Post-Doctoral Research Assistant in the Wolfson Centre for Mathematical Biology (WCMB).
+44 1865 615162
University of Oxford
Andrew Wiles Building
Radcliffe Observatory Quarter
Microvessel Chaste: An Open Library for Spatial Modeling of Vascularized Tissues.
Biophysical journal issue 9 volume 112 page 1767-1772 (May 2017)
Predicting the Influence of Microvascular Structure On Tumor Response to Radiotherapy.
IEEE transactions on bio-medical engineering issue 3 volume 64 page 504-511 (March 2017)
Mechanical Cell-Cell Communication in Fibrous Networks: The Importance of Network Geometry.
Bulletin of mathematical biology issue 3 volume 79 page 498-524 (March 2017)
Simulating Tumour Vasculature at Multiple Scales
2014 6TH INTERNATIONAL ADVANCED RESEARCH WORKSHOP ON IN SILICO ONCOLOGY AND CANCER INVESTIGATION (IARWISOCI) (2014) Full text available
I am interested in medical device design and the pathophysiology of small blood vessels in cancer. I develop and apply high performance scientific software to solve challenging 3D, multi-physics problems in these areas. Addressing problems of interest usually requires a range of methods including:
- non-linear solid mechanics of metals (including plasticity, damage and micro-mechanics), synthetic and bio-polymers, and soft tissues (with anisotropy)
- complex contact problems involving large sliding contact with membranes and shells
- agent based modelling of biological cells and blood vessels
- numerical solution of reaction-diffusion systems for chemical (nutrient and drug) transport
- 3D image segmentation and particle tracking
- experiment design and global optimization
- programming for high performance computing (in particular distributed memory parallelism with MPI)
I have recently developed an open source software library for modelling vascualrized tissues https://jmsgrogan.github.io/MicrovesselChaste/ and contribute to the Chaste library for soft tissue modelling http://www.cs.ox.ac.uk/chaste/. I primarily use C++ and Python for development and have experience of all major stages of developing and releasing a (reasonably) large software project, including testing (CxxTest, Travis CI and ctest), deployment (Docker, conda and Debian packaging), cross-platform builds (cmake), version control (git, Github) and documentation (Doxygen, Sphinx, Jupyter Notebooks, web template engines). I have experience building simple, interactive 3D user interfaces for web (XTK, three.js) and standalone (VTK and wxPython) applications and have developed a framework for automated Python wrapping of a large (500k-1 Million loc) C++ codebase (a custom solution based on Boost-Python and Py++), resulting in significant usability improvements with minimal overhead.
Prizes, Awards, and Scholarships:
• 1st place in the Mathematics category in the STEM for Britain competition for early career re-
• 2nd best paper in the established researcher category, RAMI bioengineering section conference, 2012.
• RAMI bronze medal for best overall paper, RAMI bioengineering section conference, 2011.
• Best paper, Sir Bernard Crossland Symposium, 2011.
• Best presentation, NUI Galway CoEI research day, 2010 and 2011.
• Shortlisted for the Young Investigator in Biomechanics award at the Endocardiovascular Biome-
chanics Research (EBR) Congress, Marseille, France, May 2010.
• Shortlisted for the Innovative Student Engineer Ireland award (Top 5) and Best Mechanical Engi-
neering Graduate in the UK and Ireland (Top 3) at the SET awards 2009.
• Best final year project, Engineers Ireland West division, 2009.
• Frederic Barnes Waldron prize for top mechanical engineering graduate and MCS prize for best final
year project in mechanical engineering, NUI Galway, 2009.
Major / Recent Publications:
- J.A. Grogan, A.J. Connor, B. Markelc, R.J. Muschel, P.K. Maini, H.M. Byrne, J.M. Pitt-Francis, Microvessel Chaste: an open library for spatial modeling of vascularized tissues, Biophysical Journal, 112(9):1767–1772, 2017.
- J.A. Grogan, B. Markelc, A.J. Connor, R.J. Muschel, J.M. Pitt-Franices, P.K. Maini, H.M. Byrne, Predicting the influence of microvascular structure On tumour response to radiotherapy, IEEE Transactions on Biomedical Engineering, 64(3):504-511, 2017.
- D.L. Humphries, J.A. Grogan, E.A. Gaffney, Mechanical cell?cell communication in fibrous net-
works: the importance of network geometry, Bulletin of Mathematical Biology, 79(3):498–524, 2017.
- E.L. Boland, J.A. Grogan, C. Conway, P.E. McHugh, Computer Simulation of the mechanical behaviour of implanted biodegradable stents in a remodelling artery, JOM: The Journal of The Minerals, Metals and Materials Society (TMS), 68:1198–1203, 2016.
- J.A. Grogan, S.B. Leen, P.E. McHugh, Computational micromechanics of bioabsorbable magnesium stents, Journal of Mechanical Behaviour of Biomedical Materials, 34:93-105, 2014.
- J.A. Grogan, S.B. Leen, P.E. McHugh, A physical corrosion model for bioabsorbable metallic stents, Acta Biomaterialia, In Press, DOI:10.1016/j.actbio.2013.12.059, 2014.
- J.A. Grogan, D. Gastaldi, M. Castelletti, F. Migliavacca, G. Dubini, P.E. McHugh, A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments, Review of Scientific Instruments, 34:094301, 2013.
- J.A. Grogan, S.B. Leen, P.E. McHugh, Optimizing the design of a bioabsorbable metal stent using computer simulation methods, Biomaterials, 34:8049-60, 2013.
- E. Birmingham, J.A. Grogan, G.L. Niebur, L.M. McNamara, P.E. McHugh, Computational modelling of the mechanics of trabecular bone and marrow using fluid structure interaction techniques, Annals of Biomedical Engineering, 41:814-26, 2013.
- J.A. Grogan, S.B. Leen, P.E. McHugh, Influence of statistical size effects on the plastic deformation of coronary stents, Journal of Mechanical Behaviour of Biomedical Materials, 20:61-76, 2013.
- J.A. Grogan, S.B. Leen, and P.E. McHugh. Comparing coronary stent material performance on a common geometric platform through simulated benchtesting, Journal of Mechanical Behaviour of Biomedical Materials, 12:129-138, 2012.
- J.A. Grogan, B.J. O'Brien, S.B. Leen, P.E. McHugh, A corrosion model for bioabsorbable metallic stents, Acta Biomaterialia, 7:3523-33, 2011.
- F. Harewood, J. Grogan, P. McHugh, A multiscale approach to failure assessment in deployment for cardiovascular stents, Journal of Multiscale Modelling, 2:1-22, 2010.