Eamonn Gaffney. Publications.

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  1. M Xia, Qijing Shen, PK Maini, EA Gaffney, Alex Mogilner, A new local time-decoupled squared Wasserstein-2 method for training stochastic neural networks to reconstruct uncertain parameters in dynamical systems, Neural Networks, In Press
  2. AL Krause, V Klika, E Villar-Sepulveda, AR Champneys,  EA Gaffney, Pattern Localisation in the Swift-Hohenberg Equation via Slowly Varying Spatial Heterogeneity, SIAM Journal on Applied Dynamical Systems, In Press.
  3. LV Brown, M McConnell, R Rosler, L Peiser, BJ Schmidt, AV Ratushny, EA Gaffney, MC Coles, Applying population mechanistic modelling to find determinants of chimeric antigen receptor T-cells dynamics in month-one lymphoma patients, Immunotherapy Advances 5(1), (2025)
  4. J Ayensa-Jimenez, M Perez-Aliacar, M Doweidar, E Gaffney, M Doblare, An overview from physically-based to data-driven approaches of the modelling and simulation of glioblastoma progression in microfluidic devices, Archives of Computational Methods in Engineering, https://doi.org/10.1007/s11831-025-10291-y (2025). 
  5. L Heirene, H Byrne, A Sepp, EA Gaffney and J Yates, Understanding antibody–target antigen interactions and the avidity effect using mathematical modelling, .J. R. Soc. Interface 22: 20240710, https://doi.org/10.1098/rsif.2024.0710 (2025)
  6. JR Crawshaw, EA Gaffney, M Gertz, PK Maini, and A Caruso, Modelling the Ocular Pharmacokinetics and Pharmacodynamics of Ranibizumab for Improved Understanding and Data Collection Strategies in Ocular Diseases, Investigative Ophthalmology & Visual Science, 66:20 (2025).
  7. P Lamirande, EA Gaffney, M Gertz, PK Maini, JR Crawshaw and A Caruso. A first passage model of intravitreal drug delivery and residence time - influence of ocular geometry, individual variability, and injection location, Investigative Ophthalmology & Visual Science, 65:21 (2024).
  8. C Moreau, BJ Walker, RN Poon, D Soto, DI Goldman, E. Gaffney, and KY Wan. Minimal design of a synthetic cilium, Physical Review Research 6 (4), L042061 (2024).
  9. V Klika, E Gaffney, PK. Maini, On the speed of propagation in Turing patterns for reaction-diffusion systems, Physica D, 467, 134268, 2024.
  10. JP Whiteley, CP Brown, EA Gaffney, Sensitivity of cartilage mechanical behaviour to spatial variations in material properties, Journal of the Mechanical Behavior of Biomedical Materials 156, 106575, (2024).
  11. AL Krause, EA Gaffney, TJ Jewell, V Klika, BJ Walker, Turing instabilities are not enough to ensure pattern formation, Bulletin of Mathematical Biology, 86:21 (2024).
  12. A Diez, AL Krause, PK Maini, EA Gaffney, S Seirin-Lee, Turing pattern formation in reaction-cross-diffusion systems with a bilayer geometry, Bulletin of Mathematical Biology 86, 13 (2024).
  13. MP Dalwadi, C Moreau, EA Gaffney, K Ishimoto, BJ Walker, Generalised Jeffery's equations for rapidly spinning particles. Part 1. Spheroids, Journal of Fluid Mechanics, 979:A1 (2024)
  14. MP Dalwadi, C Moreau, EA Gaffney, K Ishimoto, BJ Walker, Generalised Jeffery's equations for rapidly spinning particles. Part 2. Helicoidal objects with chirality, Journal of Fluid Mechanics, 979:A2 (2024).
  15. TJ Jewell, AL Krause, PK Maini, EA Gaffney, Patterning of nonlocal transport models in biology: the impact of spatial dimension, Mathematical Biosciences, 366:109093 (2023)
  16. J Ayensa-Jimenez, MH Doweidar, EA Gaffney, M Doblare, A mathematical modelling study of chemotactic dynamics in cell cultures: the impact of spatio-temporal heterogeneity, Bulletin of Mathematical Biology, 85:98 (2023).
  17. M Dvoriashyna, A Foss, E Gaffney, R Repetto, Mathematical modelling of ocular epithelial transport: a review, Modeling and Artificial Intelligence in Ophthalmology, 5:1-17 (2023).
  18. K Ishimoto, EA Gaffney, DJ Smith, Squirmer hydrodynamics near a periodic surface topography, Frontiers in cell and developmental biology 11, 1123446, 2023
  19. BJ Walker, K Ishimoto, EA Gaffney, Hydrodynamic slender-body theory for local rotation at zero Reynolds number, Physical Review Fluids 8 (3), 034101 (2023)
  20. JD Glover, ZR Sudderick, BBJ Shih, C Batho-Samblas, L Charlton, ..., EA Gaffney, ...., D Headon. The developmental basis of fingerprint pattern formation and variation, Cell 186 (5), 940-956. (2023)
  21. BJ Walker, K Ishimoto, EA Gaffney, Systematic parameterizations of minimal models of microswimming, Physical Review Fluids 8 (3), 034102, 2023
  22. AL Krause, EA Gaffney, BJ Walker, Concentration-Dependent Domain Evolution in Reaction-Diffusion Systems, Bulletin of Mathematical Biology 14, (2023)
  23. V Klika, EA Gaffney, Upscaling the Poisson-Nernst-Planck equations for ion transport in weakly heterogeneous charged porous media, Applied Mathematics Letters, 137, 108482, (2023).
  24. DB de Souza, HA Araujo, GC Duarte-Filho, EA Gaffney, FAN Santos, and EP Raposo, Fock-space approach to stochastic susceptible-infected-recovered models, Phys. Rev. E (2022) 106:014136
  25. LV Brown, MC Coles, M McConnell, AV Ratushny, EA Gaffney, Analysis of cellular kinetic models suggest that physiologically based model parameters may be inherently, practically unidentifiable, Journal of Pharmacokinetics and Pharmacodynamics (2022) 49:539-556
  26. A Sargood, EA Gaffney, AL Krause, Fixed and Distributed Gene Expression Time Delays in Reaction-Diffusion Systems, Bull. Math Bio (2022) 84:98, 29 pages.
  27. L Brown, J Wagg, R Darley, A van Hateren, T Elliott, E Gaffney, M Coles, De-risking clinical trial failure through mechanistic simulation, Immunotherapy Advances, (2022) 2:1-15.
  28. M Dvoriashyna, AJE Foss, EA Gaffney, R Repetto, A mathematical model of aqueous humor production and composition, Investigative Ophthalmology and Visual Science, (2022) 63:1-11.
  29. BJ Walker, K Ishimoto, C Moreau, EA Gaffney, MP Dalwadi, Emergent rheotaxis of shape-changing swimmers in Poiseuille flow, J. Fluid Mechanics (2022), doi.org/10.1017/jfm.2022.474
  30. EA Gaffney, MP Dalwadi, C Moreau, K Ishimoto, BJ Walker, Canonical orbits for rapidly deforming planar microswimmers in shear flow, Physical Review Fluids (2022) 7, L022101
  31. JE Jansen, D Aschenbrenner, HH Uhlig, MC Coles, EA Gaffney, A method for the inference of cytokine interaction networks, PLoS computational biology (2022) 18, e1010112
  32. BJ Walker, K Ishimoto, EA Gaffney, C Moreau, The control of particles in the Stokes limit, Journal of Fluid Mechanics (2022), doi.org/10.1017/jfm.2022.253
  33. JP Whiteley, CP Brown, EA Gaffney, Modelling articular cartilage: the relative motion of two adjacent poroviscoelastic layers, Mathematical Medicine and Biology: A Journal of the IMA, (2022), doi: 10.1093/imammb/dqac005
  34. BJ Walker, K Ishimoto, EA Gaffney, C Moreau, MP Dalwadi, The effects of rapid yawing on simple swimmer models and planar Jeffery's orbits, Physical Review Fluids, (2022) 7, 023101.
  35. AL Krause, EA Gaffney, PK Maini, V Klika, Modern perspectives on near-equilibrium analysis of Turing systems, Phil. Trans. R. Soc. A (2021) 379:20200268
  36. AL Krause, EA Gaffney, PK Maini, V Klika, Introduction to recent progress and open frontiers in Turing's theory of morphogenesis, Phil. Trans. R. Soc. A (2021) 379:20200280
  37. AE Kmieciak, LV Brown, MC Coles, J Wagg, A Phipps, EA Gaffney, Predicted limited redistribution of T cells to secondary lymphoid tissue correlates with increased risk of haematological malignancies in asplenic patients, Scientific Reports (2021) 11:16394.
  38. C Moreau, K Ishimoto, EA Gaffney, BJ Walker, Control and controllability of microswimmers by a shearing flow, Royal Society Open Science (2021), 8:211141
  39. EA Gaffney, K Ishimoto, BJ Walker, Modelling Motility: The Mathematics of Spermatozoa, Frontiers in Cell and Developmental Biology, (2021) 9:710825
  40. AL Krause, V Klika, PK Maini, D Headon, EA Gaffney, Isolating Patterns in Open Reaction-Diffusion Systems, Bull. Math. Bio. (2021), 83:doi10.1007/s11538-021-00913-4
  41. V Tokarova, AS Perumal, M Nayak, H Shum, O Kaspar, K Rajendran, M Mohammadi, C Tremblay, EA Gaffney, S Martel, DV Nicolau, Patterns of bacterial motility in microfluidics-confining environments, PNAS (2021), 118:2013925118
  42. TE Woolley, AL Krause, EA Gaffney, Bespoke Turing Systems, Bull. Math. Bio. (2021) 83:doi10.1007/s11538-021-00870-y
  43. BJ Walker, K Ishimoto, EA Gaffney, Regularised non-uniform segments and efficient no-slip elastohydrodynamics, Journal of Fluid Mechanics (2021), 915, doi:10.1017/jfm.2021.139.
  44. LV Brown, EA Gaffney, A Ager, J Wagg, MC Coles, Quantifying the limits of CAR T-cell delivery in mice and men, Journal of The Royal Society Interface (2021) 18:0201013 doi:10.1098/rsif.2020.1013
  45. D Aschenbrenner, M Quaranta, S Banerjee, N Ilott, J Jansen, BA Steere, Y Chen, S Ho, K Cox, Oxford IBD Cohort Investigators, CV Arancibia-Carcamo, M Coles, E Gaffney, S Travis, LA Denson, S Kugathasan, J Schmitz, F Powrie, S Sansom, HH Uhlig, Deconvolution of monocyte responses in inflammatory bowel disease reveals an IL-1 cytokine network that regulates IL-23, Gut (2021), 70:1023-1036.
  46. BJ Walker, K Ishimoto, EA Gaffney, Efficient simulation of filament elastohydrodynamics in three dimensions, Physical Review Fluids (2020), 5:123103, doi:10.1103/PhysRevFluids.5.123103
  47. GC Duarte, FAN Santos, EA Gaffney, Fock-space methods for diffusion: Capturing volume exclusion via Fermionic statistics, Physical Review E (2020), 102:052101, doi:10.1103/PhysRevE.102.052101
  48. AL Krause, V Klika, J Halatek, PK Grant, TE Woolley, N Dalchau, EA Gaffney, Turing Patterning in Stratified Domains, Bull. Math. Bio. (2020), 82, doi:10.1007/s11538-020-00809-9.
  49. K Ishimoto, EA Gaffney, BJ Walker. Regularized representation of bacterial hydrodynamics. Physical Review Fluids (2020), doi:10.1103/PhysRevFluids.5.093101
  50. S Seirin-Lee, EA Gaffney, A Dawes, CDC-42 interactions with Par proteins are critical for proper patterning in polarization, Cells (2020), DOI: 10.3390/cells9092036.
  51. SN Calver, EA Gaffney, EJ Walsh, WM Durham, JM Oliver, On the thin-film asymptotics of surface-tension-driven microfluidics, Journal of Fluid Mechanics (2020), 901, 10.1017/jfm.2020.532.
  52. BJ Walker, K Ishimoto, EA Gaffney, A regularised slender-body theory of non-uniform filaments, Journal of Fluid Mechanics (2020), 899:10.1017/jfm.2020.434
  53. A Osojnik, EA Gaffney, M Davies, JWT Yates, HM Byrne, Identifying and characterising the impact of excitability in a mathematical model of tumour-immune interactions, Journal of Theoretical Biology (2020), 501:110250
  54. MF Adamer, HH Harrington, EA Gaffney, TE Woolley, Coloured Noise from Stochastic Inflows in Reaction-Diffusion Systems, Bull. Math. Bio. (2020), 82, 10.1007/s11538-020-00719-w
  55. BJ Walker, S Phuyal, K Ishimoto, CK Tung, EA Gaffney, Computer-assisted beat-pattern analysis and the flagellar waveforms of bovine spermatozoa, Royal Society Open Science (2020) 7:200769
  56. AL Krause, V Klika, TE Woolley, EA Gaffney, From One Pattern into Another: Analysis of Turing Patterns in Heterogeneous Domains via WKBJ, J. Roy Soc. Interface (2020) 20190621.
  57. M Dvoriashyna, AJE Foss, EA Gaffney, R Repetto, Fluid and Solute Transport across the Retinal Pigment Epithelium: a Theoretical Model, J. Roy Soc. Interface (2020) 20190735
  58. S Egginton, RWP Kissane, AA Al-Shammari, and EA Gaffney, Quantifying fiber type-specific local capillary supply, J. Applied Physiology, (2020) 128:458-459.
  59. JP Whiteley, EA Gaffney, Modelling the Inclusion of Swelling Pressure in a Tissue Level Poroviscoelastic Model of Cartilage Deformation, Mathematical Medicine And Biology: A Journal Of The IMA, (2020) https://doi.org/10.1093/imammb/dqaa001
  60. BJ Walker, K Ishimoto, H Gadelha, EA Gaffney, Filament mechanics in half-space via regularised Stokeslet segments, Journal of Fluid Mechanics (2019), 879:803-833.
  61. JE Jansen, EA Gaffney, J Wagg, MC Coles, Combining Mathematical Models With Experimentation to Drive Novel Mechanistic Insights Into Macrophage Function, Frontiers In Immunology (2019) 10.3389/fimmu.2019.01283
  62. BJ Walker, K Ishimoto, EA Gaffney, Pairwise hydrodynamic interactions of synchronized spermatozoa, Physical Review Fluids, (2019) 093101.
  63. BJ Walker, RJ Wheeler, K Ishimoto, EA Gaffney, Boundary behaviours of Leishmania mexicana: A hydrodynamic simulation study, Journal of Theoretical Biology (2019) 462:311-320.
  64. H Gadelha, EA Gaffney, Flagellar ultrastructure suppresses buckling instabilities and enables mammalian sperm navigation in high-viscosity media, J Roy Soc interface (2019), https://doi.org/10.1098/rsif.2018.0668
  65. WKW Ho, L Freem, D Zhao, KJ Painter, TE Woolley, EA Gaffney, MJ McGrew, A Tzika, MC Milinkovitch, P Schneider, A Drusko, F Matthaus, JD Glover, KL Wells, JA Johansson, MG Davey, HM Sang, M Clinton, DJ Headon, Feather arrays are patterned by interacting signalling and cell density waves, PLOS Biology (2019), 17, DOI: 10.1371/journal.pbio.3000132.
  66. V Klika and JP Whiteley and CP Brown and EA Gaffney, The combined impact of tissue heterogeneity and fixed charge for models of cartilage: the one-dimensional biphasic swelling model revisited, Biomechanics and Modeling in Mechanobiology, (2019) doi: 10.1007/s10237-019-01123-7.
  67. Abdullah A Al-Shammari, Roger WP Kissane, Simon Holbek, Abigail Louise Mackey, Thomas R Andersen, Eamonn A Gaffney, Michael Kjaer, Stuart Egginton, Integrated method for quantitative morphometry and oxygen transport modeling in striated muscle, J Appl Physiol (2019) 126(3):544-557
  68. BJ Walker, RJ Wheeler, K Ishimoto, EA Gaffney, Response of monoflagellate pullers to a shearing flow: A simulation study of microswimmer guidance, Physical Review E (2018) 063111
  69. Kenta Ishimoto, Eamonn A Gaffney, Hydrodynamic Clustering of Human Sperm in Viscoelastic Fluids, Scientific reports (2018), 15600.
  70. M Dvoriashyna, AJE Foss, EA Gaffney, OE Jensen, OE, R Repetto, Osmotic and Electroosmotic Fluid Transport across the Retinal Pigment Epithelium: a Mathematical Model, Journal of Theoretical Biology (2018) 456:233-248.
  71. LV Brown, EA Gaffney, J Wagg, MC Coles, Applications of Mechanistic Modelling to Clinical and Experimental Immunology: An emerging technology to accelerate immunotherapeutic discovery and development, Clinical and Experimental Immunology, (2018) 193:284-292.
  72. V. Klika, M Kozak, EA Gaffney, Domain Size Driven Instability: Self-Organisation in Systems with Advection, SIAM Journal on Applied Mathematics (2018), 78(5), 2298-2322.
  73. K Ishimoto, EA Gaffney, An elastohydrodynamical simulation study of fillament and spermatozoan swimming driven by internal couples, IMA J. Appl. Math (2018), 83:655-679.
  74. LA Hutton-Smith, EA Gaffney, HM Byrne, A Caruso, PK Maini, and NA Mazer, Theoretical Insights Into the Retinal Dynamics of VEGF in Patients Treated with Ranibizumab, Based on an Ocular Pharmacokinetic/Pharmacodynamic Model, Molecular Pharmaceutics, (2018), 15:2770-2784.
  75. DL Humphries, JA Grogan, EA Gaffney, The mechanics of phantom Mikado networks, Journal of Physics Communications (2018) 2, UNSP 055015
  76. AL Krause, V Kilika, TE Woolley, EA Gaffney, Heterogeneity induces spatiotemporal oscillations in reaction-diffusion systems, Physical Review E (2018), 97, 052206
  77. C Willshire, AJ Bron, EA. Gaffney, EI Pearce, Basal Tear Osmolarity as a metric to estimate body hydration and dry eye severity, Progress in Retinal and Eye Research (2018) 64:56-64.
  78. K Ishimoto, H Gadelha, EA Gaffney, DJ Smith, JC Kirkman Brown, Human sperm swimming in a high viscosity mucus analogue, J. Theoretical Biology, (2018) 446:1-10.
  79. L Brown, EA Gaffney, J. Wagg, M Coles, An In Silico Model of Cytotoxic T-Lymphocyte Activation in the Lymph Node Following Short Peptide Vaccination, J. Royal Society Interface (2018) 15 20180041; DOI: 10.1098/rsif.2018.0041
  80. TE Woolley, J Belmonte-Beitia, G F Calvo, JW Hopewell, EA Gaffney, B Jones, Changes in the retreatment radiation tolerance of the spinal cord with time after the initial treatment, International Journal of Radiation Biology, (2018) 94:515-531
  81. PA Roberts, EA Gaffney, JP Whiteley, PJ Luthert, AJE Foss, HM Byrne, Predictive Mathematical Models for the Spread and Treatment of Hyperoxia-induced Photoreceptor Degeneration in Retinitis, Investigative Ophthalmology & Visual Science, (2018) 59:1238-1249
  82. K Ishimoto, EA Gaffney, Boundary element methods for particles and microswimmers in a linear viscoelastic fluid, Journal of Fluid Mechanics (2017) 831:228-251.
  83. V Klika, EA Gaffney, History dependence and the continuum approximation breakdown: the impact of domain growth on Turing's instability, Proc Roy Soc A (2017) 20160744.
  84. LA Hutton-Smith, EA Gaffney, HM Byrne, PK Maini, K Gadkar, NA Mazer, Ocular Pharmacokinetics of Therapeutic Antibodies Given by Intravitreal Injection: Estimation of Retinal Permeabilities Using a 3-Compartment Semi-Mechanistic Model, Mol. Pharm (2017), 14:2690-2698.
  85. TE Woolley, EA Gaffney, A. Goriely, Random blebbing motion: A simple model linking cell structural properties to migration characteristics Phys Rev E (2017) 96, 012409
  86. PA Roberts, EA Gaffney, PJ Luthert, AJE Foss, HM Byrne, Mathematical models of retinitis pigmentosa: The oxygen toxicity hypothesis, J. Theoretical Biology, (2017) 425:53-71.
  87. M.A. Gilbert, S.M. White, J.M. Bullock, E.A. Gaffney, Speeding Up The Simulation of Population Spread Models, Methods in Ecology and Evolution, (2017) 8:501-510.
  88. K Ishimoto, H Gadelha, EA Gaffney, DJ Smith, JC Kirkman Brown, Coarse-Graining the Fluid Flow around a Human Sperm, Physical Review Letters (2017) 118:124501
  89. Reply to Baveye and Darnault: Useful models are simple and extendable, KZ Coyte, H Tabuteau, EA Gaffney, KR Foster, WM Durham, PNAS, (2017) 114:E2804-E2805.
  90. Y. Chen, M. Chen , EA Gaffney, CP Brown, Effect of crosslinking in cartilage-like collagen microstructures, Journal of the Mechanical Behavior of Biomedical Materials, (2017) 66:138-143.
  91. DL Humphries, JA Grogan, EA Gaffney, Mechanical Cell-Cell Communication in Fibrous Networks: The Importance of Network Geometry, Bulletin of Mathematical Biology (2017) 79:498-524.
  92. Microbial competition in porous environments can select against rapid biofilm growth, KZ Coyte, H Tabuteau, EA Gaffney, KR Foster, WM Durham, PNAS, (2017) 114:E110-E170.
  93. F. Yi, EA Gaffney, S Seirin Lee, The Bifurcation Analysis of Turing Pattern Formation Induced by Delay and Diffusion in The Schnakenberg System, Journal Discrete and Continuous Dynamical System B, (2017) 247:647-668.
  94. K Ishimoto, EA Gaffney, Mechanical tuning of mammalian sperm behaviour by hyperactivation, rheology and substrate adhesion: a numerical exploration, J. Royal Society Interface (2016), 13:20160633.
  95. LG Hutchinson, H-J Mueller, EA Gaffney, PK Maini, J Wagg, A Phipps, C Boetsch, HM Byrne, B Ribba, Modeling Longitudinal Preclinical Tumor Size Data to Identify Transient Dynamics in Tumor Response to Antiangiogenic Drugs, CPT Pharmacometrics Syst. Pharmacol (2016), doi:10.1002/psp4.12142
  96. LA Hutton-Smith, EA Gaffney, HM Byrne, PK Maini, D Schwab, NA Mazer, A mechanistic model of the intravitreal pharmacokinetics of large molecules and the pharmacodynamic suppression of ocular vascular endothelial growth factor levels by ranibizumab in patients with neovascular age-related macular degeneration, Molecular pharmaceutics (2016) 13:2941-50.
  97. LG Hutchinson, EA Gaffney, PK Maini, J Wagg, A Phipps, HM Byrne, Vascular phenotype identification and anti-angiogenic treatment recommendation: A pseudo-multiscale mathematical model of angiogenesis, Journal of Theoretical Biology (2016) 398:162-180.
  98. PA Roberts, EA Gaffney, PJ Luthert, AJE Foss, HM Byrne, Retinal Oxygen Distribution and the Role of Neuroglobin, Journal of Mathematical Biology, (2016) 73:1-38.
  99. V Klika, EA Gaffney*, YC Chen, CP Brown, An overview of multiphase cartilage mechanical modelling and its role in understanding function and pathology, Journal of The Mechanical Behavior Of Biomedical Materials (2016) 62: 139-157 [*Equal first authors].
  100. PA Roberts, EA Gaffney, PJ Luthert, AJE Foss, HM Byrne, Mathematical And Computational Models Of The Retina In Health, Development And Disease, Progress in Retinal And Eye Research (2016) 53:48-69.
  101. K Ishimoto, J Cosson, EA Gaffney, A Simulation Study of Sperm Motility Hydrodynamics Near Fish Eggs and Spheres, Journal of Theoretical Biology, 389: 187-197 (2016).
  102. FAN Santos, H Gadelha, EA Gaffney, Fock space, symbolic algebra and analytical solutions for small stochastic systems, Physical Review E, (2015) 062714.
  103. H Shum, EA Gaffney, Hydrodynamic analysis of flagellated bacteria swimming in corners of rectangular channels Physical Review E 92: 063016 (2015).
  104. TE Woolley, EA Gaffney, A. Goriely, Membrane shrinkage and cortex remodelling are predicted to work in harmony to retract blebs, Royal Society Open Science, (2015).DOI: 10.1098/rsos.150184, 15 pages.
  105. Duffy B, Thiyagalingam J, Walton S, Smith DJ, Trefethen A, Kirkman-Brown JC, Gaffney EA, Chen M. Glyph-Based Video Visualization for Semen Analysis. IEEE Trans Vis Comput Graph. (2015) 21: 980-993
  106. D Hauton, J Winter, AA Al-Shammari, EA Gaffney, RD Evans, S Egginton, Maternal hypoxia decreases capillary supply and increases metabolic inefficiency leading to divergence in myocardial oxygen supply and demand, PLOS One (2015), DOI: 10.1371/journal.pone.0127424
  107. H Shum, EA Gaffney, Hydrodynamic analysis of flagellated bacteria swimming near one and between two no-slip plane boundaries, Physical Review E (2015) 91:033012
  108. K. Ishimoto, EA Gaffney, Fluid flow and sperm guidance: a simulation study of hydrodynamic sperm rheotaxis, Journal of the Royal Society Interface(2015), 12:20150172.
  109. D Hauton, J Winter, AA Al-Shammari, EA Gaffney, RD Evans, S Egginton, Changes to both cardiac metabolism and performance accompany acute reductions in functional capillary supply, Biochimica et Biophysica Acta (BBA)-General Subjects, (2015) 1850:681-690.
  110. K Korvasov, EA Gaffney, PK Maini, MA Ferreira, V Klika, Investigating the Turing conditions for diffusion-driven instability in the presence of a binding immobile substrate, Journal of Theoretical Biology, (2015) 367:286-195.
  111. EA Gaffney, S Seirin Lee*, The Sensitivity of Turing Self-Organisation to Biological Feedback Delays: 2D Models of Fish Pigmentation, Mathematical Medicine and Biology, (2015) 32:56-78. [*Equal First Authors]
  112. MA Gilbert, EA Gaffney, JM Bullock, SM White, Spreading speeds for plant populations in landscapes with low environmental variations, Journal of Theoretical Biology (2014), 363:436-452
  113. EH Ooi, DJ Smith, H Gadelha, EA Gaffney, J. Kirkman-Brown The mechanics of hyperactivation in adhered human sperm, Royal Society Open Science 2014, doi 10.1098/rsos.140230
  114. JB McGillen, CJ Kelly, A Martinez-Gonzalez, NK Martin, EA Gaffney, PK Maini, Victor M Perez-Garcia, Glucose-lactate metabolic cooperation in cancer: Insights from a spatial mathematical model and implications for targeted therapy, Journal of Theoretical Biology (2014) 361:190-203
  115. K Ishimoto, EA Gaffney, A study of spermatozoan swimming stability near a surface. Journal of Theoretical Biology (2014) 360 187-199.
  116. TE Woolley, PK Maini and EA Gaffney, Is pigment cell pattern formation in zebrafish a game of cops and robbers? Pigment Cell & Melanoma Research (2014) 27:686-687.
  117. K Ishimoto, EA Gaffney, Swimming efficiency of spherical squirmers: Beyond the Lighthill theory. Phys Rev E (2014), 90 012704
  118. TE Woolley, EA Gaffney, SL Waters, JM Oliver, RE Baker, A Goriely, Three mechanical models for blebbing and multi-blebbing, IMA Journal of Applied Mathematics (2014) 79:636-660.
  119. AA Al-Shammari, EA Gaffney, S Egginton, Modelling capillary oxygen supply capacity in mixed muscles: Capillary domains revisited, Journal of Theoretical Biology, (2014) 356:47-61
  120. DC Markham, MJ Simpson, PK Maini, EA Gaffney, RE Baker, Comparing methods for modelling spreading cell fronts Journal of Theoretical Biology (2014) 353:95-103.
  121. S Manzano, EA Gaffney, M Doblare, AH Doweidar, Cartilage Dysfunction in ALS Patients as Side Effect of Motion Loss: 3D Mechano-Electrochemical Computational Model, Biomed Research International 179070 (2014)
  122. JB McGillen, EA Gaffney, NK Martin, PK Maini, A general reaction-diffusion model of acidity in cancer invasion, J. Math. Biol. (2014), 68:1199-1224
  123. MA Gilbert, SM White, JM Bullock, EA Gaffney, Spreading speeds for stage structured plant populations in fragmented landscapes, Journal of Theoretical Biology (2014), 349:135-49.
  124. TE Woolley, EA Gaffney, JM Oliver, RE Baker, SL Waters, A Goriely, Cellular blebs: pressure-driven, axisymmetric, membrane protrusions, Biomechanics and Modeling in Mechanobiology (2014), 13:463-476
  125. K Ishimoto, EA Gaffney, Squirmer dynamics near a boundary. Phys Rev E 88, 062702 (2013).
  126. DC Markham, MJ Simpson, PK Maini, EA Gaffney, RE Baker, Incorporating spatial correlations into multispecies mean-field models, Phys. Rev E88, 052713 (2013).
  127. H. Gadelha, E. A. Gaffney, and A. Goriely, The counterbend phenomenon in flagellar axonemes and cross-linked filament bundles, PNAS 2013 110 (30) 12180-12185.
  128. S. Seirin Lee, RE Baker, EA Gaffney, SM White, Modelling Aedes aegypti mosquito control via transgenic and sterile insect techniques: Endemics and emerging outbreaks, J. Theor. Biol. (2013), 331 p78-90.
  129. VS Zubkov, CJW Breward, EA Gaffney, Meniscal Fluid Dynamics near Marx's Line, Bull. Math. Bio., (2013) 75, p1524-1543.
  130. J Belmonte-Beitia, TE Woolley, JG Scott, PK Maini, EA Gaffney, Modelling biological invasions: Individual to population scales at interfaces, J. Theoretical Biology, (2013) 334:1-12.
  131. MP Curtis, EA Gaffney, The Three Sphere Swimmer in a Nonlinear Viscoelastic Medium, Phys Rev E 87, 043006 (2013)
  132. S. Seirin Lee, RE Baker, EA Gaffney, SM White, Optimal barrier zones for stopping the invasion of Aedes aegypti mosquitoes via transgenic or sterile insect techniques, Theor. Ecol. (2013), 6, p427-442.
  133. MP Curtis, JC Kirkman-Brown, TJ Connolly, EA Gaffney, Modelling a tethered mammalian sperm cell undergoing hyperactivation, Journal of Theoretical Biology (2012) 309, p1-10
  134. EA Gaffney, NAM Monk, RE Baker, S Seirin Lee, Reply to Correspondence: No Oscillations in Real Activator-Inhibitor Systems in Accomplishing Pattern Formation. Bull Math Biol. (2012) 74:2268-2271.
  135. H Shum, EA Gaffney, The effects of flagellar hook compliance on motility of monotrichous bacteria: a modeling study, Physics of Fluids (2012) Volume: 24 Issue: 6 Pages: 061901 (19 pp.)
  136. VS Zubkov, CJW Breward, EA Gaffney, Coupling fluid and solute dynamics within the ocular surface tear film: a modelling study of black line osmolarity, Bull. Math. Bio (2012) 74, p2062-93
  137. NK Martin, IF Robey, EA Gaffney, RJ Gillies, RA Gatenby, PK Maini, Predicting the Safety and Efficacy of Buffer Therapy to Raise Tumour pHe: An Integrative Modelling Study, British J. of Cancer (2012), 7, 1280-1287.
  138. AA Al-Shammari, EA Gaffney, S Egginton, Re-evaluating the Use of Voronoi Tessellations in the Assessment of Oxygen Supply from Capillaries in Muscle. Bull. Math. Bio (2012) 74, p2204-31
  139. MJ Tindall, EA Gaffney, PK Maini, JP Armitage, Theoretical insights into bacterial chemotaxis WIREs Syst Biol Med (2012) 4, p247-259.
  140. H Colin-Harper, TE Woolley, L Dyson, A Patel, P Potter, RE Baker, EA Gaffney, PK Maini, PR Dash, K Patel, Age Related changes in speed and mechanism of adult stem cell migration, Stem Cells (2012), 30, p1182-1195.
  141. PK Maini, TE Woolley, RE Baker, EA Gaffney and S Seirin Lee, Turing's model for biological pattern formation and the robustness problem, Interface Focus (2012), 2, p487-496
  142. J. McGillen, NK Martin, IF Robey, EA Gaffney, PK Maini, Applications of mathematical analysis to tumour acidity modelling, U. Kyoto RIMS Kokyuroku Bessatsu, May 2012, 31-60.
  143. PDMH Verhaegen, J van Marle, A Kuehne, HJ Schouten, EA Gaffney, PK Maini, E Middelkoop, PPM van Zuijlen, Collagen bundle morphometry in skin and scar tissue: a novel distance mapping method provides superior measurements compared to Fourier analysis, Journal of Microscopy, (2012) 245 p82-89.
  144. TE Woolley, RE Baker, EA Gaffney, PK Maini, S Seirin-Lee, Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems, Phys. Rev. E (2012) 85 051914
  145. V Klika, RE Baker, D Headon, EA Gaffney, The influence of receptor-mediated interactions on reaction-diffusion mechanisms of cellular self-organisation, Bulletin of Mathematical Biology (2012) p 935-957.
  146. TE Woolley, RE Baker, EA Gaffney, PK Maini, Stochastic reaction and diffusion on growing domains: Understanding the breakdown of robust pattern formation, Phys. Rev. E 84, (2011) 046216 [16 pages]
  147. TE Woolley, RE Baker, EA Gaffney, PK Maini, Influence of stochastic domain growth on pattern nucleation for diffusive systems with internal noise, Phys. Rev. E 84, 041905 (2011) [13 pages]
  148. EAJ Boston, EA Gaffney, The influence of toxicity constraints in models of chemotherapeutic protocol escalation Math Med Biol (2011) 28 p357-384.
  149. C. Venkataraman, T. Sekimura, EA Gaffney, PK Maini, A.Madzvamuse, Modeling parr-mark pattern formation during the early development of Amago trout Phys. Rev. E 84, 041923 (2011) [13 pages]
  150. S Seirin Lee, EA Gaffney, RE Baker, The dynamics of Turing patterns for morphogen-regulated growing domains with cellular response delays, Bulletin of Mathematical Biology, (2011), 73 p2527-2551
  151. TE Woolley, RE Baker, EA Gaffney, PK. Maini, Power spectra methods for a stochastic description of diffusion on deterministically growing domains Phys. Rev. E (2011) 84, 021915 [15 pages]
  152. DJ Smith, EA Gaffney, H Shum, H Gadelha, JC Kirkman-Brown, Comment on the Article by J. Elgeti, U. B. Kaupp, and G. Gompper: Hydrodynamics of Sperm Cells Near Surfaces, Biophysical J. (2011) 100(9) p2318-2320
  153. AJ Bron, N Yokoi, EA Gaffney, JM Tiffany, A solute gradient in the tear meniscus. I. A hypothesis to explain Marx's line. The Ocular Surface (2011) 9 p70-91.
  154. AJ Bron, N Yokoi, EA Gaffney, JM Tiffany, A solute gradient in the tear meniscus. II Implications for lid margin disease, including meibomian gland dysfunction. The Ocular Surface (2011) 9 p92-97.
  155. J Schofield, EA Gaffney, RA Gatenby, PK Maini, Tumour angiogenesis: The gap between theory and experiments, J. Theoretical Biology, (2011) 274, p97-102.
  156. NK Martin, EA Gaffney, RA Gatenby, RJ Gillies, IF Robey, PK. Maini, A Mathematical Model of Tumour and Blood pHe Regulation: The HCO3 /CO2 Buffering System, Math Biosci (2011) 230 p1-11.
  157. EA Gaffney, H Gadelha, DJ Smith, JR Blake, JC Kirkman-Brown, Mammalian Sperm Motility: Observation and Theory. Annual Reviews of Fluid Mechanics, (2011), 43, p501-528.
  158. NK Martin, EA Gaffney, RA Gatenby, PK Maini, Tumour-Stromal Interactions in Acid-Mediated Invasion: A Mathematical Model, Journal Of Theoretical Biology, (2010), 267, p461-470.
  159. NK Martin, EA Gaffney, RA Gatenby, PK Maini, Leaky Vessels As A Potential Source Of Stromal Acidification In Tumours, Journal Of Theoretical Biology (2010), 267 p454-460.
  160. S Egginton, EA Gaffney, Tissue capillary supply - it's quality not quantity that counts!, Experimental Physiology (2010), 95, p971-979.
  161. S Seirin Lee, EA Gaffney, Aberrant Behaviours of Reaction Diffusion Self-organisation Models on Growing Domains in the Presence of Gene Expression Time Delays, Bulletin of Mathematical Biology (2010), 72, p2161-2179.
  162. H Gadelha, EA Gaffney, DJ Smith, JC Kirkman-Brown, Nonlinear instability in flagellar dynamics: a novel modulation mechanism in sperm migration?, J. Royal Society Interface (2010) 7 p1689-1697.
  163. S Seirin Lee, EA Gaffney, NAM Monk, The Influence of Gene Expression Time Delays on Gierer-Meinhardt Pattern Formation Systems, Bulletin of Mathematical Biology (2010), 72, p2139-2160.
  164. H Shum, EA Gaffney, DJ Smith, Modelling bacterial behaviour close to a no-slip plane boundary: the influence of bacterial geometry, Proc Roy Soc A (2010) 466 p1725-1748.
  165. P Moreo, EA Gaffney, JM Garcia-Anzar, M Doblare, On the modelling of biological patterns with mechanochemical models: insights from analysis and computation, Bulletin of Mathematical Biology (2010), 72, p400-431.
  166. A Madzvamuse, EA Gaffney, PK Maini, Stability analysis of reaction-diffusion systems with time-dependent coefficients on growing domains, Journal Of Mathematical Biology (2010), 61, p133-164
  167. EA Gaffney, JM Tiffany, N Yokoi, AJ Bron, A Mass and Solute Balance Model for Tear Volume and Osmolarity in The Normal And The Dry Eye, Progress in Retinal And Eye Research (2010), 29, p59-78.
  168. DJ Smith, EA Gaffney, JR Blake, Mathematical modelling of cilia-driven transport of biological fluids, Proceedings of the Royal Society A (2009), 465, p2417-2439.
  169. AJ Bron, N Yokoi, EA Gaffney, JM Tiffany, Predicted Phenotypes of Dry Eye - Proposed Consequences of its Natural History, The Ocular Surface (2009) 7, p78-92.
  170. DJ Smith, EA Gaffney, H Gadelha, N Kapur, JC Kirkman-Brown, Bend propagation in the flagella of migrating human sperm, and its modulation by viscosity, Cell Motility & The Cytoskeleton (2009), 66, 220-236.
  171. DJ Smith, EA Gaffney, JR Blake, JC Kirkman-Brown, Human sperm accumulation near surfaces: a simulation study, J. Fluid Mechanics (2009), 621, p289-320.
  172. HC Monro, EA Gaffney, Modelling chemotherapy resistance in palliation and failed cure, J. Theoretical Biology (2009), 257, p292-302.
  173. DJ Smith, EA Gaffney, JR Blake, Modelling mucociliary clearance, Respiratory Physiology & Neurobiology (2008) 163, p178-188.
  174. RE Baker, EA Gaffney, PK Maini, Partial differential equations for self-organization in cellular and developmental biology, Nonlinearity (2008), 21, R251-290.
  175. DJ Smith, JR Blake, EA Gaffney, Fluid mechanics of nodal flow due to embryonic primary cilia, Journal of The Royal Society Interface (2008) 5, p567-573
  176. EA Gaffney, JK Heath, MZ Kwiatkowska, A Mass Action Model of a Fibroblast Growth Factor Signaling Pathway and Its Simplification, Bulletin of Mathematical Biology (2008) 68, p99-130.
  177. DJ Smith, EA Gaffney, JR Blake, Discrete cilia modelling with singularity distributions, Bulletin of Mathematical Biology (2007) 69, p1477-1510.
  178. DJ Smith, EA Gaffney, JR. Blake, A model of tracer transport in airway surface liquid, Bulletin of Mathematical Biology (2007) 69, p817-836.
  179. DJ Smith, EA Gaffney and JR Blake, A visco-elastic traction layer model of muco-ciliary transport, Bulletin Mathematical Biology, (2007) 69, p289-327.
  180. EA Gaffney, NAM Monk, Gene Expression Time Delays and Turing Pattern Formation Systems, Bulletin Mathematical Biology (2006), p99-130.
  181. EA Gaffney, The Mathematical Modelling of Adjuvant Chemotherapy Scheduling: Incorporating the Effects of Protocol Rest Phases and Pharmacokinetics. Bulletin of Mathematical Biology (2005) 67, p563-611.
  182. EA Gaffney, The Application Of Matematical Modelling To Aspects Of Adjuvant Chemotherapy Scheduling, Journal of Mathematical Biology (2004) 48, p375-422.
  183. EA Gaffney, K. Pugh, PK Maini, F. Arnold, Investigating A Simple Model Of Wound Healing Angiogenesis, J. of Mathematical Biology (2002) 45 p337-374.
  184. E. Crampin, EA Gaffney, P.K. Maini, Mode Doubling And Tripling In Reation-Diffusion Patterns On Growing Domains: A Piecewise Linear Model, J. of Mathematical Biology (2002) 44 p107-128.
  185. EA. Gaffney, On Conditions For The Stability Of A Two Component Mixed Quasimonotone Reaction Diffusion Equation, J. of Mathematical Analysis and Applications (2001) 256, p513-524.
  186. EA Gaffney, PK Maini, JA Sherratt, S.Tuft, The Mathematical Modelling Of Cell Kinetics In Corneal Epithelial Wound Healing And Comparison With Experiment, Journal of Theoretical Biology (1999) 197, p15-40.
  187. EA Gaffney, PK Maini, C. McCaig, M. Zhao, J. Forrester, Modelling corneal epithelial wound closure in the presence of physiological electric fields via a moving boundary formalism, IMA Journal of Mathematics Applied in Medicine and Biology (1999) 16, p369-393.
  188. E. Crampin, EA Gaffney, PK Maini, Reaction and Diffusion on Growing Domains: Scenarios for Robust Pattern Formation, Bulletin Mathematical Biology (1999) 61, p1093-1120.
  189. EA Gaffney, PK Maini, JA Sherratt, PD Dale, Wound healing in the corneal epithelium: biological mechanisms and mathematical models, Journal of Theoretical Medicine (1997), 1:13-23.
  190. EA Gaffney, Massive hard thermal loops in curved space-time, Nuclear Physics B (1996) 476: 275-309.
  191. EA Gaffney, Quark hard thermal loops in curved spacetime, Nuclear Physics B (1996) 459:311-334.
  192. J Frenkel, EA Gaffney, JC Taylor, High-temperature field theory in curved spacetime, Nuclear Physics B (1995) 439: 131-143.
  193. E Gaffney, Hard Thermal Loops, Weak Gravitational Fields and The Quark Gluon Energy Momentum Tensor, Nuclear Physics B (1995) 442: 268-298.

Book Chapters/Proceedings

  1. Dvoriashyna, M., Foss, A.J.E., Gaffney,  E.A and Repetto, R. 2022. Mathematical models of water transport across ocular epithelial layers in ‘Modelling of Mass Transport Processes in Biological Media’ edited by Sid Becker, Andrey Kuznetsov, Filippo de Monte, Giuseppe Pontrelli and Dan Zhao. Publisher: Elsevier. ISBN: 978044315653
  2. K Ishimoto, EA Gaffney, Modelling Spermatozoan Swimming: Its Capabilities and Limitations for Contributing to The Understanding of Sperm Guidance, Flagellar mechanics and sperm guidance, Ch.9, Flagellar mechanics and sperm guidance, Ed. J. Cosson, Bentham Science Publishers, (2015).
  3. PK Maini, TE.Woolley, EA Gaffney, RE Baker, Turing's Theory of Developmental Pattern Formation, The Once and Future Turing, Ch 9, p137-149, edited by S.B. Cooper & A. Hodges, Cambridge University Press 2015
  4. AA Al-Shammari, EA Gaffney, S Egginton, Modelling Oxygen Capillary Supply to Striated Muscle Tissues, in Springer Proceedings in Mathematics & Statistics 87, Advances in Applied Mathematics, 2014
  5. Shum H, Gaffney EA. Ch.2 in: MJ Kim, E Steager, A Agung Julius eds. Mathematical models for individual swimming bacteria in Microbiorobotics: biologically inspired microscale robotic systems. Elsevier, 2012. ISBN: 9781455778911
  6. M Kwiatkowska, G Norman, D Parker, O Tymchyshyn, JK Heath, EA Gaffney, Simulation And Verification For Computational Modelling Of Signalling Pathways, Proceedings of the 2006 Winter Simulation Conference, L. F. Perrone, F. P. Wieland, J. Liu, B. G. Lawson, D. M. Nicol, and R. M. Fujimoto, eds, (2006)
  7. JR Blake, EA Gaffney, Modelling aspects of tracer transport in muco-ciliary flows, In Cilia, Mucus and Mucociliary Interactions, 26, M Salathe (Editor), New York, Marcel Dekker, 291-302. (2001).




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