Model Reference Description: Model (IKA_voltage_clamp_model)

<source/>
Voltage clamp of the IKA current.
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
Pubmed reference: 17486452
Comment [created by David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore]:
A voltage clamp experiment examining the behaviour of the A-type potassium current from the Corrias & Buist (2007) smooth muscle cell model.
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IKA voltage clamp experiment
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
Comment:
The main component encapsulating the voltage clamp experiment for the A-type potassium current.
Vm=[1.0mV]⁢Vm_dimensionless
Vm
Units: mV
Metadata
Comment:
The actual membane potential clamp transient.
Vm_dimensionless
Defined as: y
Units: dimensionless
Metadata
Comment:
The non-dimensional linear ramp boundary condition defined by the generic ramp protocol. Converted to a dimensional membrane potential for use.
Vm_initial
Initial value: -80.0
Units: dimensionless
Metadata
Comment:
The starting value for the voltage clamp. The maximum value is determined by the simulation metadata and the rate variable. It is dimensionless as we are using a generic linear ramp protocol so will need to convert to mV before use.
rate
Initial value: 1.0
Units: per_ms
Metadata
Comment:
The rate at which the linear ramp boundary condition advances the membrane potential as we integrate over time.
<source/>
The actual definition of the time variable.
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
time
Initial value: 0.0
Units: ms
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parameters
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
Comment:
The model parameters - in this case we use all default values. Here we just define the parameters needed for the calculation of EK.
one
Initial value: 1.0
Units: dimensionless
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IKA
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-26
Publisher: Division of Bioengineering, National University of Singapore
Comment [created by David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore]:
Here we calculate the A-type potassium current. We expect the time, membrane potential, and conductance to be set externally, and we provide access to the gating variables and the calculated current. This component encapsulates all others in this model and thus acts as an interface to the gating variable components, both local and imported.
Comment [created by David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore]:
The activation gate (xA1) is a standard Hodgkin-Huxley type gate. The inactivation gate (xA2), however, has been shown to never completely inactivate hence requiring a slight modification to the standard HH inactivation gating kinetics.
Imported as: IKA
Untitled metadata
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
IKA=g_KA⁢xA1⁢xA2⁢(Vm−EK)
tau_xA1=([31.8ms]+[175.0ms]⁢e[-0.5dimensionless]⁢(Vm+[44.4mV]/[22.3mV])[2.0dimensionless])⁢Tcorrection
IKA
Units: pA
g_KA
Defined as: g_KA
Units: nS
xA1
Defined as: gate
Units: dimensionless
xA2
Defined as: xA2
Units: dimensionless
Vm
Defined as: Vm
Units: mV
EK
Defined as: reversal_potential
Units: mV
tau_xA1
Units: ms
Tcorrection
Defined as: Tcorrection_K
Units: dimensionless
Q10 temperature correction factor for the IKA current
Comment [created by David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore]:
We expect this variable to be assigned the nescessary scale factor value for scaling the channel time constants to the current model temperature.
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ramp
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
Comment [created by David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore]:
Here we define a simple linear relationship dy/dt = k, specifying the change in y over time with a slope of k.
Imported as: clamp_protocol
Untitled metadata
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
dydtime=k
y
Initial value: y_initial
Units: dimensionless
The dimensionless ramp variable.
time
Defined as: time
Units: ms
The time variable over which y is to be integrated.
k
Defined as: rate
Units: per_ms
The time slope of the linear relationship.
y_initial
Defined as: Vm_initial
Units: dimensionless
The initial value of y.
<source/>
Default model parameter values
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-09-05
Publisher: Division of Bioengineering, National University of Singapore
Comment:
Here we define the complete set of default parameter values.
Modification [modified by David Nickerson]:
Adding parameter data for the IKA current.
Modified: 2007-11-26
Modification [modified by David Nickerson]:
Separating out the calculation of the Ca temperature correction factor.
Modified: 2007-11-26
Imported as: default_parameters
Untitled metadata
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
Tcorrection_Ca=Q10Ca(T−T_Ca/[10.0K])
Tcorrection_K=Q10K(T−T_K/[10.0K])
tau_d=tau_d_base⁢Tcorrection_Ca
tau_f=tau_f_base⁢Tcorrection_Ca
tau_xA2=tau_xA2_base⁢Tcorrection_K
Tcorrection_Ca
Units: dimensionless
Q10 temperature correction factor for calcium.
Q10Ca
Initial value: 2.1
Units: dimensionless
Metadata
Pubmed reference: 10099682
Comment:
Q10 value used to adjust the L-type calcium voltage dependent gating time constants to current temperature.
T
Initial value: 310.0
Units: K
Metadata
Comment:
The current temperature at which the model is defined.
T_Ca
Initial value: 297
Units: K
Metadata
Pubmed reference: 1703570
Comment:
The temperature at which the L-type calcium voltage dependent gating time constants were measured.
Tcorrection_K
Units: dimensionless
Q10 temperature correction factor for potassium.
Q10K
Initial value: 1.5
Units: dimensionless
Q10 value used to adjust the potassium voltage dependent gating time constants to current temperature.
Pubmed reference: 10394625
T_K
Initial value: 297
Units: K
tau_d
Units: ms
Metadata
Comment:
Actual time constant of activation gate of the L-type calcium current, adjusted to current temperature.
tau_d_base
Initial value: 0.47
Units: ms
Metadata
Comment:
The base time constant for the activation gate of the L-type calcium current, measured at a room temperature of 297 K.
tau_f
Units: ms
Metadata
Comment:
Actual time constant of inactivation gate of the L-type calcium current, adjusted to current temperature.
tau_f_base
Initial value: 86.0
Units: ms
Metadata
Pubmed reference: 1703570
Biological Entity: pyloric myocyte
Species: canine
Comment:
The base time constant for the inactivation gate of the L-type calcium current, measured at a room temperature of 297 K.
tau_xA2
Units: ms
Metadata
Comment:
Actual time constant of inactivation gate of the A-type potassium current, adjusted to current temperature.
tau_xA2_base
Initial value: 90.0
Units: ms
Metadata
Pubmed reference: 12381815
Biological Entity: gastric smooth muscle cell
Species: mouse
Comment:
The base time constant for the inactivation gate of the A-type potassium current, measured at a room temperature of 297 K.
Cai_rest
Initial value: 1.0e-4
Units: mM
Metadata
Comment:
The resting level of intracellular calcium. In the original C code this was evaluated as the value of [Ca]i some time interval before the first stimulus - perhaps should also implement that in this version of the model?
Cao
Initial value: 2.5
Units: mM
Extracellular calcium ion concentration.
Biological Entity: taenia coli
Species: guinea pig
Ko
Initial value: 5.9
Units: mM
Extracellular potassium ion concentration.
Biological Entity: taenia coli
Species: guinea pig
Ki
Initial value: 164.0
Units: mM
Intracellular potassium ion concentration.
Biological Entity: taenia coli
Species: guinea pig
g_CaL
Initial value: 65.0
Units: nS
Metadata
Pubmed reference: 1312782
Biological Entity: gastric smooth muscle
Species: canine
Comment:
Maximal conductance of the L-type calcium current.
d_V_half
Initial value: 17.0
Units: mV
Metadata
Pubmed reference: 7683715
Biological Entity: oesophageal muscularis mucosae
Species: New Zealand White rabbit
Comment:
Half maximal potential for voltage-dependent activation gate for L-type calcium current.
d_k
Initial value: 4.3
Units: mV
Metadata
Comment:
Slope factor for voltage dependence of L-type calcium current activation gate.
f_V_half
Initial value: 43.0
Units: mV
Metadata
Comment:
Half maximal potential for voltage-dependent inactivation gate for L-type calcium current.
f_k
Initial value: 8.9
Units: mV
Metadata
Comment:
Slope factor for voltage dependence of L-type calcium current inactivation gate.
hCa
Initial value: 201.4e-6
Units: mM
Metadata
Pubmed reference: 1312782
Biological Entity: gastric smooth muscle
Species: canine
Comment:
Calcium concentration for half maximal activation of the calcium dependent L-type calcium current inactivation gate.
sCa
Initial value: 13.1e-6
Units: mM
Metadata
Pubmed reference: 1312782
Biological Entity: gastric smooth muscle
Species: canine
Comment:
Slope factor for the calcium dependence of the calcium dependent L-type calcium current inactivation gate.
tau_fCa
Initial value: 2.0
Units: ms
Metadata
Pubmed reference: 14656705
Biological Entity: cardiac myocyte
Species: Homo sapiens
Comment:
Time constant for the calcium dependent L-type calcium current inactivation gate.
g_KA
Initial value: 9.0
Units: nS
Maximal conductance of A-type potassium channel.
Pubmed reference: 1383498
Biological Entity: gastric myocyte
Species: guinea pig
xA1_V_half
Initial value: 26.5
Units: mV
Half maximal potential for voltage-dependent activation gate for A-type potasium current.
Pubmed reference: 12381815
Biological Entity: gastric smooth muscle cell
Species: mouse
xA1_k
Initial value: 7.9
Units: mV
Slope factor for voltage dependence of A-type calcium current activation gate.
Pubmed reference: 12381815
Biological Entity: gastric smooth muscle cell
Species: mouse
xA2_V_half
Initial value: 65.0
Units: mV
Half maximal potential for voltage-dependent inactivation gate for A-type potasium current.
Pubmed reference: 12381815
Biological Entity: gastric smooth muscle cell
Species: mouse
xA2_k
Initial value: 6.2
Units: mV
Slope factor for voltage dependence of A-type calcium current inactivation gate.
Pubmed reference: 12381815
Biological Entity: gastric smooth muscle cell
Species: mouse
<source/>
Default model initial values
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-09-05
Publisher: Division of Bioengineering, National University of Singapore
Comment:
Here we define the complete set set of default initial conditions for the model's differental variables.
Modification [modified by David Nickerson]:
Adding A-type potassium current gating variable initial conditions.
Modified: 2007-11-27
Imported as: default_initial_conditions
Untitled metadata
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
d_initial
Initial value: 4.54e-5
Units: dimensionless
f_initial
Initial value: 0.871
Units: dimensionless
fCa_initial
Initial value: 1.0
Units: dimensionless
xA1_initial
Initial value: 0.0
Units: dimensionless
xA2_initial
Initial value: 1.0
Units: dimensionless
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one_ion
Creator: David Nickerson (d.nickerson@auckland.ac.nz) Bioengineering Institute, The University of Auckland
Created: 2004-12-27
Publisher: Bioengineering Institute, The University of Auckland
Comment:
Calculate the Nernst reversal potential for one ionic specie. We expect the temperature, valence and ionic concentrations to be defined by the model importing this component. We make the gas and Faraday's constants available for others to use.
Imported as: EK
Untitled metadata
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-27
Publisher: Division of Bioengineering, National University of Singapore
reversal_potential=(R⁢T/z⁢F)⁢ln(extracellular_concentration/intracellular_concentration)
reversal_potential
Units: mV
R
Initial value: 8314.472
Units: gas_constant
T
Defined as: T
Units: K
z
Defined as: one
Units: dimensionless
F
Initial value: 96485.0
Units: faradays_constant
extracellular_concentration
Defined as: Ko
Units: mM
intracellular_concentration
Defined as: Ki
Units: mM
<source/>
Standard Hodgkin-Huxley activation gate kinetics
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-09-04
Publisher: Division of Bioengineering, National University of Singapore
Comment:
The standard definition of a HH type activation gate. This component should be imported and all parameters defined.
Imported as: xA1_gate
Untitled metadata
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-26
Publisher: Division of Bioengineering, National University of Singapore
Comment:
Import the standard HH type activation gate for use as the A-type K current voltage dependent activation gate (xA1).
dgatedtime=gate_inf−gate/gate_tau
gate_inf=[1.0dimensionless]/[1.0dimensionless]+e−(V_half+Vm/k)
gate
Initial value: gate_initial
Units: dimensionless
Metadata
Comment:
This is the actual gating variable representing a standard HH type activation gate.
time
Defined as: time
Units: ms
Metadata
Comment:
The time variable needs to be defined for the activation gate component.
gate_inf
Units: dimensionless
Metadata
Comment:
The steady state activation gate value.
gate_tau
Defined as: tau_xA1
Units: ms
Metadata
Comment:
The activation gate time constant.
V_half
Defined as: xA1_V_half
Units: mV
Metadata
Comment:
The membrane potential at which the activation gate is half maximally activated.
Vm
Defined as: Vm
Units: mV
Metadata
Comment:
The membrane potential variable needs to be defined for the activation gate component.
k
Defined as: xA1_k
Units: mV
Metadata
Comment:
The slope factor for the voltage dependence of the activation gate.
gate_initial
Defined as: xA1_initial
Units: dimensionless
Metadata
Comment:
The initial value for the activation gate needs to be defined.
<source/>
xA2_gate
Creator: David Nickerson (david.nickerson@nus.edu.sg) Division of Bioengineering, National University of Singapore
Created: 2007-11-26
Publisher: Division of Bioengineering, National University of Singapore
Comment:
A slight modification on the standard Hodgkin-Huxley gating kinetics for the IKA inactivation gate, xA2.
dxA2dtime=xA2_inf−xA2/tau_xA2
xA2_inf=[0.9dimensionless]/[1.0dimensionless]+exA2_V_half+Vm/xA2_k+[0.1dimensionless]
xA2
Initial value: xA2_initial
Units: dimensionless
time
Defined as: time
Units: ms
xA2_inf
Units: dimensionless
tau_xA2
Defined as: tau_xA2
Units: ms
xA2_V_half
Defined as: xA2_V_half
Units: mV
Vm
Defined as: Vm
Units: mV
xA2_k
Defined as: xA2_k
Units: mV
xA2_initial
Defined as: xA2_initial
Units: dimensionless

Units definitions

mV
(1000⁢second-3) ⁢(kilogram) ⁢(metre2) ⁢(ampere-1)
dimensionless
dimensionless
per_ms
0.001⁢second-1
ms
1000⁢second
pA
1e+12⁢ampere
nS
(1e+09⁢second3) ⁢(kilogram-1) ⁢(metre-2) ⁢(ampere2)
K
kelvin
mM
(1e+09⁢mole) ⁢(1e-09⁢metre-3)
gas_constant
(kelvin-1) ⁢(1e+12⁢second-2) ⁢(kilogram) ⁢(1e-09⁢mole-1) ⁢(metre2)
faradays_constant
(1e+09⁢second) ⁢(1e-09⁢mole-1) ⁢(ampere)
Created: 05:35:47 2008-02-05 (UTC) by CellMLSimulator