Cells

Cells contains the cell objects which encompass mathematicals and code of the electrophysiological cardiomyocycte cell models. Each model is derived from a publication where the mathmatical equations are presented along with the results and validation for the model. Typically, the easiest way to create a cell object is through the PyLongQt.cellMap dictionary, or through Protocol.setCellByName().

class PyLongQt.Cells.Br04

Mouse Ventricular (Bondarenko 2004)

Bondarenko, V. E. “Computer Model of Action Potential of Mouse Ventricular

Myocytes.” AJP: Heart and Circulatory Physiology, vol. 287, no. 3, 2004, pp.

H1378–403, doi:10.1152/ajpheart.00185.2003.

class PyLongQt.Cells.Cell

Base class for cells built on py:class:CellKernel. Provides selections of variables & constants to be tracked and saved during the simulation

property constantSelection

The selection of constants to be tracked during the simulation

property variableSelection

The selection of variables to be tracked during the simulation

class PyLongQt.Cells.CellKernel

Base class for all cell objects. This class provides the interface for interacting and manipulating cells. Further, the Cell class adds additional functionallity to cells relevant to i/o

property ACap

Capacitive cell surface area

property AGeo

Geometric cell surface area

property Cm

Cell capacitance (uF/cm^2)

property FDAY

Faraday’s constant (C/mol)

property RGAS

R gass constant

property Rcg

Ratio of capacitive to geometric area

property Rmyo

Myoplasmic resistivity

property TEMP

Cell temperature (K)

property Vcell

Cell volume ()

property Vmyo

Cell Myoplasmic volume (uL)

property apTime

What is this

property cellLength

Cell length (cm). Cells are modeled as cylinders.

property cellRadius

Cell radius (cm). Cells are modeled as cylinders.

clone(self: PyLongQt._PyLongQt.Cells.CellKernel) → PyLongQt._PyLongQt.Cells.CellKernel

Create a copy/clone of the cell

property dVdt

Change in voltage over change in time from the last timestep

property dt

The current timestep (ms)

property dtmax

Maximum timestep size (ms)

property dtmed

Medium timestep size (ms)

property dtmin

Minimum timestep size (ms)

property dvcut

What is this(mV/ms)

externalStim(self: PyLongQt._PyLongQt.Cells.CellKernel, stimulus: float) → None

Apply a stimulus to the cell :stimulus: The current (pA/pF) to apply to the cell. Will be applied for only the timestep when it is called.

getOption(self: PyLongQt._PyLongQt.Cells.CellKernel, name: str) → bool

Get the status of one of the cells options.

name

The name of the option

property iCat

The total calcium current (pA/pF)

property iKt

The total potassium current (pA/pF)

property iNat

Total sodium current (pA/pF)

property iTot

The total current (pA/pF)

property iTotold

The total current from the previous timestep

optionsMap(self: PyLongQt._PyLongQt.Cells.CellKernel) → Dict[str, bool]

Options which modify the cell model. The options map contains all possible options

and their statuses. ..Note: Some options may be mutually exclusive.

property pars

The constants for the cell. Constants are values which will not change throughout the simulation. Some of these values can be set using PyLongQt.Protocols.Protocol.pvars. Different cell models will have different constants.

setOption(self: PyLongQt._PyLongQt.Cells.CellKernel, name: str, value: bool) → None

Set one of the cells options.

name

The name of the option

value

Whether the option should be true or false

setV(self: PyLongQt._PyLongQt.Cells.CellKernel, voltage: float) → None

Set transmembrane voltage

property t

The current time (ms)

tstep(self: PyLongQt._PyLongQt.Cells.CellKernel, stim_time: float) → float

Increment the cell’s time by dt.

stim_time

the time (ms) when the next stimulus will occur. This is used to determine the appropriate timestep size.

property type

The name of the cell model

updateConc(self: PyLongQt._PyLongQt.Cells.CellKernel) → None

Update the cell’s ion concentrations and signaling molecules

updateCurr(self: PyLongQt._PyLongQt.Cells.CellKernel) → None

Update the cell’s ion channel and flux currents

updateV(self: PyLongQt._PyLongQt.Cells.CellKernel) → float

Update the cell’s transmembrane voltage.

property vOld

The transmembrane voltage (mV)

property vars

The variables for the cell. Variables are values which will change throughout the simulation. Different cell models will have different variables.

class PyLongQt.Cells.CoupledInexcitableCell

Coupled Inexcitable Cell ..Note: No Publication

class PyLongQt.Cells.Courtemanche98

Human Atrial (Courtemanche 1998)

Courtemanche, Marc, et al. “Ionic Mechanisms Underlying Human Atrial Action

Potential Properties: Insights from a Mathematical Model.” The American Journal

of Physiology, vol. 275, no. 1 Pt 2, July 1998, pp. H301-21,

http://www.ncbi.nlm.nih.gov/pubmed/9688927.

class PyLongQt.Cells.FaberRudy

Mammalian Ventricular (Faber-Rudy 2000)

Faber, Gregory M., and Yoram Rudy. “Action Potential and Contractility Changes

[Na+](i) Overloaded Cardiac Myocytes: A Simulation Study.” Biophysical Journal,

vol. 78, no. 5, Elsevier, 2000, pp. 2392–404,

doi:10.1016/S0006-3495(00)76783-X.

class PyLongQt.Cells.GpbAtrial

Human Atrial (Grandi 2011)

Grandi, E., et al. “Human Atrial Action Potential and Ca2+ Model: Sinus Rhythm

and Chronic Atrial Fibrillation.” Circulation Research, vol. 109, no. 9, 2011,

pp. 1055–66, doi:10.1161/CIRCRESAHA.111.253955.

class PyLongQt.Cells.GpbAtrialOnal17

Human Atrial (Onal 2017)

Onal, Birce, et al. “Ca 2+ /Calmodulin Kinase II-Dependent Regulation of Atrial

Myocyte Late Na+ Current, Ca 2+ Cycling and Excitability: A Mathematical

Modeling Study.” American Journal of Physiology - Heart and Circulatory

Physiology, 2017, p. ajpheart.00185.2017, doi:10.1152/ajpheart.00185.2017.

updateIna(self: PyLongQt._PyLongQt.Cells.GpbAtrialOnal17) → None

class PyLongQt.Cells.GpbVent

Human Ventricular (Grandi 10)

Grandi, Eleonora, et al. A Novel Computational Model of the Human Ventricular

Action Potential and Ca Transient. 2009, doi:10.1016/j.yjmcc.2009.09.019.

class PyLongQt.Cells.GridCell

Grid Cell

Henriquez, C. S., & Plonsey, R. (1987). Effect of resistive discontinuities

on waveshape and velocity in a single cardiac fibre. Medical & Biological

Engineering & Computing, 25(4), 428–438. https://doi.org/10.1007/BF02443364

class PyLongQt.Cells.HRD09BorderZone

Canine Ventricular Border Zone (Hund-Rudy 2009)

Hund, T. J., Decker, K. F., Kanter, E., Mohler, P. J., Boyden, P. A., Schuessler,

R. B., … Rudy, Y. (2008). Role of activated CaMKII in abnormal calcium homeostasis

and INa remodeling after myocardial infarction: Insights from mathematical modeling.

Journal of Molecular and Cellular Cardiology, 45(3), 420–428.

https://doi.org/10.1016/j.yjmcc.2008.06.007

class PyLongQt.Cells.HRD09Control

Canine Ventricular (Hund-Rudy 2009)

Hund, T. J., Decker, K. F., Kanter, E., Mohler, P. J., Boyden, P. A., Schuessler,

R. B., … Rudy, Y. (2008). Role of activated CaMKII in abnormal calcium homeostasis

and INa remodeling after myocardial infarction: Insights from mathematical modeling.

Journal of Molecular and Cellular Cardiology, 45(3), 420–428.

https://doi.org/10.1016/j.yjmcc.2008.06.007

class PyLongQt.Cells.InexcitableCell

Inexcitable Cell ..Note: No Publication

class PyLongQt.Cells.Ksan

Mouse Sinus Node (Kharche 2011)

Kharche, Sanjay, et al. “A Mathematical Model of Action Potentials of Mouse

Sinoatrial Node Cells with Molecular Bases.” American Journal of

Physiology-Heart and Circulatory Physiology, vol. 301, no. 3, Sept. 2011, pp.

H945–63, doi:10.1152/ajpheart.00143.2010.

class PyLongQt.Cells.Kurata08

Rabbit Sinus Node (Kurata 2008)

Kurata, Yasutaka, et al. “Regional Difference in Dynamical Property of

Sinoatrial Node Pacemaking: Role of Na+channel Current.” Biophysical Journal,

vol. 95, no. 2, 2008, pp. 951–77, doi:10.1529/biophysj.107.112854.

class PyLongQt.Cells.OHaraRudy

class PyLongQt.Cells.OHaraRudyEndo

Human Ventricular Endocardium (O’Hara-Rudy 2011)

O’hara, Thomas, et al. “Simulation of the Undiseased Human Cardiac Ventricular

Action Potential: Model Formulation and Experimental Validation.” PLoS Comput

Biol, vol. 7, no. 5, American Heart Association, 2011, pp. 1002061–302,

doi:10.1371/journal.pcbi.1002061.

class PyLongQt.Cells.OHaraRudyEpi

Human Ventricular Epicardium (O’Hara-Rudy 2011)

O’hara, Thomas, et al. “Simulation of the Undiseased Human Cardiac Ventricular

Action Potential: Model Formulation and Experimental Validation.” PLoS Comput

Biol, vol. 7, no. 5, American Heart Association, 2011, pp. 1002061–302,

doi:10.1371/journal.pcbi.1002061.

class PyLongQt.Cells.OHaraRudyM

Human Ventricular Mid Myocardial (O’Hara-Rudy 2011)

O’hara, Thomas, et al. “Simulation of the Undiseased Human Cardiac Ventricular

Action Potential: Model Formulation and Experimental Validation.” PLoS Comput

Biol, vol. 7, no. 5, American Heart Association, 2011, pp. 1002061–302,

doi:10.1371/journal.pcbi.1002061.

class PyLongQt.Cells.TNNP04Control

Human Ventricular (Ten Tusscher 2004)

Ten Tusscher, KHWJ H. W. J., et al. “A Model for Human Ventricular Tissue.”

American Journal of Physiology. Heart and Circulatory Physiology, vol. 286, no.

4, 2004, pp. H1573-89, doi:10.1152/ajpheart.00794.2003.

class PyLongQt.Cells.VarsParsVeiw

Interface for accessing and setting a cell’s variables or constants. Variables are values in a cell which change durring a simulation, while constants will not. Some constants may be manipulated through Protocol.pvars

__contains__(self: PyLongQt._PyLongQt.Cells.VarsParsVeiw, name: str) → bool

Checks if cell has that variable/constant. :name: The name of the variable/constant to check

__getitem__(self: PyLongQt._PyLongQt.Cells.VarsParsVeiw, name: str) → float

Gets the value of a variable/constant. :name: The name of the variable/constant

__iter__(self: PyLongQt._PyLongQt.Cells.VarsParsVeiw) → iterator

Iterate over variables/constants

__setitem__(self: PyLongQt._PyLongQt.Cells.VarsParsVeiw, name: str, value: float) → None

Sets the value of a variable/constant to a value. :name: The name of the variable/constant :value: The value to set the variable/constant to

keys(self: PyLongQt._PyLongQt.Cells.VarsParsVeiw) → Set[str]

Get the names of all variables/constants