Physics of the Heart - Michael Colman

Ageing RyR dataset (rat)

This contains super reoslution imaging datasets for RyR cluster properties in rat ventricular myocytes aged 6, 18 and 24-months.
It also includes our simple, custom Python tools for quantifying and analysing the properties of RyR cluster daya.

Spark-population CRU model.

This contains the spark-population CRU model, implemented into the Grandi atrial, Grandi ventricular, and CRN atrial cell models.
This is an isolated version of single cell models only and focussed specifically on the spark-population model.

The Multi-scale Cardiac Simulation Framework.

This contains implementations for all recent publications as well as general further functionality. Novel components include:

Models of spatio-temporal, stochastic sub-cellular calcium dynamics.
Model reduction approaches for efficient modelling of spontaneous calcium release
Human atrial cell models
Update 01/2022: Sub-cellular heterogeneity controls and maps added
Update 09/2023: Network model of intercellular coupling added, as well as some further functionality for Spontaneous Release Functions

Simple, network model of diffusion.

This contains an isolated and simple version of the network model of diffusion presented in: ‘A simple approach for image-based modelling of the heart that enables robust simulation of highly heterogeneous electrical excitation’ Sci. Rep., vol. 13, no. 1, Art. no. 1, Sep. 2023, doi: 10.1038/s41598-023-39244-w

Human atrial cell models.

This contains the novel and previously published models associated with publication "Description of the human atrial action potential derived from a single, congruent data source: Novel computational models for integrated experimental-numerical study of atrial arrhythmia mechanisms" Front. Physiol 2018.

Update 06/2019: New version of the code also includes tissue models.

Structural model of spatio-temporal calcium handling.

This contains the novel model assocaited with the publication: "A Computational Model of Spatio-Temporal Cardiac Intracellular Calcium Handling with Realistic Structure and Spatial Flux Distribution from Sarcoplasmic Reticulum and T-tubules Reconstructions" PLOS Comp. Biol 2018.

Note: Yet to be updated into new code format and included in the full MSCSF. Keep posted!

Sub-cellular heterogeneity analysis toolkit.

This contains the toolkit developed for the analysis of sub-cellular heterogeneity, as presented in the following studies: "Increased SERCA2a sub-cellular heterogeneity in right-ventricular heart failure inhibits excitation-contraction coupling and modulates arrhythmogenic dynamics" Philosophical Transactions of the Royal Society B: Biological Sciences. ISSN 0962-8436 (In Press), and "Multi-scale approaches for the simulation of cardiac electrophysiology: I - sub-cellular and stochastic calcium dynamics from cell to organ" Methods (Elsevier) 2021 Volume 185, January 2021, Pages 49-59

This toolkit is designed to be compatible with the MSCSF, and specific heterogeneity maps associated with the above studies are provided with that code download.