Engineering Computational Biology Group
School of Computer Science and Software Engineering
The University of Western Australia
35 Stirling Highway, Crawley WA 6009, Australia
Summary of Professional Experience:
- Ph.D. in Engineering. The University of Sydney (1990)
- B.E. in Civil Engineering (First Class Honours). The University of Sydney
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
in biomedical engineering, building on his biological knowledge
four years as a medical student. Significant projects undertaken to
(i) development of a theoretical model describing calcium oscillations
smooth muscle cells (ii) development of a new conceptual approach to
identifying women at risk of preterm birth and (iii) development of
models describing the behaviour of cartilage (with A/Prof Bruce
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
a growing list of papers on oxygen transport in the kidney (with A/Prof
Evans and A/Prof Bruce Gardiner), Wnt signaling relevant to colon
colon crypt mechanics (with Prof Tony Burgess, A/Prof Bruce Gardiner.
Wee Tan and Richard Van der Wath) and bleb function in the eye (with
Bruce Gardiner, Prof Jonathon Crowston and Dr Michael
has been developing a new model describing the processes of bone
and mechano-signal transduction in bone (with A/Prof Peter Pivonka, Dr
Scheiner and Dr Pascal Buenzli), and published extensively on this
work is applicable to understanding disease processes like osteoporosis
cancer matatasis to the bone microenvironment. David has recently
developing models of tendon homeostasis and repair (with A/Prof Bruce
Prof Minghao Zheng, Prof Jaike Xu, Dr Jonas Rubenson and Prof David
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
David has served as A/Dean Research (University of Newcastle),
Teaching and Learning and Head of Department (University of Melbourne),
Dean Faculty of Engineering Computing and Mathematics, The University
Western Australia. David served on the Australian Research Council's
Experts, and was Chair of the Engineering and Environmental Science
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
completed course Leading Organisational Change and Renewal at Harvard
Business School and completed the Advanced Management Program at
Harvard Business School
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.
- 1992-1993 Mr. Mark Taylor MEng Expansive soils Lower Hunter Awarded 1993
- 1992-1997 Dr Paul Kau PhD Fluoride transport through clay soils Awarded
- 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
- 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 -
- 1998-2005 Brook Ewers PhD Electrical and Mechanical Behaviours of Clay
- 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
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
3. SMITH, D.W. (2001).
Geotechnical and Geoenvironmental Engineering. 6th Ed. 521
4. SMITH, D.W. (2002).
Writing Science: A Guide to Scientific Writing for Research Engineers.
3rd Ed. 220 pages.
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
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,
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
G.R., BOURANTAS, G.C., WITTEK, A., MILLER, K., SMITH, D.W., and GARDINER, B.S. (2019), (book
chapter) A Discrete Element Method for Modelling Cell Mechanics: Application to the Simulation of Chondrocyte Behavior in the Growth Plate, in Computational Biomechanics for Medicine: Measurements, Models, and Predictions, Springer International Publishing p. 93–103
10. SMITH, D.W., GARDINER, B.S., ZHANG,
L., and GRODZINSKY, A.J. (2019). Articular Cartilage Dynamics Pub. Springer Singapore (ISBN 978-981-13-1473-5 DOI 10.1007/978-981-13-1474-2), 738 pages.
Refereed Journal Publications 1989-2018
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.
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.
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.
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,
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.
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.
P.W. and SMITH, D.W. (1995), ‘Pollution Control Strategy Employing an
Interception–Sorption Trench’ Australian Geomechanics, Vol. 27, p.
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.
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.
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.
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.
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.
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.
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.
S. G., ALLMAN M. A., and SMITH, D. W., (1999)
‘Mound shapes beneath covered areas.’ Australian Geomechanics,
Vol. 34, No. 3 p. 5–14.
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.
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.
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.
D.W. (2000) ‘Geotechnical Design and Numerical Modelling’ Australian
Geomechanics, Vol. 35, No.4, p. 7–32.
D.W. (2001), ‘Granular Temperature’ ASCE International Journal of
Geomechanics Vol. 1 No. 1 p. 41–64.
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.
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.
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.
24. 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.
D.W. and FLETCHER, H (2002) ‘Reactive Walls: an overview’ Australian
Geomechanics, Vol. 37 No. 4 p. 85-98.
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.
J., SMITH, D.W., FITYUS, S.G. and SHENG, D. (2003), Numerical Analysis of Neutron Mositure Probe Measurements’ ASCE International Journal of Geomechanics, Vol
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.
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.
C., SMITH, D.W. and FITYUS, S.G. (2004) ‘Coupled Multi-ion Electrodiffusion
Analysis for Clay Soils’ Canadian Geotechnical Journal, Vol 41(2): p.
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.
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.
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.
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.
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.
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.
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.
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.
H., SMITH, D.W. and PIVONKA, P. (2006), ‘A geochemical model for the adsorption
of fluoride onto alumina’ ASCE Journal of Environmental Engineering 132
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.
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),
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
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.
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.
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.
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.
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.
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.
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
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)
51. NARSILIO GA, SMITH DW,
PIVONKA P (2010) Estimating vertical and lateral pressures in periodically structured montmorillonite clay particles. Anais Da Academia Brasilerira De Ciencias
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:
53. 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
3.2 Bioengineering and Medical Journal
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
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.
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.
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
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.
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.
60. ZHANG L., GARDINER, B., SMITH, D.W., PIVONKA, P.,
GRODZINSKY, A. (2008). IGF uptake with competitive binding in articular cartilage. Journal
of Biological Systems 16(2):175-195.
61. 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
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.
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.
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.
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.
A., GRAYDEN, D., ZHU, Y., SMITH, D.W. (2008). A Continuous Wavelet Transform
Algorithm for Peak Detection, Electrophoresis Vol 29, Issue 20,
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
68. 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,
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.
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.
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.
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.
73. 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
74. BUENZLI, P. PIVONKA, P. SMITH D.W. (2011).
structure of cell distribution in cortical Bone Multicellular Units: a
mathematical model. BONE 48(4), pp 918-926, 2011.
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.
76. 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.
77. 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:
78. 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.
79. 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.
80. (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.
81. 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.
82. 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
B.S., Thompson, S.L., Ngo, J.P. Smith, D.W., Abdelkader
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.
84. (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.
85. 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.
86. 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.
87. (2013). Modeling the Insulin-Like Growth Factor System in Articular Cartilage.
PLoS ONE 8(6): e66870. doi:10.1371/journal.pone.0066870.
88. (2013). A conceptual framework for computational models of Achilles tendon homeostasis.
Systems Biology and Medicine 5(5): 523-538. DOI: 10.1002/wsbm.1229.
89. (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.
90. (2013). Computational Model for the Analysis of Cartilage and Cartilage Tissue Constructs.
Tissue Engineering and Regenerative Medicine. doi: 10.1002/term.1751.
91. 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.
92. (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 .
93. (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.
94. (2014). Urinary oxygen tension: a clinical window on the health of the renal medulla?
Am J Physiol Regul Integr Comp Physiol 306: R45-R50.
95. (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.
96. (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.
97. (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.
98. (2014). Analysis of Wnt signaling beta-catenin spatial dynamics in HEK293T cells.
BMC Systems Biology 8(44). DOI: 10.1186/1752-0509-8-44.
99. (2014). Time evolution of deformation in a human cartilage under cyclic loading.
Annals of Biomedical Engineering 45(5): 1166-1177.
100. (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.
101. (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.
102. (2015). Cyclic mechanical stimulation rescues rabbit Achilles tendon from degeneration in a bioreactor system.
Journal of Orthopaedic Research doi: 10.1002/jor.22960.
103. (2016). Controlling seepage in discrete particle simulations of biological systems.
Computer Methods in Biomechanics and Biomedical Engineering PMID 26629728.
104. (2016). Adaptive remodeling of Achilles tendon: A multi-scale computational model.
PLOS Computational Biology 12 (9): PMID:27684554. doi: 10.1371/journal.pcbi.
105. (2016). Predicting knee osteoarthritis.
Annals of Biomedical Engineering 44 (1): 222-233. PMCID: PMC4690844. DOI: 10.1007/s10439-015-1393-5.
106. (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.
107. (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.
108. (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.
109. (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.
110. (2017). Predicting tenocyte expression profiles and average molecular concentrations in Achilles tendon ECM from tissue strain and fiber damage.
Biomechanics and Modeling in Mechanobiology16 (4): 1329-1348. DOI: 10.1007/s10237-017-0890-x .
111. (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.
112. (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.
113. (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.
114. (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. DOI: 10.1016/j.jmbbm.2017.05.018.
115. (2017). Estimating outflow facility through pressure dependent pathways of the human eye.
PLOS ONE DOI: 10.1371/journal.pone.0188769.
116. (2018). Renal haemodynamics and oxygenation during and after cardiac surgery and cardiopulmonary bypass.
Acta Physiologica 222 (3)DOI: 10.1111/apha.12995.
117. (2018). Effect of collagen length distribution and timing for repair on the active TGF-β concentration in tendon.
Connective Tissue Research DOI: 10.1080/03008207.2018.1432605.
118. (2018). Three-dimensional morphometric analysis of the renal vasculature.
American Journal of Physiology-Renal Physiology314 (5): F715-F725.
119. (2018). A model of oxygen transport in the rat renal medulla.
American Journal of Physiology-Renal Physiology.
120. (2019). Editorial: Stimulation of erythropoietin release by hypoxia and hypoxemia: similar but different. Kidney International 95(1): 23-25
121. (2019). Efficient solution methods for modelling slowly evolving mechanical phenomena in cells and tissues using the discrete element method. Engineering Analysis with Boundary Elements 100: 175-184
122. (2019). The investigation of fluid flow in cartilage contact gap. Journal of the Mechanical behaviour of Biomedical Materials DOI: 10.1016/j.jmbbm.2019.04.008.
123. (2019). Estimating three-dimensional outflow and pressure gradients within the human eye. PLOS ONE DOI: 10.1371/journal.pone.0214961.
Research Grants: Brief Grant History
- 1998-2000 ARCLG Decontamination of a fluoride polluted aquifer DW Smith
- 1999-2001 ARCLG Contaminant transport of inorganics through soil
- 1999-2001 RMC A quantitative model for the timing of parturition DW Smith
- 1999-2001 RMC Contaminant transport through a deforming porous DW Smith
- 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
- 2001-2003 ARC DP Contaminant transport through a deforming porous DW
- 2004 LIEF Atomic force microscopy for soft interfaces (with ten others)
- 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
- 2010-2012 NHMRC Hypoxia is the common pathway to renal failure
- 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
- 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.
- 2018-2020 ARC-DP Physiology of oxygen transport in the mammalian kidney $392,664.
- 2018-2020 ARC-DP Interaction between consolidation and lubrication of synovial joints $352,616.