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 42 articles , 1 standard article )

Showing results 1 to 20 of 42.
Sorted by year (citations)

1 2 3 next

  1. Bouchnita, Anass; Hellander, Stefan; Hellander, Andreas: A 3D multiscale model to explore the role of EGFR overexpression in tumourigenesis (2019)
  2. Cervi, Jessica; Spiteri, Raymond J.: A comparison of fourth-order operator splitting methods for cardiac simulations (2019)
  3. Chernyshenko, Alexey Y.; Danilov, A. A.; Vassilevski, Y. V.: Numerical simulations for cardiac electrophysiology problems (2019)
  4. Farrell, P. E.; Hake, J. E.; Funke, S. W.; Rognes, M. E.: Automated adjoints of coupled PDE-ODE systems (2019)
  5. Green, Kevin R.; Bohn, Tanner A.; Spiteri, Raymond J.: Direct function evaluation versus lookup tables: when to use which? (2019)
  6. 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)
  7. 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)
  8. 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)
  9. Cervi, Jessica; Spiteri, Raymond J.: High-order operator splitting for the bidomain and monodomain models (2018)
  10. Emerick, Brooks; Schleiniger, Gilberto; Boman, Bruce M.: Multi-scale modeling of APC and (\beta)-catenin regulation in the human colonic crypt (2018)
  11. 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)
  12. 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)
  13. Yan, Huaming; Konstorum, Anna; Lowengrub, John S.: Three-dimensional spatiotemporal modeling of colon cancer organoids reveals that multimodal control of stem cell self-renewal is a critical determinant of size and shape in early stages of tumor growth (2018)
  14. Cooper, Fergus R.; Baker, Ruth E.; Fletcher, Alexander G.: Numerical analysis of the immersed boundary method for cell-based simulation (2017)
  15. Coudière, Yves; Turpault, Rodolphe: Very high order finite volume methods for cardiac electrophysiology (2017)
  16. Emerick, Brooks; Schleiniger, Gilberto; Boman, Bruce M.: A kinetic model to study the regulation of (\beta)-catenin, APC, and axin in the human colonic crypt (2017)
  17. Quarteroni, Alfio; Lassila, Toni; Rossi, Simone; Ruiz-Baier, Ricardo: Integrated heart -- coupling multiscale and multiphysics models for the simulation of the cardiac function (2017)
  18. Shoffner, S. K.; Schnell, Santiago: Approaches for the estimation of timescales in nonlinear dynamical systems: timescale separation in enzyme kinetics as a case study (2017)
  19. Campos, J. O.; Oliveira, R. S.; dos Santos, R. W.; Rocha, B. M.: Lattice Boltzmann method for parallel simulations of cardiac electrophysiology using GPUs (2016)
  20. Corrado, Cesare; Lassoued, Jamila; Mahjoub, Moncef; Zemzemi, Néjib: Stability analysis of the POD reduced order method for solving the bidomain model in cardiac electrophysiology (2016)

1 2 3 next

Further publications can be found at: