Pras Pathmanathan
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Dr
Pras
Pathmanathan
Research Officer
pras@cs.ox.ac.uk
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Interests
I am a jointly a researcher in the Computational Biology Group, a multi-disciplinary group based in the Department of Computer Science, and a research fellow at the Center for Devices and Radiological Health, Food and Drug Administration (FDA). As of May 2012 I am based at the FDA just outside of Washington DC.
I work in the modelling of biological function, generally at the cellular or organ levels. My main research interests are modelling cardiac electro-physiological activity, cardiac mechanical activity and soft-tissue mechanics in general, mostly from a numerical methods and mathematical modelling view, and with extensive use of nonlinear elasticity theory and the finite element method. I am also involved in work on discrete cellular modelling (with applications in advancing understanding of the onset of cancer) and lung modelling. I am heavily involved with the Chaste (Cancer, Heart and Soft Tissue Environment) project, in which we have developed a powerful, efficient, general and reliable tool for solving computationally-demanding problems in biological modelling. I am also an Associate Fellow in the 2020 Science Program.
Numerical Methods and Object-Oriented Design:
This 6 hour course, run summer 2011, describes numerical schemes for solving ODEs and PDEs, and discusses how to implement solvers in an object-oriented manner. General designs are described, as well as (slightly simplified) descriptions of the designs used in Chaste. Solid mechanics problems are discussed in the latter lectures.
All lectures - all lectures (no transitions) - lecture 1 - lecture 2 - lecture 3 - lecture 4 - lecture 5 - lecture 6
Object-Oriented Scientific Computing:
This 4 hour course, run summer 2012 in the University of Maryland, Dept of Bioengineering, is related but different to the above. It describes numerical schemes for solving ODEs and PDEs, how to implement solvers in an object-oriented manner, and introduces some real-world applications of numerical solvers.
Lecture 1 - Lecture 2 - Lecture 3 - Lecture 4 - Applications - Biomechanics applications - Example code
Publications: see here
for a more up-to-date list than that given below.
Selected Publications
| Chaste: an open source C++ library for computational physiology and biology G.R. Mirams‚ C.J. Arthurs‚ M.O. Bernabeu‚ R. Bordas‚ J. Cooper‚ A. Corrias‚ Y. Davit‚ S−J. Dunn‚ A.G. Fletcher‚ D.G. Harvey‚ M.E. Marsh‚ J. M. Osborne‚ P. Pathmanathan‚ J. Pitt−Francis‚ J. Southern‚ N. Zemzemi and D.J. Gavaghan In PLoS Computational Biology. Vol. 9. No. 3. Pages e1002970. 2013. Details | BibTeX | DOI (10.1371/journal.pcbi.1002970) | Link |
| Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials N Zemzemi‚ MO Bernabeu‚ J Saiz‚ J Cooper‚ P Pathmanathan‚ GR Mirams‚ J Pitt−Francis and B Rodriguez In British Journal of Pharmacology. Vol. 168. No. 3. Pages 718−733. 2013. |
| Computational modelling of cardiac electro−physiology: explanation of the variability of results from different numerical solvers P. Pathmanathan‚ M. Bernabeu‚ S. Niederer‚ D. Gavaghan and D. Kay In Int. J. Numerical Methods in Biomedical Engineering. Vol. 28. No. 8. Pages 890−903. 2012. |
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Chaste | |
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