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Updating model tree
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@MichaelClerx
MichaelClerx committed Aug 4, 2024
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Expand Up @@ -31,6 +31,32 @@ Models are omitted if they contain spatial propagation, either in larger tissues
Whether or not a modification counts as a "model" is entirely subjective.
No strict criteria are used here, I just tried to make it useful.

See also:
- [Noble, Garny, Noble (2012) How the Hodgkin-Huxley equations inspired the Cardiac Physiome Project](https://doi.org/10.1113/jphysiol.2011.224238)
- [Amuzescu, Airini et al., Radu (2021) Evolution of mathematical models of cardiomyocyte electrophysiology](https://doi.org/10.1016/j.mbs.2021.108567)

Some reductions:
- Fitzugh 1961 reduces HH to a "Bonhoeffer-Van der Pol" model
- Nagumo 1962 makes Fitzhugh 1961 suitable for propagation
- Morris & Lecar 1981 create a reduced HH-like model of a Ca-driven AP
- Winfree 1991 provides a great overview of spiral wave models, including Belousov-Zhabotinsky
- Varghese 1993 reduces DiFrancesco 1985
- Aliev & Panfilov 1996
- Fenton & Karma 1998 derive an FN-like model
- Bernus 2002 reduces Priebe 1998
- Mitchell & Schaeffer 2003
- Ten Tusscher 2006b reduces Ten Tusscher 2006
- Bueno-Orovio 2008 adds an equation to Fenton 1998
- Tran 2009 reduces Luo 1991
- Balakrishnan 2015 develop a reduced whole heart model
- Gray & Pathmanathan 2016 create a minimal but fully parametrisable AP model
- Corrado 2017, Carrado & Niederer 2016, Corrado 2018
- ...

Some CaRU-based models:
- Greenstein 2002
- Tanskanen 2005

## 1962 Noble mPf
Base: HH1952
| [Paper](https://doi.org/10.1113/jphysiol.1962.sp006849) Noble (1962) A Modification of the Hodgkin-Huxley Equations Applicable to Purkinje Fibre Action and Pacemaker Potentials
Expand Down Expand Up @@ -166,6 +192,7 @@ Modifications:
- INaK new formulation
- Rescaled gK1
- ...
- CICR

## 1995 Zeng GV
Base: [1994 Luo GV](#1994-luo-gv)
Expand Down Expand Up @@ -200,6 +227,9 @@ Base: Mostly new?
Base: [Luo 1994](#1994-luo-gv)
| [Paper](https://doi.org/10.1016/s0006-3495(98)77832-4) Jafri, Rice, Winslow (1998) Cardiac Ca2 Dynamics; The Roles of Ryanodine Receptor Adaptation and Sarcoplasmic Reticulum Load

Modifications:
- Elements of Keizer & Levine 1996 Ca-induced Ca release model

## 1998 Noble GV
Base: [Noble 1991](#1991-noble-gv)
| Code for this paper is inside "Oxsoft Heart"
Expand Down Expand Up @@ -232,6 +262,8 @@ Base: [Jafri 1998](#1998-jafri-gv)
| [Paper](https://doi.org/10.1016/s0006-3495(00)76783-x) Faber, Rudy (2000) Action Potential and Contractility in [Na+]i Overloaded Cardiac Myocytes

## 2000 Greenstein CV
Base: [Winslow 1999](#1999-winslow-cv)
| [Paper](https://doi.org/10.1161/01.res.87.11.1026) Greenstein, Wu et al., Winslow (2000) Role of the calcium-independent transient outward current Ito1 in shaping action potential morphology and duration

## 2000 Ramirez CA
Base: [Courtemanche 1998](#1998-courtemanche-ha)
Expand Down Expand Up @@ -261,7 +293,6 @@ Modifications:

## 2002 Fenton mV
## 2002 Fox CV
## 2002 Greenstein CV

## 2002 Kneller CA
Base: [Ramirez 2000](#2000-ramirez-ca)
Expand Down Expand Up @@ -388,6 +419,13 @@ Bits:
## 2005 Michailova CV
## 2006 Cortassa mV
## 2006 Fink HV

## 2006 Greenstein CV
Base: [Greenstein 2000](#2000-greenstein-cv) (via Greenstein 2002 local control model)

Modifications:
- Ensemble behaviour of CaRUs using Hinch 2004 approximation

## 2006 Iribe GV
## 2006 Mangoni MS
## 2006 Pasek LV
Expand Down Expand Up @@ -424,6 +462,10 @@ Known as: Faber-Rudy
Base: [Shannon 2004](#2004-shannon-rv)
| [Paper](https://doi.org/10.1529/biophysj.107.114868) Grandi, Puglisi et al., Bers (2007) Simulation of Ca-calmodulin-dependent protein kinase II on rabbit ventricular myocyte ion currents and action potentials

## 2007 Iyer HV
Base: [Iyer 2004](#2004-iyer-hv)
| [Paper](https://doi.org/10.1161/01.res.0000258468.31815.42) Iyer, Hajjar, Armoundas (2007) Mechanisms of Abnormal Calcium Homeostasis in Mutations Responsible for Catecholaminergic Polymorphic Ventricular Tachycardia

## 2007 Livshitz CV
**Included**
| Base: [Hund 2004](#2004-hund-cv)
Expand Down Expand Up @@ -596,6 +638,13 @@ Base: [Decker 2009](#2009-decker-cv)

Known as: PRd

## 2011 Moreno HV
Base: [Ten Tusscher 2006](#2006-ten-tusscher-hv)
| [Paper](https://doi.org/10.1126/scitranslmed.3002588) Moreno, Zhu et al., Clancy (2011) A computational model to predict the effects of class I anti-arrhythmic drugs on ventricular rhythms

Modifications:
- New INa model (new WT and drug-bound)

## 2011 O'Hara HV
**Included**
| Base: [Hund 2004](#2004-hund-cv)
Expand Down Expand Up @@ -650,6 +699,17 @@ Modifications:
- Replaced INa with Courtemanche 1998 one
- Modified IK1 (changed gK1 and a)

## Asakura 2014 HV
Base: [Grandi 2010](#2010-grandi-hv), CaRU reduction used by [Greenstein 2006](#2006-greenstein-cv)
| [Paper](https://doi.org/10.1016/j.pbiomolbio.2014.08.008) Asakura, Cha et al., Noma (2014) EAD and DAD mechanisms analyzed by developing a new human ventricular cell model

Modifications:
- Contraction from Negroni and Lascano, 2008
- Hinch 2004 approximation for LCC-RyR coupling
- INa and INaL: mode-switching causes fixed fractions INa and INaL "mode"
- IK1 from Ishihara & Yan 2007 and Yan & Ishihara 2005
- ...

## 2014 Chang HA
Base: [Grandi 2011](#2011-grandi-pandit-voigt-ha)
| [Original OpenCARP code](https://doi.org/10.6084/m9.figshare.1201512)
Expand All @@ -670,7 +730,8 @@ Base: [Yang 2012 mouse](2012-yang-mv)
| [Paper](https://doi.org/10.1016/j.yjmcc.2013.11.001) Yang, Polanowska-Grabowska et al., Saucerman (2014) PKA catalytic subunit compartmentation regulates contractile and hypertrophic responses to beta-adrenergic signaling

## 2015 Himeno HV
Base: Several! Interesting one to look at
Base: [Asakura 2014](#2014-asakura-hv)
Not sure if simulating individual CaRUs or not!

## 2015 Negroni RV
Base: [Shannon 2004](#2004-shannon-rv), [Soltis 2010](#2010-soltis-rv)
Expand Down Expand Up @@ -715,6 +776,10 @@ Modifications:

## 2016 Varela CA

## Aguilar 2017 A
Base: [Courtemanche 1998](#1998-courtemanche-ha)
| [Paper](https://doi.org/) Aguilar, Feng et al., Nattel (2017) Rate-dependent role of IKur in human atrial repolarization and atrial fibrillation maintenance

## 2017 Bartos RV
Base: [Negroni 2015](#2015-negroni-rv)
| [Original matlab code](https://github.com/drgrandilab/Bartos-et-al-2017-Rabbit-Ventricular-Model-with-Updated-IKs)
Expand Down Expand Up @@ -827,19 +892,31 @@ Base: [Dutta 2017](#2017-dutta-hv)
Known as: BPS2020

Modifications:
- New ICaL formulation
- New ICaL formulation (from Passini 2012 CINC)
- ...

## 2020 Paci Hi
**Included**
| Base: [Paci 2018](#2018-paci-hi)
| [Paper](https://doi.org/10.1016/j.bpj.2020.03.018) Paci, Passini et al., Entcheva (2020) All-Optical Electrophysiology Refines Populations of In Silico Human iPSC-CMs for Drug Evaluation

## 2020 Sengul Ayan LV
Base: [Jafri 1998](#1998-jafri-gv) but mostly new
| [Paper]() Sengul Ayan, Sircan et al., Yaras (2020) Mathematical model of the ventricular action potential and effects of isoproterenol-induced cardiac hypertrophy in rats

Modifications:
- 5 parameter reformulation of most currents

## 2020 Tomek HV
Base: [Tomek 2019](#2019-tomek-hv)
| [Original Matlab and official CellML](https://github.com/jtmff/torord)
| [Paper](https://doi.org/10.1101/2020.06.01.127043) Tomek, Bueno-Orovio, Rodriguez (2020) ToR-ORd-dynCl; an update of the ToR-ORd model of human ventricular cardiomyocyte with dynamic intracellular chloride

Known as: ToR-ORd-dynCl

Modifications:
- Chloride homeostasis

## 2020 Trovato HP
**Included**
| Base: [O'Hara 2011](#2011-ohara-hv), [Li 2011](#2011-li-cp)
Expand Down Expand Up @@ -894,6 +971,11 @@ Modifications:
- Added Land 2017 contraction model
- ...

## 2022 Doste HV
Base: [Tomek 2020](#2020-tomek-hv), [Heijman 2011](#2011-heijman-cv)
| [Original matlab code](https://github.com/rdoste/ToR-ORd-BARS)
| [Paper](https://doi.org/10.1016/j.yjmcc.2022.08.361) Doste, Coppini, Bueno-Orovio (2022) Remodelling of potassium currents underlies arrhythmic action potential prolongation under beta-adrenergic stimulation in hypertrophic cardiomyopathy

## 2022 Kohjitani Hi
Base: [Himeno 2015](#2015-himeno-hv)
| [Paper](https://doi.org/10.1038/s41598-022-23398-0) Kohjitani, Koda et al., Kimura (2022) Gradient-based parameter optimization method to determine membrane ionic current composition in human induced pluripotent stem cell-derived cardiomyocytes
Expand Down Expand Up @@ -926,12 +1008,3 @@ Base: [Morotti 2017](#2016-morotti-ha)
| [Original C++ code](https://github.com/drgrandilab/Ni-et-al-2023-Human-Atrial-Signaling-Model)
| [Paper](https://doi.org/10.1093/cvr/cvad118) Ni, Morotti et al., Grandi (2023) Integrative human atrial modelling unravels interactive PKA and CaMKII signalling as key determinants of atrial arrhythmogenesis









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