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. 2017 May 3;12(5):e0172292.
doi: 10.1371/journal.pone.0172292. eCollection 2017.

BeatBox-HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology

Mario Antonioletti  1 , Vadim N Biktashev  2   3 , Adrian Jackson  1 , Sanjay R Kharche  2   4 , Tomas Stary  2 , Irina V Biktasheva  2   5
Affiliations

BeatBox-HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology

Mario Antonioletti et al. PLoS One. .

Abstract

The BeatBox simulation environment combines flexible script language user interface with the robust computational tools, in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level, so that cell excitation, tissue/anatomy models, stimulation protocols may be included into a BeatBox script, and simulation run either sequentially or in parallel (MPI) without re-compilation. BeatBox is a free software written in C language to be run on a Unix-based platform. It provides the whole spectrum of multi scale tissue modelling from 0-dimensional individual cell simulation, 1-dimensional fibre, 2-dimensional sheet and 3-dimensional slab of tissue, up to anatomically realistic whole heart simulations, with run time measurements including cardiac re-entry tip/filament tracing, ECG, local/global samples of any variables, etc. BeatBox solvers, cell, and tissue/anatomy models repositories are extended via robust and flexible interfaces, thus providing an open framework for new developments in the field. In this paper we give an overview of the BeatBox current state, together with a description of the main computational methods and MPI parallelisation approaches.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. BeatBox formalism paradigm [7].
Fig 2
Fig 2. BeatBox “Ring of devices”.
The ring of devices set up by sample.bbs script (see Listing 2 in the Appendix).
Fig 3
Fig 3. Numerical convergence of the solution of the problem Eqs (21)–(25).
Slope lines are with slopes 1, 2 and best fits with slopes 1.564 for L∞, and 1.719 for L2.
Fig 4
Fig 4. Numerical convergence of the solution of the problem Eqs (30)–(36).
Slope lines: slope 2 (black) and best fits with slopes 2.009 for L∞, and 1.9889 for L2.
Fig 5
Fig 5. Schematic of the domain partitioning in MPI implementation of BeatBox.
Solid circles represent nodes on which actual computations are done, empty circles are the “halo” points, the rectangles denote the exchange buffers and the solid black line represents the boundary of an irregular computational domain (excitable tissue).
Fig 6
Fig 6. Log-log plots: The wall clock time per one time step in the simulation job, vs the number of cores.
(a) Full box; (b) Rabbit ventricle geometry, (c) Human atrium geometry. In all plots, “with ppm” stands for performance including file output via ppmout device, “without ppm” stands for pure computations, and “ideal” is the perfect-scaling extrapolation of the performance achieved on the smallest number of cores.
Fig 7
Fig 7. Scroll wave generation from ischaemic border zone.
Generation of a scroll wave out of microscopic re-entries in excitable medium with random, space- and time-dependent distribution of parameters, modelling movement of ischaemic border zone during reperfusion [69]; Beeler-Reuter [50] kinetics.
Fig 8
Fig 8. Drift along a thickness step.
Drift of scroll wave along a thickness step [67], FitzHugh-Nagumo kinetics.
Fig 9
Fig 9. Drift in a realistic human atrium geometry.
Drift of scroll wave in a realistic human atrium geometry [61], Courtemanche et al. [47] kinetics. (a) Trajectories of spontaneous drift, caused purely by the anatomy features [62]; (b) Trajectories of resonant drift, caused by feedback-controlled electrical stimulation [70].
Fig 10
Fig 10. Scroll waves of excitation in a DT-MRI based model of human foetal heart.
A snapshot of excitation pattern with scroll wave filaments in human foetal heart anatomy [71], FitzHugh-Nagumo kinetics. The surface of the heart is shown semitransparent, colour-coded depending on the values of the u and v variable as shown in the colourbox on the right. The yellow lines are the scroll filaments inside the heart. The human foetal heart DT-MRI data sets used in the BeatBox simulation presented here were provided by E. Pervolaraki et al. [71]. The simulation shown is part of the ongoing project on cardiac re-entry dynamics in DT-MRI based model of human foetal heart. The full paper by R.A. Anderson, F.C. Wen, A.V. Holden, E. Pervolaraki, and I.V. Biktasheva is in preparation.
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Grants and funding

Engineering and Physical Sciences Research Council (UK), https://www.epsrc.ac.uk/, supported the recent HPC development of the BeatBox cardiac simulation environment, including design, data collection and analysis, submission of the manuscript; grant number EP/I029664, VNB, IVB. Engineering and Physical Sciences Research Council (UK), https://www.epsrc.ac.uk/, supported development of the BeatBox cardiac simulation environment, including design, data collection and analysis, submission of the manuscript; grant number EP/N014391/1, VNB. Engineering and Physical Sciences Research Council (UK), https://www.epsrc.ac.uk/, supported development of the BeatBox cardiac simulation environment, including design, data collection and analysis, submission of the manuscript; grant number EP/P008690/1, IVB.

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