wormsim 0.0.1__py3-none-any.whl

wormsim/components/mechanism/modfile/slo2_unc2.mod

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+TITLE slo2 current for C. elegans neuron model (suppose to interact with unc2)
+
+
+COMMENT
+channel type: calcium-related potassium channel
+
+slo2-unc2 1:1 stoichiometry
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+    (molar) = (1/liter)  : moles do not appear in units
+    (uM) = (micromolar)
+}
+
+
+NEURON {
+    SUFFIX slo2_unc2
+    USEION k READ ek WRITE ik
+    RANGE gbslo2, minf, tm, mcavinf, tmcav, hcavinf, thcav, m, hcav, mcav
+}
+
+
+PARAMETER {
+    : slo2
+    gbslo2 = 1 (nS/um2)
+    wyx = 0.019 (1/mV)
+    wxy = -0.024 (1/mV)
+    wom = 0.90 (1/ms)
+    wop = 0.027 (1/ms)
+    kxy = 93.45 (uM/um2)
+    nxy = 1.84
+    kyx = 3294.55 (uM/um2)
+    nyx = 0.00001
+    canci = 0.05 (uM/um2) : calcium concentration When the calcium channel is closed
+
+    : unc2
+    vhm = -12.2 (mV)
+    ka = 4.0 (mV)
+    vhh = -52.5 (mV)
+    ki = 5.6 (mV)
+    atm = 1.5 (ms)
+    btm = -8.2 (mV)
+    ctm = 9.1 (mV)
+    dtm = 15.4 (mV)
+    etm = 0.1 (ms)
+    ath = 83.8 (ms)
+    bth = 52.9 (mV)
+    cth = -3.5 (mV)
+    dth = 72.1 (ms)
+    eth = 23.9 (mV)
+    fth = -3.6 (mV)
+
+    : cain
+    FARADAY = 96485 (coul) : moles do not appear in units
+	gsc = 0.04 (nS)   : single channel conductance, assumed equal to 40 pS for both L-type and P/Qtype calcium channels
+    r = 0.013 (um)       : radius of the nanodomain
+    dca = 250 (um2/s) : calcium diffusion coefficient
+    kb = 500 (1/uM/s) : intracellular buffer rate constant
+    btot = 30 (uM)    : total intracellular buffer concentration
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    tm (ms)
+    mcavinf
+    tmcav (ms)
+    hcavinf
+    thcav (ms)
+}
+
+
+STATE {
+    m
+    hcav
+    mcav
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    ik = gbslo2 * m * hcav * (v + 80) : ek=-80
+}
+
+
+INITIAL {
+    setparames(v)
+    hcav = hcavinf
+    mcav = mcavinf
+    m = minf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    mcav' = (mcavinf - mcav) / tmcav
+    hcav' = (hcavinf - hcav) / thcav
+    m' = (minf - m) / tm    
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    LOCAL alpha, beta, wm, wp, fm, fp, kom, kop, kcm, cain
+    : unc2 model
+    mcavinf = 1 / (1 + exp(-(v - vhm) / ka))
+    hcavinf = 1 / (1 + exp((v - vhh) / ki))
+    tmcav = atm / (exp(-(v - btm) / ctm) + exp((v - btm) / dtm)) + etm
+    thcav = ath / (1 + exp(-(v - bth) / cth)) + dth / (1 + exp((v - eth) / fth))
+    : cain
+    if (v < 60) {
+        cain = -gsc * (v - 60) * 10^9 / (8 * 3.1415926 * r * dca * FARADAY) * exp (-r / sqrt(dca / (kb * btot)))
+    } else {
+        cain = 0.0001
+    }
+    : slo2-unc2 model
+    alpha = mcavinf / tmcav
+    beta = 1 / tmcav - alpha
+    wm = wom * exp(-wyx * v)
+    wp = wop * exp(-wxy * v)
+    fm = 1 / (1 + (cain / kyx) ^ nyx)
+    fp = 1 / (1 + (kxy / (cain)) ^ nxy)
+    kom = wm * fm
+    kop = wp * fp
+    kcm = wm * 1 / (1 + (canci / kyx) ^ nyx)
+    minf = mcav * kop * (alpha + beta + kcm) / ((kop + kom) * (kcm + alpha) + beta * kcm)
+    tm = (alpha + beta + kcm) / ((kop + kom) * (kcm + alpha) + beta * kcm)
+}

wormsim/components/mechanism/modfile/unc2.mod

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+TITLE unc2 current for C. elegans neuron model
+
+
+COMMENT
+channel type: voltage-gated calcium channel
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+}
+
+
+NEURON {
+    SUFFIX unc2
+    USEION ca READ eca WRITE ica
+    RANGE gbunc2, minf, hinf, tm, th, m, h
+}
+
+
+PARAMETER {
+    gbunc2 = 1 (nS/um2)
+    vhm = -12.2 (mV)
+    ka = 4.0 (mV)
+    vhh = -52.5 (mV)
+    ki = 5.6 (mV)
+    atm = 1.5 (ms)
+    btm = -8.2 (mV)
+    ctm = 9.1 (mV)
+    dtm = 15.4 (mV)
+    etm = 0.1 (ms)
+    ath = 83.8 (ms)
+    bth = 52.9 (mV)
+    cth = -3.5 (mV)
+    dth = 72.1 (ms)
+    eth = 23.9 (mV)
+    fth = -3.6 (mV)
+}
+
+
+ASSIGNED {
+    v (mV)
+    eca (mV)
+    ica (pA/um2)
+    minf
+    hinf
+    tm (ms)
+    th (ms)
+}
+
+
+STATE {
+    m
+    h
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ica = gbunc2 * m * h * (v - eca)
+    ica = gbunc2 * m * h * (v - 60) :eca=60 mV
+}
+
+
+INITIAL {
+    setparames(v)
+    m = minf
+    h = hinf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    m' = (minf - m) / tm
+    h' = (hinf - h) / th
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = 1 / (1 + exp(-(v - vhm) / ka))
+    hinf = 1 / (1 + exp((v - vhh) / ki))
+    tm = atm / (exp(-(v - btm) / ctm) + exp((v - btm) / dtm)) + etm
+    th = ath / (1 + exp(-(v - bth) / cth)) + dth / (1 + exp((v - eth) / fth))
+}