Chaste

Chaste: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library. Recent work has described the software engineering and computational infrastructure that has been set up as part of the Cancer, Heart and Soft Tissue Environment (Chaste) project. Chaste is an open source software package that currently has heart and cancer modelling functionality. This software has been written using a programming paradigm imported from the commercial sector and has resulted in a code that has been subject to a far more rigorous testing procedure than that is usual in this field. In this paper, we explain how new functionality may be incorporated into Chaste. Whiteley has developed a numerical algorithm for solving the bidomain equations that uses the multi-scale (MS) nature of the physiology modelled to enhance computational efficiency. Using a simple geometry in two dimensions and a purpose-built code, this algorithm was reported to give an increase in computational efficiency of more than two orders of magnitude. In this paper, we begin by reviewing numerical methods currently in use for solving the bidomain equations, explaining how these methods may be developed to use the MS algorithm discussed above. We then demonstrate the use of this algorithm within the Chaste framework for solving the monodomain and bidomain equations in a three-dimensional realistic heart geometry. Finally, we discuss how Chaste may be developed to include new physiological functionality-such as modelling a beating heart and fluid flow in the heart-and how new algorithms aimed at increasing the efficiency of the code may be incorporated.


References in zbMATH (referenced in 50 articles , 2 standard articles )

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  1. Hamis, Sara; Yates, James; Chaplain, Mark A. J.; Powathil, Gibin G.: Targeting cellular DNA damage responses in cancer: an in vitro-calibrated agent-based model simulating monolayer and spheroid treatment responses to ATR-inhibiting drugs (2021)
  2. Miller, Claire; Crampin, Edmund; Osborne, James M.: Maintaining the proliferative cell niche in multicellular models of epithelia (2021)
  3. Sophie Theis, Magali Suzanne, Guillaume Gay: Tyssue: an epithelium simulation library (2021) not zbMATH
  4. Cooper et al.: Chaste: Cancer, Heart and Soft Tissue Environment (2020) not zbMATH
  5. Mathias, Sonja; Coulier, Adrien; Bouchnita, Anass; Hellander, Andreas: Impact of force function formulations on the numerical simulation of centre-based models (2020)
  6. Pravdin, Sergei F.; Epanchintsev, Timofei I.; Nezlobinskii, Timur V.; Panfilov, Alexander V.: Induced drift of scroll waves in the Aliev-Panfilov model and in an axisymmetric heart left ventricle (2020)
  7. Bouchnita, Anass; Hellander, Stefan; Hellander, Andreas: A 3D multiscale model to explore the role of EGFR overexpression in tumourigenesis (2019)
  8. Cervi, Jessica; Spiteri, Raymond J.: A comparison of fourth-order operator splitting methods for cardiac simulations (2019)
  9. Chernyshenko, Alexey Y.; Danilov, A. A.; Vassilevski, Y. V.: Numerical simulations for cardiac electrophysiology problems (2019)
  10. Farrell, P. E.; Hake, J. E.; Funke, S. W.; Rognes, M. E.: Automated adjoints of coupled PDE-ODE systems (2019)
  11. Green, Kevin R.; Bohn, Tanner A.; Spiteri, Raymond J.: Direct function evaluation versus lookup tables: when to use which? (2019)
  12. Jiang, J.; Garikipati, K.; Rudraraju, S.: A diffuse interface framework for modeling the evolution of multi-cell aggregates as a soft packing problem driven by the growth and division of cells (2019)
  13. P. J., Murray; F. A., Carrieri; J. K., Dale: Cell cycle regulation of oscillations yields coupling of growth and form in a computational model of the presomitic mesoderm (2019)
  14. Abidi, Yassine; Bellassoued, Mourad; Mahjoub, Moncef; Zemzemi, Nejib: On the identification of multiple space dependent ionic parameters in cardiac electrophysiology modelling (2018)
  15. Almet, Axel A.; Hughes, Barry D.; Landman, Kerry A.; Näthke, Inke S.; Osborne, James M.: A multicellular model of intestinal crypt buckling and fission (2018)
  16. Cervi, Jessica; Spiteri, Raymond J.: High-order operator splitting for the bidomain and monodomain models (2018)
  17. Emerick, Brooks; Schleiniger, Gilberto; Boman, Bruce M.: Multi-scale modeling of APC and (\beta)-catenin regulation in the human colonic crypt (2018)
  18. Hurtado, Daniel E.; Rojas, Guillermo: Non-conforming finite-element formulation for cardiac electrophysiology: an effective approach to reduce the computation time of heart simulations without compromising accuracy (2018)
  19. Kursawe, Jochen; Baker, Ruth E.; Fletcher, Alexander G.: Approximate Bayesian computation reveals the importance of repeated measurements for parameterising cell-based models of growing tissues (2018)
  20. Razumov, Artem A.; Ushenin, Konstantin S.; Butova, Ksenia A.; Solovyova, Olga E.: The study of the influence of heart ventricular wall thickness on pseudo-ECG (2018)

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Further publications can be found at: http://www.cs.ox.ac.uk/chaste/publications.html