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    Professor David Smith

    Engineering Computational Biology Group 
    School of Computer Science and Software Engineering
    The University of Western Australia
    35 Stirling Highway, Crawley  WA 6009, Australia

    Email: david.smith@uwa.edu.au
    Phone: +61 8 6488 5531
    Fax: +61   8 6488 1089
    Web: http://biomed.csse.uwa.edu.au

    Photo of David
    Qualifications:
    • Ph.D. in Engineering. The University of Sydney (1990)
    • B.E. in Civil Engineering (First Class Honours). The University of Sydney (1986)
    Summary of Professional Experience:
    After initially studying medicine for four years, David graduated with a First Class Honours Degree in Civil Engineering from The University of Sydney in 1986. In 1990, he was awarded a PhD from The University of Sydney for numerical analysis of a proposal to dispose of radioactive waste in the ocean floor. Since that time, David has been a career academic, teaching civil engineering at the University of Newcastle (AU) biomedical engineering at the University of Melbourne, and researching geotechnical, geoenvironmental and biomedical problems. He was appointed Professor of Biomedical and Environmental Engineering at the University of Melbourne in 2004 and Research Professor of Biomedical Engineering at the University of Western Australia in 2009.

    David has researched consolidation and transport behaviour of clays soils, and is an expert in the field. For his PhD thesis, he developed Green's functions describing the thermoconsolidation behaviour of clay. David has developed detailed geochemical transport models, and derived new analytic solutions for the solution of the advective-reactive transport equation. New theoretical models of soil behaviour have been developed, the most significant published contributions being: (i) a new set of transport equations appropriate for a deforming porous medium (e.g. engineered landfill liner systems); (ii) new transport equations and appropriate boundary conditions taking into account spatially varying dispersivity;  (iii) developing micro-macroscale modeling approaches to better understand fundamental dissipative and transport mechanics in charged porous media and (iv) developing a numerical model of neutron-diffusion through soils for neutron probe calibration.

    Though fundamental geoenvironmental research has been a key focus, this work has been complemented by applied research. The most significant practical contributions are: (i) modeling contaminant transport through engineered liner systems landfills, (ii) modelling fluoride transport through aquifers; (iii) developing a strategy for decontamination of fluoride polluted aquifer by sorption onto alumina; (iv) developing a strategy for decontamination of a hydrocarbon polluted aquifer by sorption onto granulated tyre rubber; (v) setting up a field site to investigate expansive clay soils and the effect they have on house foundations and (vi) investigating the suitability of soft clay soils for electro-osmosis. In the last few years, David has developed original micromechanical and numerical models. the most significant of these are: (i) describing the transport of ions through a charged porous medium; (ii) quantifying the effects of anion exclusion and cation inclusion on mass transport through clay soils; (iii) describing the coupling of a diffuse-double layer with the Navier-Stokes equation.

    Over the last fourteen years, David has been developing his research interests in biomedical engineering, building on his biological knowledge obtained during four years as a medical student. Significant projects undertaken to date are: (i) development of a theoretical model describing calcium oscillations in smooth muscle cells (ii) development of a new conceptual approach to identifying women at risk of preterm birth and (iii) development of theoretical models describing the behaviour of  cartilage (with A/Prof Bruce Gardiner, Dr Lihai Zhang and Prof Alan Grodzinsky). David has published extensively on cartilage, and received numerous national competitive grants on this topic. He developed a model describing respiratory appendage development in drosophila. More recently he has published a growing list of papers on oxygen transport in the kidney (with A/Prof Roger Evans and A/Prof Bruce Gardiner), Wnt signaling relevant to colon cancer and colon crypt mechanics (with Prof Tony Burgess, A/Prof Bruce Gardiner. Drs Chin Wee Tan and Richard Van der Wath) and bleb function in the eye (with A/Prof Bruce Gardiner, Prof Jonathon Crowston and Dr Michael Coote).  David has been developing a new model describing the processes of bone remodeling, and mechano-signal transduction in bone (with A/Prof Peter Pivonka, Dr Stefan Scheiner and Dr Pascal Buenzli), and published extensively on this topic. This work is applicable to understanding disease processes like osteoporosis and cancer matatasis to the bone microenvironment. David has recently commenced developing models of tendon homeostasis and repair (with A/Prof Bruce Gardiner, Prof Minghao Zheng, Prof Jaike Xu, Dr Jonas Rubenson and Prof David Lloyd).

    Research Interests:
    David is generally interested in all problems in computational biology, including cellular signal transduction, bone, cartilage, tendon, cell mechanics, physiology of the kidney, problems in developmental biology and others. Furthermore, he is interested in all kinds of geotechnical and geoenvironmental engineering problems, but particularly multiscale models for clay soils. Experience as per published papers listed below.

    Departmental Research Group involvement:

    • Engineering Computational Biology Group
    Administrative Experience

    David has served as A/Dean Research (University of Newcastle), A/Dean Teaching and Learning and Head of Department (University of Melbourne), and Dean Faculty of Engineering Computing and Mathematics, The University of Western Australia. David served on the Australian Research Council's College of Experts, and was Chair of the Engineering and Environmental Science Panel in 2007, and as Chair of the New Zealand Health Research Council Panel BMAC4 in 2012-13.He is a member of the Australian Institute of Company Directors, and completed course Leading Organisational Change and Renewal at Harvard Business School and completed the Advanced Management Program at Harvard Business School (AMP179).

    Memberships and Affiliations:
    • Fellow, The Institution of Engineers, Australia. FIEAust
    • Engineers Australia Chartered Professional Engineer (specialisations in civil and environmental engineering) NPER-3 registered. CPEng
    • Member, American Society of Civil Engineers. MASCE
    • Member Australian Institute of Company Directors, MAICD.

    Students Supervised

    • 1992-1993 Mr. Mark Taylor MEng Expansive soils Lower Hunter Awarded 1993
    • 1992-1997 Dr Paul Kau PhD Fluoride transport through clay soils Awarded 1997
    • 1994-2000 Dr Stephen Fityus PhD Transport processes in partially saturated soils Awarded 2000
    • 1997-2000 Dr Glen Peters PhD Contaminant Transport Through a Deforming Porous Medium Awarded 2002
    • 1998-2003 Heath Fletcher PhD Decontamination of a fluoride polluted aquifer using alumina Awarded 2003
    • 2000-2003 Fiona Robinson MEng The use of rubber as a sorbent for hydrocarbons Awarded 2003
    • 1999-2003 Mark Reitsma PhD Frictional behaviour of soils using the Atomic Force Microscope Awarded 2003
    • 1997-2003 Shaun McGrath PhD Identification of women likely to have preterm birth Discontinued
    • 2002-2003 Hlwan Moe MEng Air flow through granular media Under examination
    • 1998-2005 Tim Lewis PhD Contaminant Transport Through a Deforming Porous Medium To submit 2005
    • 1999-2005 Emily Slatter PhD Development of a Suction Oedometer - submitted 2005
    • 1998-2005 Brook Ewers PhD Electrical and Mechanical Behaviours of Clay Soils
    • 2005-2008 Lihai Zhang, PhD Cartilage Modeling
    • 2007-2011 Chin Wee Tan PhD Wnt signaling pathway in colon cancer
    • 2007-2011 Yan Wang PhD Computational Model of Multiple Myeloma: Bone Interactions

    Publications

    1. Course Notes and Thesis

    1     SMITH, D.W., (1990). Boundary Element Analysis of Heat Flow and Consolidation for Geotechnical Applications. PhD thesis, 292 pages.

    2     SMITH, D.W. (2000). Soil Mechanics 5th Ed. 169 pages.

    3     SMITH, D.W. (2001). Geotechnical and Geoenvironmental Engineering. 6th Ed. 521 pages.

    4     SMITH, D.W. (2002). Writing Science: A Guide to Scientific Writing for Research Engineers. 3rd Ed. 220 pages.

    2. Edited Books and Book Chapters

    5     SMITH, D.W. and CARTER, J.P. (2000). Developments in Theoretical Geomechanics—The John Booker Memorial Symposium. Pub. Balkema, 760 pages.

    6     SMITH, D.W. FITYUS, S.G. and ALLMAN, M.A. (2001). ANZ GeoEnvironment 2001 Conference 830 pages.

    7.  ZHANG, L.,  GARDINER, B.S., SMITH, D.W., PIVONKA, P. and GRODZINSKY, A.J.(2010), (book chapter) The Transport of Insulin-like Growth Factor through Cartilage, in Porous Media Applications in Biological Systems and Biotechnology, Editor K. Vafai, CRC, 1st Edition, Dec 2010.

    8.  Evans, R.G.,  Smith, J.A., Gardiner, B.S., Smith, D.W., Thrift, A.G., Lankadeeva, Y.R., May, C.N. and Cochrane, A.D. (2016), (book chapter) Hypoxia as a biomarker of kidney disease. Diseases of the Kidney, in Biomarkers of Disease: Methods, Discoveries and Applications, Editors Preedy V.R. & Patel V.B, Springer-Verlag, Berlin p. 83–105 .

    3. Refereed Journal Publications 1989-2017

    1.     SMITH, D.W. and BOOKER, J.R., (1989), ‘Boundary Integral Analysis of Transient Thermoelasticity’, International Journal of Numerical and Analytical Methods in Geomechanics, Vol. 13, p. 283–302.

    2.     SMITH, D.W. and BOOKER, J.R., (1993), ‘Green’s Functions for a Fully Coupled Thermoporoelastic Material’, International Journal of Numerical and Analytical Methods in Geomechanics, Vol. 17, p. 139–163.

    3.     SMITH, D.W., ROWE, R.K., and BOOKER, J.R., (1993), ‘The Analysis of a Polluted Aquifer Decontamination using an Interception Sorption Strategy, Computers and Geotechnics, Vol. 15, p. 163–186.

    4.     SMITH, D.W. ROWE, R.K., and BOOKER, J.R., (1993) ‘The Analysis of Pollution Migration Through Soil With Linear Hereditary Time–Dependent Sorption’, International Journal of Numerical and Analytical Methods in Geomechanics, Vol. 17, 255–274.

    5.     ALLMAN, M.A., SMITH, D.W. and SLOAN, S.W. (1994), ‘The Establishment of a Reactive Soil Field Site near Newcastle’, Australian Geomechanics, Vol. 26 p. 46–56.

    6.     SLOAN, S.W., SMITH, D.W., YU, H.S. and ALLMAN, M.A. (1994), ‘Research at Newcastle on Computational Geomechanics’ Australian Geomechanics, Vol. 26, p. 42–45.

    7.     HITCHCOCK, P.W. and SMITH, D.W. (1995), ‘Pollution Control Strategy Employing an Interception–Sorption Trench’ Australian Geomechanics, Vol. 27, p. 60–67.

    8.     SMITH, D.W. and BOOKER, J.R., (1996), ‘Boundary Integral Analysis of Thermoporoelasticity’, International Journal of Numerical and Analytical Methods in Geomechanics, Vol. 20, p. 457–488.

    9.     KAU, P.M.H., SMITH, D.W., BINNING, P., (1997), ‘Fluoride Retention by Kaolin Clay Liners in Waste Storage’, Journal of Contaminant Hydrology, Vol. 28 p. 267–288.

    10.  KAU, P.M.H., SMITH, D.W. and BINNING, P.J. (1997), The Dissolution of Kaolin by Acidic Fluoride Wastes, Soil Science., Vol. 162. No. 12, p. 896–911.

    11.  HITCHCOCK, P.W., and SMITH, D.W. (1998), ‘Implications of Non–equilibrium Sorption on the Interception–sorption trench remediation strategy’, Geoderma, Vol. 84, Nos 1–3, p. 109–121.

    12.  KAU, P.M.H., SMITH, D.W. and BINNING, PJ. (1998), ‘Experimental sorption of fluoride by kaolinite and bentonite’, Geoderma, Vol. 84 Nos 1–3, p. 65–89.

    13.  KAU, P.M.H., BINNING, P.J., HITCHCOCK, P.W. and SMITH, D.W., (1999), ‘Experimental Analysis of Fluoride Diffusion and Sorption onto Clays’, Journal of Contaminant Hydrology, Vol. 36. p. 131–151.

    14.  SHENG, D. and SMITH, D.W., (1999), ‘Analytic Solutions to the Advective Contaminant Transport Equation with Non–Linear Sorption’, International Journal of Numerical and Analytical Methods in Geomechanics. Vol. 23 No. 9, 853–880.

    15.  FITYUS, S. G., ALLMAN M. A., and SMITH, D. W., (1999)  ‘Mound shapes beneath covered areas.’ Australian Geomechanics, Vol. 34, No. 3 p. 5–14.

    16.  FITYUS, S.G., SMITH, D.W. and BOOKER, J.R., (1999), ‘Contaminant Migration Through and Unsaturated Soil Beneath a Landfill’, Canadian Geotechnical Journal, Vol. 36 p. 330–354.

    17.  SHENG, D. and SMITH, D.W., (1999), ‘Numerical Modelling of Competitive Components Transport with Nonlinear Adsorption’, International Journal of Numerical and Analytical Methods in Geomechanics Vol. 24, No.1, p. 47–71.

    18.  Kau. P.M.H., SMITH, D.W. and BINNING, PJ (1999) The dissolution of kaolin by acidic fluoride wastes. Soil Science, Vol 62(12)  p. 896-911.

    19.  SMITH, D.W., (2000), ‘One-dimensional Contaminant Transport Through a Deforming Porous Media: Theory and a Solution for a Quasi–steady–state Problem’, International Journal of Numerical and Analytical Methods in Geomechanics Vol. 24, p. 693–722.

    20.  SMITH, D.W. (2000) ‘Geotechnical Design and Numerical Modelling’ Australian Geomechanics, Vol. 35, No.4, p. 7–32.

    21.  SMITH, D.W. (2001), ‘Granular Temperature’ ASCE International Journal of Geomechanics Vol. 1 No. 1 p. 41–64.

    22.  PETERS, G. and SMITH, D.W. (2001), ‘Boundary Conditions for the Advection–Dispersion Equation.’ International Journal of Numerical and Analytical Methods in Geomechanics Vol 25, No. 7 Published Online: 4 May 2001.

    23.  FITYUS, S. G. and SMITH, D. W. (2001), ‘Solution Of The Unsaturated Soil Moisture Equation Using Repeated Transforms.’ International Journal for Numerical and Analytical Methods in Geomechanics.  Vol 25, No. 7 Published Online: 4 May 2001.

    24.  SHENG, D. and SMITH, D.W., (2002), ‘2-D Finite Element Analysis of Multi-component Contaminant Transport’, ASCE International Journal of Geomechanics Vol. 2 No.1 p. 113-134.

    25.  PETERS, G. and SMITH, D.W. (2002), ‘Contaminant Transport Through a Deforming Porous Media’ International Journal of Numerical and Analytical Methods in Geomechanics Vol. 26. p. 683-717.

    26.  SMITH, D.W. and FLETCHER, H (2002) ‘Reactive Walls: an overview’ Australian Geomechanics, Vol. 37 No. 4 p. 85-98.

    27.  Li, J., SMITH, D.W. and FITYUS, S.G (2003), ‘The effect of an gap between the access tube and the soil during neutron probe measurement’ Australian Journal of Soil Research Vol. 41. p. 151-164.

    28.  Li, J., SMITH, D.W., FITYUS, S.G. and SHENG, D. (2003), Numerical Analysis of Neutron Mositure Probe MeasurementsASCE International Journal of Geomechanics, Vol 3/1 p.11-20.

    29.  SHENG, D., SLOAN, S.W., GENS, A. and SMITH, D.W. (2003) Finite Element Formulation and Algorithms for Unsaturated Soils Part I: Theory. International Journal of Numerical and Analytical Methods in Geomechanics Vol. 27 p. 445-465.

    30.  SHENG, D., SMITH, D.W., SLOAN, S.W. and GENS, A. (2003) Finite Element Formulation for Unsaturated Soils Part II: Verification and Application. International Journal of Numerical and Analytical Methods in Geomechanics, Vol. 27 p. 467-490.

    31.  JUNGNICKEL, C., SMITH, D.W. and FITYUS, S.G. (2004) ‘Coupled Multi-ion Electrodiffusion Analysis for Clay Soils’ Canadian Geotechnical Journal, Vol 41(2): p. 287-298.

    32.  PETERS, G. and SMITH, D.W. (2004), ‘The Influence of Advective Transport on Coupled Chemical and Mechanical Consolidation of Clays’ Mechanics of Materials Vol 36 (5) p. 467-486.

    33.  FITYUS, S.G. and SMITH, D.W, (2004), ‘The development of a residual soil profile from a mudstone in a temperate climate’ Engineering Geology Vol 74 p 39-56.

    34.  SMITH, D.W., PIVONKA, P., JUNGNICKEL, C. and FITYUS, S.G. (2004) ‘Theoretical Analysis of Anion Exclusion and Diffusive Transport Through a Platy Clay Soil’ Transport in Porous Media Vol. 57 p. 251-277.

    35.  FITYUS, S. G. and SMITH, D. W. and ALLMAN, M. A. (2004) ‘Results from a Reactive Soil Field Site near Newcastle, Australia’ ASCE Journal of Geotechnical and Geoenvironmental Engineering Volume 130, Issue 7, pp. 686-695.

    36.  SMITH, D.W. and REITSMA, M. (2004), ‘A conceptual model explaining the residual frictional angle in montmorillonitic clay soils’ Australian Geomechanics Vol. 39. No. 2 p. 111-119.

    37.  PIVONKA, P., HELLMICH, C. and SMITH, D.W, (2004), ‘Is chloride diffiusivity of cement pastes   mainly governed by paste-specific microporosity and paste independent molecular structuring of water?—arguments from a scale transition analysis’ Cement and Concrete Research 4 (12): 2251-2260.

    38.  PIVONKA, P. and SMITH, D.W. (2005), 'Investigation of nanoscale electrohydrodynamic transport phenomena in charged porous media' International Journal for Numerical Methods in Engineering 63 (14): 1975-1990.

    39.  HUANG, W., FITYUS, S.G., BISHOP, D., SMITH, D.W. and SHENG, D. (2006) A finite element parametric study of the consolidation behaviour of a trial embankment on soft clay. ASCE International Journal of Geomechanics Vol. 5 No. 6:328-341.

    40.  FLETCHER, H., SMITH, D.W. and PIVONKA, P. (2006), ‘A geochemical model for the adsorption of fluoride onto alumina’ ASCE Journal of Environmental Engineering 132 (2): 229-246.

    41.  REITSMA, M., CAIN, R. BIGGS, S. and SMITH, D.W. (2006) ‘Observed transition from linear to non-linear friction-load behavior using a Lateral Force Microscope’ Applied Surface Science Vol 252, 4964-4968.

    42.  REITSMA, M., CAIN, R.G., BIGGS, S. and SMITH, D.W. (2006) Wear of a single asperity using a Lateral Force Microscope. Tribology Letters 24(3), 257-263.

    43.  WELLS, T, FITYUS, S.G., SMITH, D.W. (2006) The indirect estimation of saturated hydraulic conductivity of soils, using measurements of gas permeability. I. Laboratory testing with dry granular soils. Australian Journal of Soil Research 44(7) p. 719-­725

    44.  PIVONKA, P, SMITH, D.W. and GARDINER, B.  (2007) ‘Investigation of Donnan Equilibrium in charged porous materials-a scale transition analysis’ Transport in Porous Media No. 2 Vol 69,  p. 215-237.

    45.  WELLS, T., FITYUS, S.G., SMITH, D.W. (2007) The use of in situ air flow measurements to study permeability in cracked clay soils. ASCE Journal of Geotechnical and Geoenvironmental Engineering. 133(12), 1577-1586.

    46.  NARSILIO, G., Li, R., PIVONKA, P. and SMITH, D.W. (2007) Comparative Study of Methods Used to Estimate Ionic Diffusion Coefficients Using Migration Tests. Cement and Concrete Research Vol 37, Iss. 8 Pages 1152-1163.

    47.  LEWIS, T. PIVONKA, P., and SMITH, D.W.. (2009) Theoretical investigation of the effects of consolidation on contaminant transport through clay barriers. International Journal for Numerical and Analytical Methods in Geomechanics 33(1), 95-116.

    48.  LEWIS, T., PIVONKA, P, and SMITH, D.W. (2009). Parametric sensitivity analysis of coupled mechanical consolidation and contaminant transport through clay barriers. Computers and Geotechnics. 36(1-2), 31-40.

    49.  SMITH, D.W., NARSILIO, GA, PIVONKA, P. (2009) Numerical particle-scale study of the swelling pressure in clays. KSCE Journal of Civil Engineering 13(4) 273-279.

    50.  PIVONKA P, NARSILIO GA, LI RN, SMITH DW, GARDINER B, (2009) Electrodiffusive Transport in Charged Porous Media: From the Particle-Level Scale to the Macroscopic Scale Using Volume Averaging, Journal of Porous Media 12(2),101-118.

    51.  NARSILIO, GA, BUZZI, O., FITYUS, SG, SMITH, D.W. (2009) Upscaling of Navier-Stokes equations in porous media: theoretical and experimental approach. Computers and Geotechnics Vol. 36(7) 1200-1206.

    52.  NARSILIO GA, SMITH DW, PIVONKA P (2010) Estimating vertical and lateral pressures in periodically structured montmorillonite clay particles. Anais Da Academia Brasilerira De Ciencias   Volume: 82   Issue: 1   Pages: 13-24.

    53.  MOHAJERI A, NARSILIO GA, PIVONKA P, SMITH, D.W. (2010) Numerical estimation of effective diffusion coefficients for charged porous materials based on micro-scale analyses  Computers and Geotechnics.  Volume: 37: 3   Pages: 280-287.

    54.  SCHEINER, S. PIVONKA, P. SMITH, D.W. (2012) Electro-diffusive transport in macroscopic porous media: Estimation of effective transport properties using numerical upscaling. Computer and Geotechnics http://dx.doi.org/10.1016/j.compgeo.2012.08.002.

    3.2   Bioengineering and Medical Journal Publications

     55.  McGRATH S, McLEAN M, SMITH D, BISITS A, GILES W, SMITH R. (2002). Maternal plasma corticotropin-releasing hormone trajectories vary depending on the cause of preterm delivery. American Journal of Obstetrics and Gynecology. 2002 186(2):257-60.

    56.  IMTIAZ, M., SMITH, D.W., Van-HELDEN, D.F. (2002). A theoretical model of slow wave regulation using voltage–dependent synthesis of inositol 1,4,5–triphosphate. Biophysical Journal, Vol 83 p. 1877-1890.

    57.  ADEEB, S. ALI, A., SHRIVE, N., FRANK, C. and SMITH, D.W. (2004). Modeling the behaviour of ligaments: A technical note. Computer Methods in Biomechanics and Biomedical Engineering 7(1), 33-42.

    58.  IMTIAZ, M., KATNIK, C. SMITH, D.W., Van-HELDEN, D.F. (2006). Role of voltage–dependent store Calcium release in the synchronization of calcium oscillations. Biophysical Journal 90 (1): 1-23

    59.  GARDINER, B., SMITH, D.W., PIVONKA, P., GRODZINSKY, A., FRANK, E. and ZHANG, L. (2007). Solute transport in cartilage undergoing cyclic deformation, Computer Methods of Biomechanics and Biomedical Engineering Vol. http://www.informaworld.com/smpp/title~content=t713455284~db=all~tab=issueslist~branches=10 - v1010, Issue 4. p. 265 - 278.

    60.  ZHANG, L, GARDINER, B., SMITH, D.W., PIVONKA, P., GRODZINSKY, A., (2007). The effect of cyclic deformation and solute binding on solute transport in cartilage, Archives of Biochemistry and Biophysics 457(1):47-56.

    61.  ZHANG L., GARDINER, B., SMITH, D.W., PIVONKA, P., GRODZINSKY, A. (2008). The role of competitive binding in solute transport in cyclic deformed cartilage. Journal of Biological Systems 16(2):175-195.

    62.  ZHANG, L.,  B.S. GARDINER, D.W. SMITH, P. PIVONKA, A.J. GRODZINSKY (2008). An integrated model of IGF-I mediated biosynthesis in deforming articular cartilage, Issue on Micro and Nanomechanics of Biological and Bio-inspired Materials Journal of Engineering Mechanics-ASCE 135(5) 439-449.

    63.  PIVONKA, P., ZIMAK, J., SMITH, D.W., GARDINER, B., DUNSTAN, C.B., SIMS, N.A., MARTIN, T.J., MUNDY, G. (2008). Identification of Model Structure And Control Mechanisms For Bone Multicellular Units:  A Theoretical Study. BONE Vol 43 p. 249-263.

    64.  ZHANG, L, GARDINER, B., SMITH, D.W., PIVONKA, P., GRODZINSKY, A., (2008). A fully coupled poro-elastic reactive-transport model of cartilage. Molecular & Cellular Biomechanics 5(2), 133-153.

    65.  EVANS, R.G. GARDINER, BS. SMITH, DW. O’CONNOR, PM. (2008). Intra-renal oxygenation: unique challenges and the biophysical basis of homeostasis, American Journal of Physiology – Renal, Vol 295, Issue 5, p. F1259-F1270.

    66.  EVANS, R.G. GARDINER, BS. SMITH, DW. O’CONNOR, PM. (2008). Methods for studying the physiology of kidney oxygenation Clinical and Experimental Pharmacology and Physiology, Vol 35, p. 1405-1412.

    67. WEE, A., GRAYDEN, D., ZHU, Y., SMITH, D.W. (2008). A Continuous Wavelet Transform Algorithm for Peak Detection,  Electrophoresis Vol 29, Issue 20, p.4215-4225.

    68.  GENG, G., JOHNSTON, L.A., YAN, E, BRITTO, J.M. SMITH, D.W. WALKER, D.W. EGAN G. (2009).  Biomechanical mechanisms for cortical folding, Biomechanisms for modeling cortical cerebral folding. Journal of Medical Image Analysis. Vol 13(6) 920-930.

    69.  SMITH R, SMITH, J. SHEN, X, ENGEL, P., BOWMAN, M., McGRATH S, BISSETS, A, McELDUFF, P., GILES, W., SMITH, D.W. (2009).  The Onset of Human Labor is Associated with a Fall in the Ratio of Progesterone to Estrogens and an Increase in the Estriol to Estradiol Ratio. Journal of Clinical Endocrinology and Metabolism Vol 94, Issue 6, 2066-2074.

    70.  ZHANG, L, GARDINER, B., SMITH, D.W., PIVONKA, P., GRODZINSKY, A., (2009). Integrated Model of IGF-I Mediated Biosynthesis in a Deformed Articular Cartilage. Engineering Mechanics-ASCE 135(5) 439-449.

    71.  PIVONKA, P., ZIMAK, J., SMITH, D.W., GARDINER, B., DUNSTAN, C.B., SIMS, N.A., MARTIN, T.J., MUNDY, G. (2010). Theoretical investigation of the role of the RANK-RANKL-OPG system in bone remodeling. Journal of Theoretical Biology Vol 262, p, 306-316.

    72.  GARDINER, B.S., SMITH, D.W., COOTE, M.A, CROWSTON, J.G. (2010). Computational modeling of intra-ocular pressure following glaucoma surgery. PLOS ONE.  Volume: 5   Issue: 10 Article Number: e13178. doi:10.1371/journal.pone.0013178.

    73.  ZHANG, L., GARDINER, B.S. SMITH, D.W., PIVONKA, P. GRODZINSKY, A. (2010). On the role of diffusible binding partners in modulating transport and concentration of protein in tissues. Journal of Theoretical Biology Volume: 263   Issue: 1   Pages: 20-29.

    74.  SOKOLOWSKI P, SAISON F, GILES W., McGRATH S, SMITH D.W., SMITH J, SMITH R. (2010). Human Uterine Wall Tension Trajectories and the Onset of Parturition, PLOS ONE Volume: 5 Issue: 6 Article Number: e11037. doi:10.1371/journal.pone.0011037

    75.  BUENZLI, P. PIVONKA, P. SMITH D.W. (2011). Spatio-temporal structure of cell distribution in cortical Bone Multicellular Units: a mathematical model. BONE 48(4), pp 918-926, 2011.

    76.  GARDINER, B.S., SMITH, D.W., O’CONNOR, P.M., EVANS, R. (2011). A Mathematical Model of Diffusional Shunting of Oxygen from Arteries to Veins in the Kidney. American Journal of Physiology—Renal Phyisology 300: F1339-1352. doi:10.1152/ajprenal.00544.2010.

    77.  WANG, Y. PIVONKA, P, BUENZLI, PR, SMITH, D.W., DUNSTAN, C.R. (2011). Computational Modeling of Interactions between Multiple Myeloma and the Bone Microenvironment. PLoS ONE 6(11): e27494. doi:10.1371/journal.pone.0027494.

    78.  GARDINER, BS., ZHANG, L, SMITH, DW., PIVONKA, P., GRODZINSKY, AJ (2011). A mathematical model for targeting chemicals to tissues by exploiting complex degradation, Biology Direct,  Volume: 6     Article Number: 46   DOI: 10.1186/1745-6150-6-46.

    79.  BUENZLI, PR., JEON, J., PIVONKA, P., SMITH, DW, CUMMINGS, PT., (2012). Investigation of microscopic bone resorption in cortical Basic Multicellular Units using a lattice-based computational model. BONE Vol 50, Issue 1 , Pages 378-389.

    80.  TAN, C.W., GARDINER, B.S., HIROKAWA, Y. LAYTON, M.J., SMITH, D.W., BURGESS, A.W. (2012). Wnt Signalling Pathway Parameters for Mammalian Cells. PLoS ONE 7(2): e31882. doi:10.1371/journal.pone.0031882.

    81.  SMITH DW, GARDINER BS, DUNSTAN C (2012) Bone Balance within a Cortical BMU: Local Controls of Bone Resorption and Formation. PLoS ONE 7(7): e40268. doi:10.1371/journal.pone.0040268.

    82.  Tao, W., Gardiner, B.S., Lin, Z., Rubenson, J., Wang, A., Kirk, T.B., Xu, J., Smith D., Lloyd, D., Zheng, MH. (2012).  Bioreactor design for tendon/ligament engineering. Tissue Engineering Part B 19(2). doi:10.1089/ten.teb.2012.0295.

    83.  Buenzli, P.R., Pivonka, P., Gardiner, B.S., Smith D.W. (2012). Modelling the anabolic response of bone using a cell population model. Journal of Theoretical Biology 307:42–52. doi.org/10.1016/j.jtbi.2012.04.019

    84.  Gardiner, B.S., Thompson, S.L., Ngo, J.P. Smith, D.W., Abdelkader A, Broughton B.R., Bertram J.F., Evans R.G. (2012). Diffusive oxygen shunting between vessels in the preglomerular renal vasculature: anatomic observations and computational modeling. American Journal of Physiology—Renal Phyisology 303: F605-F618. 10.​1152/​ajprenal.​00186.​2012

    85.  Nguyen, D.Q., Ross, C.M., Li, Y.Q., Pandav, S., Gardiner, B.S., Smith, D.W., How A.C., Crowston J.G., Coote, M.A. (2012). A Model to Measure Fluid Outflow in Rabbit Capsules Post Glaucoma Implant Surgery. Investigative Ophthalmology & Visual Science 53(11): 6914-6919. doi: 10.1167/iovs.12-10438.

    86.  Tao, W., Gardiner, B.S., Lin, Z., Rubenson, J., Wang, A., Kirk, T.B., Xu, J., Smith D., Lloyd, D., Zheng, MH. (2013). Programmable mechanical stimulation on tendon homeostasis in a bioreactor system. Biotechnology & Bioengineering 110(5). doi:10.1002/bit.24809.

    87.  Evans, R.G., Ince, C., Joles, J., Smith D.W., May, C., O’Connor, P., Gardiner, B. (2013). Haemodynamic influences on kidney oxygenation: The clinical implications of integrative physiology accepted Clinical and Experimental Pharmacology and Physiology 40: 106-122.

    88.  Zhang, L., Smith, D.W., Gardiner, B.S. and Grodzinsky, A.J.(2013). Modeling the Insulin-Like Growth Factor System in Articular Cartilage. PLoS ONE 8(6): e66870. doi:10.1371/journal.pone.0066870.

    89.  Smith, D.W., Gardiner, B.S., Rubenson, J., Kirk, T.B., Lloyd, D., Zheng, MH., Besier, T.(2013). A conceptual framework for computational models of Achilles tendon homeostasis. Systems Biology and Medicine 5(5): 523-538. DOI: 10.1002/wsbm.1229.

    90.  Van der Wath, R., Gardiner, B.S., Smith, D.W. Burgess, T. (2013). Cell Organisation in the Colonic Crypt: a Theoretical Comparison of the Pedigree and Niche Concepts. PLoS ONE 8(9): e73204. doi:10.1371/journal.pone.0073204.

    91.  Smith, D.W., Gardiner, B.S., Davidson, J.B. and Grodzinsky, A.J.(2013). Computational Model for the Analysis of Cartilage and Cartilage Tissue Constructs. Tissue Engineering and Regenerative Medicine. doi: 10.1002/term.1751.

    92.  TAN, C.W., HIROKAWA, Y., GARDINER, B.S., SMITH, D.W., BURGESS, A.W. (2013) Colon Cryptogenesis: Asymmetric Budding. PLoS ONE 8(10). doi:10.1371/journal.pone.0078519.

    93.  Scheiner, S. Pivonka, P. Smith, D.W., Dunstan, C.R.(2014). Mathematical modeling of postmenopausal osteoporosis and its treatment by the anti-catabolic drug denosumab. International Journal Numerical Methods in Biomedical Engineering 30(1): 1-27 .

    94.  Buenzli, P.R., Pivonka, P. and Smith, D.W. (2014). Bone refilling in bone multicellular units: Insights into tetracycline double labelling from a computational model. Biomechanics and Modeling in Mechanobiology 13(1): 185-203. DOI: 10.1007/s10237-013-0495-y.

    95.  Evans, R.G., Smith J.A., Wright, C., Gardiner, B.S., Smith, D.W. and Cochrane, A.D. (2014). Urinary oxygen tension: a clinical window on the health of the renal medulla? Am J Physiol Regul Integr Comp Physiol 306: R45-R50.

    96.  Shim, V.B., Fernandez J.W., Gamage, P.B., Regnery, C., Smith, D.W., Gardiner, B.S., Lloyd, D.G. and Besier, T.F. (2014). Subject-specific finite element analysis to characterize the influence of geometry and material properties in Achilles tendon rupture. J of Biomechanics 47: 3598-3604. DOI: 10.1016/j.jbiomech.2014.10.001.

    97.  Ngo, J.P., Kar, S., Kett, M.M., Gardiner, B.S., Pearson, J.T., Smith, D.W., Ludbrook, J., Bertram,J.F. and Evans, R.G. (2014). Vascular geometry and oxygen diffusion in the vicinity of artery-vein pairs in the kidney. American Journal of Physiology-Renal Physiology 317(10): F1111-F1122. DOI: 10.1152/ajprenal.00382.2014.

    98.  Cox, B.N.and Smith, D.W. (2014). On strain and stress in living cells. Journal of the Mechanics and Physics of Solids 71: 239-252. DOI: 10.1016/j.jmps.2014.07.001.

    99.  Tan, C.W., Gardiner, B.S., Hirokawa, Y., Smith, D.W. and Burgess, A.W. (2014). Analysis of Wnt signaling beta-catenin spatial dynamics in HEK293T cells. BMC Systems Biology 8(44). DOI: 10.1186/1752-0509-8-44.

    100.  Zhang, L., Miramini, S., Smith, D.W., Gardiner, B.S. and Grodzinsky, A.J. (2014). Time evolution of deformation in a human cartilage under cyclic loading. Annals of Biomedical Engineering 45(5): 1166-1177.

    101.  Woodhouse, F.G., Gardiner, B.S. and Smith, D.W. (2015). Short-term consolidation of articular cartilage in the long-term context of osteoarthritis. Journal of Theoretical Biology 368: 102-112. DOI: 10.1016/j.jtbi.2015.01.003.

    102.  Gardiner, B.S., Wong, K.K., Joldes, G.R., Rich, A.J. Tan, C.W., Burgess, A.W. and Smith, D.W. (2015). Discrete element framework for modelling extracellular matrix, deformable cells and subcellular components. PLoS Computational Biology 11(10): e1004544. doi: 10.1371/journal.pcbi.1004544.

    103.  Wang, T., Lin, Z., Ni, M., Day, R.E., Gardiner, B.S., Landao-Bassonga, E., Rubenson, J., Kirk, T.B., Smith, D.W., Wang, A., Lloyd, D.G., Wang, Y., Zheng, Q. and Zheng. M.H. (2015). Cyclic mechanical stimulation rescues rabbit Achilles tendon from degeneration in a bioreactor system. Journal of Orthopaedic Research doi: 10.1002/jor.22960.

    104.  Gardiner, B.S., Joldes, G.R., Wong, K.K.L., Tan, C.W. and Smith. D.W. (2016). Controlling seepage in discrete particle simulations of biological systems. Computer Methods in Biomechanics and Biomedical Engineering PMID 26629728.

    105.  Young, S.R., Gardiner, B.S., Mehdizadeh, A., Rubenson, J., Umberger, B. and Smith, D.W. (2016). Adaptive remodeling of Achilles tendon: A multi-scale computational model. PLOS Computational Biology 12 (9): PMID:27684554. doi: 10.1371/journal.pcbi.

    106.  Gardiner, B.S., Woodhouse, F.G., Besier, T.F., Grodzinsky, A.J., Lloyd, D.G., Zhang, L. and Smith, D.W. (2016). Predicting knee osteoarthritis. Annals of Biomedical Engineering 44 (1): 222-233. PMCID: PMC4690844. DOI: 10.1007/s10439-015-1393-5.

    107.  Kar, S., Smith, D.W., Gardiner, B.S., Li, Y., Wang, Y. and Grodzinsky. A.J. (2016). Modeling IL-1 induced degradation of articular cartilage. Archives of Biochemistry and Biophysics 594: 37-53. PMID:26874194. doi: 10.1016/j.abb.2016.02.008.

    108.  Sgouralis, I., Kett, M.M., Ow, C.P.C., Abdelkader, A., Layton, A.T., Gardiner, B.S., Smith, D.W., Lankadeva, Y.R. and Evans, R.G. (2016). Bladder urine oxygen tension for assessing renal medullary oxygenation in rabbits: Experimental and modelling studies. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 311(3): R532-R544. PMID: 27385734. doi: 10.1152/ajpregu.00195.2016.

    109.  Ngo, J.P., Ow, C.P.C., Gardiner, B.S., Kar, S., Pearson, J.T., Smith, D.W. and Evans, R.G. (2016). Diffusive shunting of gases and other molecules in the renal vasculature: Physiological and evolutionary significance. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology PMID: 27488891. doi: 10.1152/ajpregu.00246.2016.

    110.  Kar,S., Smith, D.W., Gardiner, B.S. and Grodzinsky, A.J. (2016). Systems based study of the therapeutic potential of small charged molecules for the inhibition of IL-1 mediated cartilage degradation. PLOS ONE 11(12): e0168047. PMID: 27977731. doi: 10.1371/journal.pone.0168047.

    111.  Mehdizadeh, A., Gardiner, B.S., Lavagnino, M. and Smith, D.W. (2017). Predicting tenocyte expression profiles and average molecular concentrations in Achilles tendon ECM from tissue strain and fiber damage. Biomechanics and Modeling in Mechanobiology 1-20.

    112.  Lee, C-J., Gardiner, B.S., Ngo, J.P., Kar, S., Evans, R.G. and Smith, D.W. (2017). Accounting for oxygen in the renal cortex: A computational study of factors that predispose the cortex to hypoxia. American Journal of Physiology-Renal Physiology DOI: 10.1152/ajprenal.00657.2016.

    113.  Lee, C-J., Gardiner, B.S., Ngo, J.P., Kar, S., Evans, R.G. and Smith, D.W. (2017). A pseudo-three-dimensional model for quantification of oxygen diffusion from pre-glomerular arteries to renal tissue and renal venous blood. American Journal of Physiology-Renal Physiology DOI: 10.1152/ajprenal.00659.2016.

    114.  Ngo, J.P., Le, B., Khan, Z., Kett, M.M., Gardiner, B.S., Smith, D.W., Melhem, M.M., Maksimenko, A., Pearson, J.T., and Evans, R.G. (2017). Micro-computed tomographic analysis of the radial geometry of intrarenal artery-vein pairs in rats and rabbits: comparison with light microscopy. Clinical and Experimental Pharmacology and Physiology DOI: 10.1111/1440-1681.12842.

    115.  Miramini, S., Smith, D.W., Zhang, L., and Gardiner, B.S. (2017). The spatio-temporal mechanical environment of healthy and injured human cartilage during sustained activity and its role in cartilage damage. Journal of the Mechanical Behavior of Biomedical Materials 74: 1-10.

    Research Grants: Brief Grant History

    • 1998-2000 ARCLG Decontamination of a fluoride polluted aquifer DW Smith PBinning $159,000
    • 1999-2001 ARCLG Contaminant transport of inorganics through soil $137,000
    • 1999-2001 RMC A quantitative model for the timing of parturition DW Smith RSmith $49,317
    • 1999-2001 RMC Contaminant transport through a deforming porous DW Smith $49,317
    • 2000 MBRF Prediction of Preterm Birth DW Smith $10,000
    • 2001 MBRF Prediction of Preterm Birth DW Smith $10,000
    • 2001 LEIF High Resolution Inductively Coupled Mass Spectrometer (with seven others) $659,000
    • 2001-2003 ARC DP Effect of Cracking on Expansive Clays DW Smith and SFityus $180,000
    • 2001-2003 ARC DP Contaminant transport through a deforming porous DW Smith $160,000
    • 2004 LIEF Atomic force microscopy for soft interfaces (with ten others) $445,000
    • 2004-2008 ARC-DP Fundamental theoretical investigation of the chemomechanical properties of clays DW Smith SFityus $495,000
    • 2004-2006 ARC-DP Fundamental theoretical and experimental investigation of cartilage mechanics DW Smith AGrodzinsky $282,000
    • 2006 NHMRC Development Grant, Computer program to predict premature birth, DW Smith R Smith, Uni of Newcastle, $388,000
    • 2008 ARC Linkage Grant, Estimating The Risk of Preterm Birth Using Blood Tests with X. Shen, DW Smith R Smith Symbion Health: $390,000
    • 2009-2011 ARC-DP Engineering cartilage homeostasis in health and disease $230,000 DW Smith
    • 2009-2011 ARC-DP Multiscale modeling of transport through deformable porous materials $450,000
    • 2009-2011 NHMRC Simulations of colon cancer $528,000
    • 2009-2011 NHMRC Regulating fluid mechanics to improve outcomes for glaucoma surgery $269,000
    • 2009-2011 Prostate Cancer Council of Aust: Prostate metatasis to bone $280,000
    • 2010-2012 NHMRC Hypoxia is the common pathway to renal failure $478,000
    • 2011-2015 ARC Linkage Project: Bioengineered scaffolds for Achilles tendinopathy treatment $840,000
    • 2012-2014 NHMRC Investigating the roles of the wnt and notch signalling systems in colon cancer crypt biology $585,000.
    • 2013-2015 NHMRC Glycomic control of cartilage extra cellular matrix turnover $682,895.
    • 2013-2015 NHMRC Bridging the gap between cartilage biology and osteoarthritis risk prediction $494,589.
    • 2014-2016 ARC-DP The comparative physiology of oxygen delivery to the kidney $505,000.
    • 2017-2019 NHMRC Towards Prevention of Acute Kidney Injury after Cardiac Surgery $770,000.
     

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