XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
% SkM_AP_KCa.ode % Simulations for skeletal muscle fiber % % ICa(S) and IK(Ca) were incorporated to simulate AP for human skeletal muscle cells. % % "Wang YJ, Lin MW, Lin AA, Wu SN. Riluzole-induced block of voltage-gated Na(+) % current and activation of BK(Ca) channels in cultured differentiated human % skeletal muscle cell. Life Sci 2007;82:11-20." % UNITS: millivolts, milliseconds, nanosiemens, microfarads % INITIAL VALUES Initial Vm=-75, m=0.0, h=1.0, n=0.0, Vt=-70, c=0.15, o=0.15, cer=200 % VALUES OF THE MODEL PARAMETERS Parm gNa_max=0.9, gcabar=0.05, gK_max=0.415, gL_max=0.0024, gkca=0.5 Parm ENa=50.0, EK=-70.0, EL=-75.0, ECa=50 Parm En=-40.0, Em=-42.0, Eh=-41.0 Parm Ct=0.04, Cm=0.0090, Rs=15.0, Am=200.0 Parm alpha_n_max=0.0229, beta_n_max=0.09616 Parm v_alpha_m=10.0, v_alpha_n=7.0, v_alpha_h=14.7 Parm alpha_m_max=0.208, beta_m_max=2.081 Parm v_beta_n=40.0, v_beta_m=18.0, v_beta_h=7.6 Parm alpha_h_max=0.0156, beta_h_max=3.382 Parm kd=0.18, alpha=4.5e-6, kpmca=0.2, pleak=0.0005, kserca=0.4 Parm d1=0.84, d2=1.0, k1=0.18, k2=0.011, bbar=0.28, abar=0.48 Parm fer=0.01, vcytver=5, fcyt=0.01 % STIMULUS Parm period=50, iStim_mag=2, iStim_beg=5, iStim_dur=1 iStim= iStim_mag * heav(mod(t,period)-iStim_beg) * heav(iStim_beg+iStim_dur-mod(t,period)) beta_n= (beta_n_max * exp(((En - Vm) / v_beta_n))) beta_m= (beta_m_max * exp(((Em - Vm) / v_beta_m))) beta_h= (beta_h_max / (1.0 + exp(((Eh - Vm) / v_beta_h)))) alpha_n= (alpha_n_max * (Vm - En) / (1.0 - exp(((En - Vm) / v_alpha_n)))) alpha_m= (alpha_m_max * (Vm - Em) / (1.0 - exp(((Em - Vm) / v_alpha_m)))) alpha_h= (alpha_h_max * exp(((Eh - Vm) / v_alpha_h))) % IK(Ca) PARAMETERS alp(Vm) = abar/(1+k1*exp(-2*d1*96.485*Vm/8.313424/(310))/c) beta(Vm) = bbar/(1+c/(k2*exp(-2*d2*96.485*Vm/8.313424/310))) tau(Vm) = 1/(alp(Vm)+beta(Vm)) ooinf(Vm) = alp(Vm)*tau(Vm) dinf = 1/(1 + exp((-24.6-Vm)/11.3)) taud = 80*(1/(cosh(-0.031*(Vm+37.1)))) alphad = dinf/taud betad = (1-dinf)/taud gca = -gcabar*Vm/(exp(0.117*Vm)-1) % CA HANDLING MECHANISMS w=c^5/(c^5+kd^5) jmem=-(alpha*ICa+kpmca*c) jleak=pleak*(cer-c) jserca=kserca*c jer=jleak-jserca % IONIC CURRENTS INa= (gNa_max * m**3 * h * (Vm - ENa)) IT= ((Vm - Vt) / Rs) IKCa=gkca*o*w*(Vm-EK) ICa= gca*d^2 IL= (gL_max * (Vm - EL)) IK= (gK_max * n * n * n * n * (Vm - EK)) % DIFFERENTIAL EQUATIONS dVm/dt = ((iStim - (INa + ICa + IK + IL + IT + IKCa)) / Cm) dm/dt = ((alpha_m * (1.0 - m)) - (beta_m * m)) dh/dt = ((alpha_h * (1.0 - h)) - (beta_h * h)) dn/dt = ((alpha_n * (1.0 - n)) - (beta_n * n)) dVt/dt = ((Vm - Vt) / (Rs * Ct)) dd/dt = (1-d)*alphad - d*betad do/dt = (ooinf(Vm)-o)/tau(Vm) dc/dt = fcyt*(jmem+jer) dcer/dt =-fer*(vcytver)*jer % AUXILLARY FUNCTIONS aux i_na=INa aux i_kca=IKCa % NUMERICAL AND PLOTTING PARAMETERS FOR XPP @ METH=Euler, DT=0.01, TOTAL=150, MAXSTOR=50000 @ YP=vm, YHI=50, YLO=-90, XLO=0, XHI=150, BOUND=5000 done
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Copyright © 2017 Matthias Koenig
Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:
- Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
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Model :
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type | FunctionDefinitions [8] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | max
|
minimum | |||
FunctionDefinition | min
|
maximum | |||
FunctionDefinition | heav
|
heavyside | |||
FunctionDefinition | mod
|
modulo | |||
FunctionDefinition | alp
|
||||
FunctionDefinition | beta
|
||||
FunctionDefinition | tau
|
||||
FunctionDefinition | ooinf
|
type | Parameters [81] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | Vm
|
F | -75.0 | None | ||||
Parameter | m
|
F | 0.0 | None | ||||
Parameter | h
|
F | 1.0 | None | ||||
Parameter | n
|
F | 0.0 | None | ||||
Parameter | Vt
|
F | -70.0 | None | ||||
Parameter | c
|
F | 0.15 | None | ||||
Parameter | o
|
F | 0.15 | None | ||||
Parameter | cer
|
F | 200.0 | None | ||||
Parameter | gNa_max
|
F | 0.9 | None | ||||
Parameter | gcabar
|
F | 0.05 | None | ||||
Parameter | gK_max
|
F | 0.415 | None | ||||
Parameter | gL_max
|
F | 0.0024 | None | ||||
Parameter | gkca
|
F | 0.5 | None | ||||
Parameter | ENa
|
F | 50.0 | None | ||||
Parameter | EK
|
F | -70.0 | None | ||||
Parameter | EL
|
F | -75.0 | None | ||||
Parameter | ECa
|
F | 50.0 | None | ||||
Parameter | En
|
F | -40.0 | None | ||||
Parameter | Em
|
F | -42.0 | None | ||||
Parameter | Eh
|
F | -41.0 | None | ||||
Parameter | Ct
|
F | 0.04 | None | ||||
Parameter | Cm
|
F | 0.009 | None | ||||
Parameter | Rs
|
F | 15.0 | None | ||||
Parameter | Am
|
F | 200.0 | None | ||||
Parameter | alpha_n_max
|
F | 0.0229 | None | ||||
Parameter | beta_n_max
|
F | 0.09616 | None | ||||
Parameter | v_alpha_m
|
F | 10.0 | None | ||||
Parameter | v_alpha_n
|
F | 7.0 | None | ||||
Parameter | v_alpha_h
|
F | 14.7 | None | ||||
Parameter | alpha_m_max
|
F | 0.208 | None | ||||
Parameter | beta_m_max
|
F | 2.081 | None | ||||
Parameter | v_beta_n
|
F | 40.0 | None | ||||
Parameter | v_beta_m
|
F | 18.0 | None | ||||
Parameter | v_beta_h
|
F | 7.6 | None | ||||
Parameter | alpha_h_max
|
F | 0.0156 | None | ||||
Parameter | beta_h_max
|
F | 3.382 | None | ||||
Parameter | kd
|
F | 0.18 | None | ||||
Parameter | alpha
|
F | 4.5e-06 | None | ||||
Parameter | kpmca
|
F | 0.2 | None | ||||
Parameter | pleak
|
F | 0.0005 | None | ||||
Parameter | kserca
|
F | 0.4 | None | ||||
Parameter | d1
|
F | 0.84 | None | ||||
Parameter | d2
|
F | 1.0 | None | ||||
Parameter | k1
|
F | 0.18 | None | ||||
Parameter | k2
|
F | 0.011 | None | ||||
Parameter | bbar
|
F | 0.28 | None | ||||
Parameter | abar
|
F | 0.48 | None | ||||
Parameter | fer
|
F | 0.01 | None | ||||
Parameter | vcytver
|
F | 5.0 | None | ||||
Parameter | fcyt
|
F | 0.01 | None | ||||
Parameter | period
|
F | 50.0 | None | ||||
Parameter | iStim_mag
|
F | 2.0 | None | ||||
Parameter | iStim_beg
|
F | 5.0 | None | ||||
Parameter | iStim_dur
|
F | 1.0 | None | ||||
Parameter | d
|
F | 0.0 | dimensionless | None | |||
Parameter | iStim
|
F | 0.0 | dimensionless | None | |||
Parameter | beta_n
|
F | 0.0 | dimensionless | None | |||
Parameter | beta_m
|
F | 0.0 | dimensionless | None | |||
Parameter | beta_h
|
F | 0.0 | dimensionless | None | |||
Parameter | alpha_n
|
F | 0.0 | dimensionless | None | |||
Parameter | alpha_m
|
F | 0.0 | dimensionless | None | |||
Parameter | alpha_h
|
F | 0.0 | dimensionless | None | |||
Parameter | dinf
|
F | 0.0 | dimensionless | None | |||
Parameter | taud
|
F | 0.0 | dimensionless | None | |||
Parameter | alphad
|
F | 0.0 | dimensionless | None | |||
Parameter | betad
|
F | 0.0 | dimensionless | None | |||
Parameter | gca
|
F | 0.0 | dimensionless | None | |||
Parameter | w
|
F | 0.0 | dimensionless | None | |||
Parameter | jmem
|
F | 0.0 | dimensionless | None | |||
Parameter | jleak
|
F | 0.0 | dimensionless | None | |||
Parameter | jserca
|
F | 0.0 | dimensionless | None | |||
Parameter | jer
|
F | 0.0 | dimensionless | None | |||
Parameter | INa
|
F | 0.0 | dimensionless | None | |||
Parameter | IT
|
F | 0.0 | dimensionless | None | |||
Parameter | IKCa
|
F | 0.0 | dimensionless | None | |||
Parameter | ICa
|
F | 0.0 | dimensionless | None | |||
Parameter | IL
|
F | 0.0 | dimensionless | None | |||
Parameter | IK
|
F | 0.0 | dimensionless | None | |||
Parameter | i_na
|
F | 0.0 | dimensionless | None | |||
Parameter | i_kca
|
F | 0.0 | dimensionless | None | |||
Parameter | t
|
model time | F | 0.0 | dimensionless | None |
type | Rules [35] | assignment | name | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
Rule | d Vm/dt
|
= | None | ||||
Rule | d m/dt
|
= | None | ||||
Rule | d h/dt
|
= | None | ||||
Rule | d n/dt
|
= | None | ||||
Rule | d Vt/dt
|
= | None | ||||
Rule | d d/dt
|
= | None | ||||
Rule | d o/dt
|
= | None | ||||
Rule | d c/dt
|
= | None | ||||
Rule | d cer/dt
|
= | None | ||||
Rule | iStim
|
= | None | ||||
Rule | beta_n
|
= | None | ||||
Rule | beta_m
|
= | None | ||||
Rule | beta_h
|
= | None | ||||
Rule | alpha_n
|
= | None | ||||
Rule | alpha_m
|
= | None | ||||
Rule | alpha_h
|
= | None | ||||
Rule | dinf
|
= | None | ||||
Rule | taud
|
= | None | ||||
Rule | alphad
|
= | None | ||||
Rule | betad
|
= | None | ||||
Rule | gca
|
= | None | ||||
Rule | w
|
= | None | ||||
Rule | jmem
|
= | None | ||||
Rule | jleak
|
= | None | ||||
Rule | jserca
|
= | None | ||||
Rule | jer
|
= | None | ||||
Rule | INa
|
= | None | ||||
Rule | IT
|
= | None | ||||
Rule | IKCa
|
= | None | ||||
Rule | ICa
|
= | None | ||||
Rule | IL
|
= | None | ||||
Rule | IK
|
= | None | ||||
Rule | i_na
|
= | None | ||||
Rule | i_kca
|
= | None | ||||
Rule | t
|
= | None |