochastic facilitation in an auditory brainstem neuron model." Physical Review E 88: 052722. Download a preprint from arxiv

    29. McDonnell M D, Li F, Amblard P O and Grant A J (2013). "Optimal sensor selection for noisy binary detection in stochastic pooling networks." Physical Review E 88:022118.

    28. McDonnell M D, Mohan A and Stricker C (2013). "Mathematical analysis and algorithms for efficiently and accurately implementing stochastic simulations of short-term synaptic depression and facilitation." Frontiers in Computational Neuroscience 7:Article Number 58.

    27. Mohan A, McDonnell M D and Stricker C (2013). "Interaction of short-term depression and firing dynamics in shaping single neuron encoding." Frontiers in Computational Neuroscience7:Article number 14.

    26. Kostal L, Lansky P and McDonnell M D (2013). "Metabolic cost of neuronal information in an empirical stimulus-response model." Biological Cybernetics 107:355-365.

    25. Prettejohn B J, Berryman M J and McDonnell M D (2013). "A model of the a ffects of authority on consensus formation in adaptive networks: impact on network topology and robustness." Physica A 392:857–868.

    24. McDonnell M D, Mohan A, Stricker C and Ward L M (2012). "Input-rate modulation of gamma oscillations is sensitive to network topology, delays and short-term plasticity." Brain Research 1434:162-177.

    23. McDonnell M D and Ward L M (2011). "The benefits of noise in neural systems: bridging theory and experiment." Nature Reviews Neuroscience 12:415-426.

    22. McDonnell M D, Ikeda S and Manton J (2011). "An introductory review of information theory in the context of computational neuroscience." Biological Cybernetics 105:55–70.

    21. Prettejohn B J, Berryman M J and McDonnell M D (2011). "Methods for generating complex networks with selected structural properties for simulations: A review and tutorial for neuroscientists." Frontiers in Computational Neuroscience 5:11 (pp 1-18).

    20. McDonnell M D, Grant A J, Land I, Vellambi B N, Abbott D and Lever K (2011) "Gain from the two-envelope problem via information asymmetry: On the suboptimality of randomized switching." Proceedings of the Royal Society A 467:2825-2851.

    19. McDonnell MD, Burkitt A N, Grayden D B, Meffin H and Alex J. Grant (2010). "A channel model for inferring the optimal number of electrodes for future cochlear implants," IEEE Transactions on Information Theory 56:928-940. DOI link.

    18. McDonnell MD, Stocks NG and Amblard PO (2010). "Communication of uncoded sensor measurements through nanoscale binary-node stochastic pooling networks," Nano Communication Networks 1:209-223.

    17. McDonnell MD, Amblard PO and Stocks NG (2010). "Bio-inspired communication:performance limits for information transmission and compression in stochastic pooling networks with binary quantizing nodes," Journal of Computational and Theoretical Nanoscience 7:876-883.

    16. McDonnell MD and Flitney AP (2009). "Signal acquisition via polarization modulation in single photon sources," Physical Review E 80:060102(R) 2009. doi link, Arxiv Preprint.

    15. McDonnell M D and Abbott D (2009). "Randomized switching in the two-envelope problem," Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 465 pp 3309–3322, 2009 abstract link

    Media coverage of the "Two-envelopes" paper:

  • ABC News in Science online: Scientists crack 'two-envelope' problem
  • Physorg.com: New Strategy Solves 'Two-Envelope' Paradox
  • Mebrana.ru: Article in Russian in popular science magazine, Membrana

    14. Nikitin A P, Stocks N G, Morse R P and McDonnell M D (2009). “Neural Population Coding Is Optimized by Discrete Tuning Curves,” Physical Review Letters 103, 138101, doi link, Arxiv Preprint. This paper selected for inclusion in Virtual Journal of Biological Physics Research.

    13. McDonnell M D and Stocks N (2009) Suprathreshold stochastic resonance. Scholarpedia, 4(6):6508 [Review Article]

    12. McDonnell M D and Abbott D(2009). “What is stochastic resonance? Definitions, misconceptions, debates, and its relevance to biology,” PLoS Computational Biology 5, Art. No. e1000348 (2009) Full text link [Review Article]

    11. McDonnell M D (2009). “Information capacity of stochastic pooling networks is achieved by discrete inputs,” Physical Review E 79, Art. No. 041107 (2009) doi link. This paper selected for inclusion in Virtual Journal of Nanoscale Science and Technology. This paper selected for inclusion in Virtual Journal of Biological Physics Research.

    10. McDonnell M D, Amblard P O and Stocks N G (2009). “Stochastic Pooling Networks,” Journal of Statistical Mechanics: Theory and Experiment, Art. No. P01012 (2009) doi link

    9. Stocks N G, Nikitin A P, McDonnell M D and Morse R P. (2009). "The role of stochasticity in an information-optimal neural population code". Journal of Physics: Conference Series, 197:012015, doi link to full text here.

    8. McDonnell M D and Stocks N G (2008). “Maximally Informative Stimuli and Tuning Curves for Sigmoidal Rate-Coding Neurons and Populations,” Physical Review Letters 101, 058103, doi link, Arxiv Preprint. This paper selected for inclusion in Virtual Journal of Biological Physics Research.

    7. McDonnell M D, Stocks N G and Abbott D (2007). “Optimal stimulus and noise distributions for information transmission via suprathreshold stochastic resonance,” Physical Review E 75, 061105, doi link, Arxiv Preprint

    6. McDonnell M D, Stocks N G, Pearce C E M and Abbott D (2006). “Optimal information transmission in nonlinear arrays through suprathreshold stochastic resonance,” Physics Letters A 352, pp. 183-189.

    5. McDonnell M D, Stocks N G, Pearce C E M and Abbott D (2005). “Quantization in the presence of large amplitude threshold noise,” Fluctuation and Noise Letters 5, pp. L457-L468.

    4. McDonnell M D, Stocks N G, Pearce C E M and Abbott D (2003). “Stochastic resonance and data processing inequality,” IEE Electronics Letters 39, pp. 1287-1288.

    3. McDonnell M D, Abbott D and Pearce C E M (2002). “An analysis of noise enhanced information transmission in an array of comparators,” Microelectronics Journal 33, pp. 1079-1089.

    2. McDonnell M D, Abbott D and Pearce C E M (2002) “A Characterization of suprathreshold stochastic resonance in an array of comparators by correlation coefficient,” Fluctuation and Noise Letters 2, pp. L205-L220.

    1. McDonnell M D, Possingham H P, Ball I R and Cousins E A (2002). “Mathematical Methods for Spatially Cohesive Reserve Design,” Environmental Modeling & Assessment 7, pp. 107-114.

    BOOK CHAPTERS:

    McDonnell M D (2009). “Applying stochastic signal quantization theory to the robust digitization of noisy analog signals", In Applications of Nonlinear Dynamics: Model and Design of Complex Systems, Eds. V. In, P. Longhini and A. Palacios, Springer, ISBN 978-3540856313 (Webpage for book)

    CONFERENCE PUBLICATIONS:

    Numerous full-length refereed conference papers are listed here


    Expertise for Media Contact

    I am able to provide media comment in the following areas of expertise:

    Discipline: Computational neuroscience

    • stochastic resonance
    • information theory

    Community Service

    Organisation Name:   The Australian Association of Computational Neuroscientists and Neuromorphic Engineers
    Type of Organisation:   Professional organisation
    Organisation URL:   http://neuroeng.org.au/wordpress/
    Level of involvement:   Founding Member
    Year from:   2012

    Organisation Name:   PLoS ONE
    Organisation URL:   http://www.plosone.org/
    Level of involvement:    Editorial Board
    Year from:   2013

    Organisation Name:   Fluctuation and Noise Letters (FNL): An Interdisciplinary Scientific Journal on Random Processes in Physical, Biological and Technological Systems
    Organisation URL:   http://www.worldscinet.com/fnl/
    Level of involvement:   Editorial Board
    Year from:   2009

    Organisation Name:   Institute of Electrical and Electronics Engineers (IEEE)
    Section:   IEEE South Australia (SA) Section, Joint Communications and Signal Processing Chapter
    Type of Organisation:   Professional organisation
    Organisation URL:   http://ewh.ieee.org/r10/s_australia/
    Level of involvement:   Chapter Vice President
    Year from:   2008
    Year to:   2010
    Comments:   (Chapter Secretary in 2008)

    Organisation Name:   ARC Communications Research Network
    Type of Organisation:   Professional organisation
    Organisation URL:   http://www.acorn.net.au/
    Level of involvement:   Local Representative for UNISA Node
    Year from:   2008
    Year to:   2009


    Research Degree Supervisor

    For information on projects and topics offered for postgraduate research by Mark McDonnell, see the projects page of the Computational and Theoretical Neuroscience Laboratory.

    I am Principle Supervisor for the following PhD students: (see CTNL People):

    1. Daniel Padilla. Project: Bayesian models of neuronal information processing (started July 2011)
    2. Gao Xiao. Project: Information theoretic approaches to optimising cochlear implant electrode design (started Februrary 2012)
    3. Brett Schmerl. Project: Modelling the complex neuronal networks of the olfactory cortex (started March 2012)
    4. Siyi Wang. Project: Information theory for molecular communication (started March 2013)
    5. Bahar Moezzi. Project: modelling of stochastic spontaneous nerve fibre activity in the auditory brainstem (started July 2013)
    6. Migel Tissera. Project: Modelling and neuromorphic applications of stochastic memristors (started July 2013)


    I am on the supervision panel for the following PhD students:

    1. Ashutosh Mohan. Project: short term synaptic plasticity in cortical neurons (located at John Curtin School of Medical Research, ANU)
    2. Nab Dahal. Project: augmented cognition (started February 2011)
    3. Kollengode Ananthakrishnan. Project: automatic speech separation



    I was principle supervisor of the following completed PhD students:

  • Dr Brenton Prettejohn, 2013, Thesis title: Understanding the underlying similarities shared by complex systems: A study of consensus formation, and neuronal network dynamics, through the application of complex network simulations.






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