University of Oxford Logo University of OxfordDepartment of Computer Science - Home

Jonathan Whiteley : Publications

By dateBy titleBy typeBibtex

[1]

The effect of membrane−regulated actin polymerization on a two−phase flow model for cell motility

L.S. Kimpton‚ J.P. Whiteley‚ S.L. Waters and J.M. Oliver

In IMA Journal of Applied Mathematics. Vol. 79. Pages 603−635. 2014.

[2]

Evaluation of the Growth Environment of a Hydrostatic Force Bioreactor for Preconditioning of Tissue−Engineered Constructs

Y. Reinwald‚ K.H.L. Leonard‚ J.R. Henstock‚ J.P. Whiteley‚ J.M. Osborne‚ S.L. Waters‚ P. Levesque and A.J. El Haj

In Tissue Engineering Part C. 2014.

[3]

Error estimation and adaptivity for incompressible hyperelasticity

J.P. Whiteley and S.J. Tavener

In International Journal for Numerical Methods in Engineering. Vol. 99. Pages 313−332. 2014.

[4]

On a poroviscoelastic model for cell crawling

L.S. Kimpton‚ J.P. Whiteley‚ S.L. Waters and J.M. Oliver

In Journal of Mathematical Biology. 2014.

[5]

Automatic simplification of systems of reaction–diffusion equations by a posteriori analysis

P.J. Maybank and J.P. Whiteley

In Mathematical Biosciences. Vol. 248. Pages 146−157. 2014.

[6]

Modelling the effect of gap junctions on tissue–level cardiac electrophysiology

D. Bruce‚ P. Pathmanathan and J.P. Whiteley

In Bulletin of Mathematical Biology. Vol. 76. Pages 431−454. 2014.

[7]

Heat or mass transfer at low Péclet number for Brinkman and Darcy flow round a sphere

C.G. Bell‚ H.M. Byrne‚ J.P. Whiteley and S.L. Waters

In International Journal of Heat and Mass Transfer. Vol. 68. Pages 247−258. 2014.

[8]

Homogenization via formal multiscale asymptotics and volume averaging: how do the two techniques compare?

Y. Davit and C.G. Bell and H.M. Byrne and L.A.C. Chapman and L.S. Kimpton and G.E. Lang and K.H.L. Leonard‚ J.M. Oliver‚ N.C. Pearson‚ R.J. Shipley‚ S.L. Waters‚ J.P. Whiteley‚ B.D. Wood and M. Quintard

In Advances in Water Resources. Vol. 62. Pages 178−206. 2013.

[9]

Multiple travelling wave solutions in a minimal model for cell motility

L.S. Kimpton‚ J.P. Whiteley‚ S.L. Waters‚ J.R. King and J.M. Oliver

In Mathematical Medicine and Biology. Vol. 30. Pages 241−272. 2013.

[10]

Heat or mass transfer from a sphere in Stokes flow at low Peclet number

C.G. Bell‚ H.M. Byrne‚ J.P. Whiteley and S.L. Waters

In Applied Mathematics Letters. Vol. 26. Pages 392−396. 2013.

[11]

Guide to Scientific Computing in C++

Joe Pitt−Francis and Jonathan Whiteley

Springer. 2012.

[12]

Error bounds on block Gauss–Seidel solutions of coupled multiphysics problems

J.P. Whiteley‚ K. Gillow‚ S.J. Tavener and A.C. Walter

In International Journal for Numerical Methods in Engineering. Vol. 88. Pages 1219−1237. 2011.

[13]

The significant effect of the choice of ionic current integration method in cardiac electrophysiological simulations

P. Pathmanathan G.R. Mirams J.A. Southern and J.P. Whiteley

In International Journal for Numerical Methods in Biomedical Engineering. Vol. 27. Pages 1751–1770. 2011.

[14]

The Influence of Bioreactor Geometry and the Mechanical Environment on Engineered Tissues

J. M. Osborne‚ R. D. O'Dea‚ J. P. Whiteley‚ H. M. Byrne and S. L. Waters

In Journal of Biomechanical Engineering. Vol. 132. No. 5. Pages 051006. May, 2010.

[15]

A numerical guide to the solution of the bidomain equations of cardiac electrophysiology

P. Pathmanathan‚ M.O. Bernabeu‚ R. Bordas‚ J. Cooper‚ A. Garny‚ J. Pitt−Francis‚ J.P. Whiteley and D.J. Gavaghan

In Progress in Biophysics and Molecular Biology. Vol. 102. No. (2−3). Pages 136−155. 2010.

[16]

A numerical method for the multiphase viscous flow equations

J.M. Osborne and J.P. Whiteley

In Computer Methods in Applied Mechanics and Engineering. Vol. 199. Pages 3402−3417. 2010.

[17]

Non−local models for the formation of hepatocyte−stellate cell aggregates

J.E.F. Green‚ S.L. Waters‚ J.P. Whiteley‚ L. Edelstein−Keshet‚ K.M. Shakesheff and H.M. Byrne

In Journal of Theoretical Biology. Vol. 267. Pages 106−120. 2010.

[18]

Cardiac electromechanics: the effect of contraction model on the mathematical problem and accuracy of the numerical scheme

P. Pathmanathan‚ S.J. Chapman‚ D.J. Gavaghan and J.P. Whiteley

In Quarterly Journal of Mechanics and Applied Mathematics. Vol. 63. No. 3. Pages 375−399. 2010.

[19]

A posteriori error analysis for the use of lookup tables in cardiac electrophysiology simulations

J. Cooper‚ J.P. Whiteley and D.J. Gavaghan

In SIAM Journal on Scientific Computing. Vol. 32. No. 4. Pages 2167−2189. 2010.

[20]

Modeling alveolar volume changes during periodic breathing in heterogeneously ventilated lungs

S.−J. Dunn and J.P. Whiteley

In Annals of Biomedical Engineering. Vol. 38. No. 9. Pages 2988−2999. 2010.

[21]

Model reduction using a posteriori analysis

J.P. Whiteley

In Mathematical Biosciences. Vol. 225. Pages 44−52. 2010.

[22]

Computational and Numerical Methods for the Accurate and Efficient Solution of the Bidomain Equations

J.P. Whiteley

In Mathematics In Industry. Vol. 15. Pages 377−382. 2010.

[23]

A Note on the Effect of the Choice of Weak Form on GMRES Convergence for Incompressible Nonlinear Elasticity Problems

P. Pathmanathan‚ J.P. Whiteley‚ S.J. Chapman and D.J. Gavaghan

In Journal of Applied Mechanics. Vol. 77. Pages 034501. 2010.

[24]

Chaste: Incorporating a Novel Multiscale Spatial and Temporal Algorithm into a Large Scale Open Source Library

M.O. Bernabeu‚ R. Bordas‚ P. Pathmanathan‚ J. Pitt−Francis‚ J. Cooper‚ A. Garny‚ D.J. Gavaghan‚ B. Rodriguez‚ J.A. Southern and J.P. Whiteley

In Phil Trans Roy Soc (A). Vol. 367. No. 1895. Pages 1907−1930. May, 2009.

[25]

Chaste: a test−driven approach to software development for biological modelling

J. Pitt−Francis‚ P. Pathmanathan‚ M.O. Bernabeu‚ R. Bordas‚ J. Cooper‚ A.G. Fletcher‚ G.R. Mirams‚ P. Murray‚ J.M. Osborne‚ A. Walter‚ S.J. Chapman‚ A. Garny‚ I.M.M. van Leeuwen‚ P.K. Maini‚ B. Rodriguez‚ S.L. Waters‚ J.P. Whiteley‚ H.M. Byrne and D.J. Gavaghan

In Computer Physics Communications. Vol. 180. No. 12. Pages 2452–2471. 2009.

[26]

Solving the Coupled System Improves Computational Efficiency of the Bidomain Equations

J.A. Southern‚ G. Plank‚ E.J. Vigmond and J.P. Whiteley

In IEEE Transactions on Biomedical Engineering. Vol. 56. No. 10. Pages 2404−2412. 2009.

[27]

A Comparison of Numerical Methods used for Finite Element Modelling of Soft Tissue Deformation

P. Pathmanathan‚ D.J. Gavaghan and J.P. Whiteley

In Journal of Strain Analysis. Vol. 44. Pages 391−406. 2009.

[28]

Discontinuous Galerkin Finite Element Methods for Incompressible Non−linear Elasticity

J.P. Whiteley

In Computer Methods in Applied Mechanics and Engineering. Vol. 198. Pages 3464−3478. 2009.

[29]

A Numerical Method for Cardiac Mechanoelectric Simulations

P. Pathmanathan and J.P. Whiteley

In Annals of Biomedical Engineering. Vol. 37(5). Pages 860−873. 2009.

[30]

An integrative computational model for intestinal tissue renewal

I.M.M. van Leeuwen‚ G.R. Mirams‚ A. Walter‚ A. Fletcher‚ P. Murray‚ J. Osborne‚ S. Varma‚ S.J. Young‚ J. Cooper‚ B. Doyle‚ J. Pitt−Francis‚ L. Momtahan‚ P. Pathmanathan‚ J.P. Whiteley‚ S.J. Chapman‚ D.J. Gavaghan‚ O.E. Jensen‚ J.R. King‚ P.K. Maini‚ S.L. Waters and H.M. Byrne

In Cell Proliferation. Vol. 42. Pages 617−636. 2009.

[31]

An Efficient Technique for the Numerical Solution of the Bidomain equations

J.P. Whiteley

In Annals of Biomedical Engineering. Vol. 36. No. 8. Pages 1398−1408. 2008.

[32]

Chaste: using agile programming techniques to develop computational biology software

J. Pitt−Francis‚ M.O. Bernabeu‚ J. Cooper‚ A. Garny‚ L. Momtahan‚ J. Osborne‚ P. Pathmanathan‚ B. Rodriguez‚ J.P. Whiteley and D.J. Gavaghan

In Philosophical Transactions of the Royal Society A: Mathematical‚ Physical and Engineering Sciences. Vol. 366. No. 1878. Pages 3111–3136. 2008.

[33]

Predicting tumor location by modeling the deformation of the breast

P. Pathmanathan‚ D.J. Gavaghan‚ J.P. Whiteley‚ S.J. Chapman and J.M. Brady

In IEEE Transactions on Biomedical Engineering. Vol. 55(10). Pages 2471−2480. 2008.

[34]

Multi−scale computational modelling in biology and physiology

J.A. Southern‚ J.M. Pitt−Francis‚ J.P. Whiteley‚ D. Stokeley‚ H. Kobashi‚ R. Nobes‚ Y. Kadooka and D.J. Gavaghan

In Progress in Biophysics and Molecular Biology. Vol. 96. Pages 60−89. 2008.

[35]

Non–linear modelling of breast tissue

J.P. Whiteley‚ D.J. Gavaghan‚ S.J. Chapman and J.M. Brady

In Mathematical Medicine and Biology. Vol. 24. Pages 327–345. 2007.

[36]

Soft tissue modelling of cardiac fibres for use in coupled mechano–electric simulations

J.P. Whiteley‚ M.J. Bishop and D.J. Gavaghan

In Bulletin of Mathematical Biology. Vol. 69. Pages 2199–2225. 2007.

[37]

Physiology driven adaptivity for the numerical solution of the bidomain equations

J.P. Whiteley

In Annals of Biomedical Engineering. Vol. 35. Pages 1510–1520. 2007.

[38]

Synchronization between arterial blood pressure and cerebral oxyhaemoglobin concentration investigated by wavelet cross–correlation

A.B. Rowley‚ S.J. Payne‚ I. Tachtsidis‚ M.J. Ebden‚ J.P. Whiteley‚ D.J. Gavaghan‚ L. Tarassenko‚ M. Smith‚ C.E. Elwell and D.T. Delpy

In Physiological Measurement. Vol. 28. Pages 161–173. 2007.

[39]

An efficient numerical technique for the solution of the monodomain and bidomain equations

J.P. Whiteley

In IEEE Transactions on Biomedical Engineering. Vol. 53. Pages 2139–2147. 2006.

[40]

Some factors affecting pulmonary oxygen transport

J.P. Whiteley

In Mathematical Biosciences. Vol. 202. Pages 115–132. 2006.

[41]

Synthesis of voltage–sensitive optical signals: application to panoramic optical mapping

M.J. Bishop‚ B. Rodriguez‚ J. Eason‚ J.P. Whiteley‚ N.A. Trayanova and D.J. Gavaghan

In Biophysical Journal. Vol. 90. Pages 2938–2945. 2006.

[42]

Oxygen transport to muscle tissue where regions of low oxygen tension exist

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Mathematical and Computer Modelling. Vol. 42. Pages 1113–1122. 2005.

[43]

The solution of inverse non–linear elasticity problems that arise when locating breast tumours

J.P. Whiteley

In Journal of Theoretical Medicine. Vol. 6. Pages 143–149. 2005.

[44]

Predicting tumour location by simulating large deformations of the breast using a 3D finite element model and nonlinear elasticity

P. Pathmanathan‚ D.J. Gavaghan‚ J.P. Whiteley‚ J.M. Brady‚ M.P. Nash‚ P.F. Nielsen and V. Rajagopal

In Proceedings of MICCAI 2004. Vol. 3217 of Lecture Notes in Computer Science. Pages 217–224. 2004.

[45]

Periodic breathing induced by arterial oxygen partial pressure oscillations

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Mathematical Medicine and Biology. Vol. 20. Pages 205–224. 2003.

[46]

Mathematical modelling of pulmonary gas transport

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Journal of Mathematical Biology. Vol. 47. Pages 79–99. 2003.

[47]

The effect of diffusion in the respiratory tree on the alveolar amplitude response technique (AART)

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Respiratory Physiology & Neurobiology. Vol. 137. Pages 81–96. 2003.

[48]

Efficient computations of gas transport in the respiratory tree

J.P. Whiteley and D.J. Gavaghan

In Mathematical Medicine and Biology. Vol. 20. Pages 91–104. 2003.

[49]

A tidal ventilation model for oxygenation in respiratory failure

J.P. Whiteley‚ A.D. Farmery‚ D.J. Gavaghan and C.E.W. Hahn

In Respiratory Physiology & Neurobiology. Vol. 136. Pages 77–88. 2003.

[50]

The effects of ventilation pattern on carbon dioxide transfer in three computer models of the airways

J.P. Whiteley‚ M.J. Turner‚ A.B. Baker‚ D.J. Gavaghan and C.E.W. Hahn

In Respiratory Physiology & Neurobiology. Vol. 131. Pages 269–284. 2002.

[51]

Mathematical modelling of oxygen transport to tissue

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Journal of Mathematical Biology. Vol. 44. Pages 503–522. 2002.

[52]

Variation of venous admixture‚ SF6 shunt‚ PaO2‚ and the PaO2/FIO2 ratio with FIO2

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In British Journal of Anaesthesia. Vol. 88. Pages 771–778. 2002.

[53]

Some factors affecting oxygen uptake by red blood cells in the pulmonary capillaries

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Mathematical Biosciences. Vol. 169. Pages 153–172. 2001.

[54]

Modelling inert gas exchange in tissue and mixed–venous blood return to the lungs

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Journal of Theoretical Biology. Vol. 209. Pages 431–443. 2001.

[55]

A mathematical model of electron transfer within the mitochondrial respiratory cytochromes

A.D. Farmery and J.P. Whiteley

In Journal of Theoretical Biology. Vol. 213. Pages 197–207. 2001.

[56]

A tidal breathing model of the inert gas sinewave technique for inhomogeneous lungs

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Respiration Physiology. Vol. 124. Pages 65–83. 2000.

[57]

The effect of inspired oxygen concentration on the ventilation–perfusion distribution in inhomogeneous lungs

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Journal of Theoretical Biology. Vol. 204. Pages 575–585. 2000.

[58]

Discovering the structure of partial differential equations from example behavior

L. Todorovski‚ S. Dzeroski‚ A. Srinivasan‚ J.P. Whiteley and D.J. Gavaghan

In Proceedings of the International Conference on Machine Learning‚ Stanford‚ USA. Pages 991–998. 2000.

[59]

The effect of the width of the ventilation–perfusion distribution on arterial blood oxygen content

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Journal of Theoretical Biology. Vol. 201. Pages 271–279. 1999.

[60]

A tidal breathing model for the multiple inert gas elimination technique

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Journal of Applied Physiology. Vol. 87. Pages 161–169. 1999.

[61]

Pulmonary blood flow measured by inspiratory inert gas concentration forcing oscillations

E.M. Williams‚ M.C. Sainsbury‚ L. Sutton‚ L. Xiong‚ A.M.S. Black‚ J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Respiration Physiology. Vol. 113. Pages 47–56. 1998.

[62]

A mathematical evaluation of the multiple breath nitrogen washout (MBNW) technique and the multiple inert gas elimination technique (MIGET)

J.P. Whiteley‚ D.J. Gavaghan and C.E.W. Hahn

In Journal of Theoretical Biology. Vol. 194. Pages 517–539. 1998.

[63]

[64]