diff --git a/examples/kinetics_fad_semmiclassical.py b/examples/kinetics_fad_semmiclassical.py index b4dcd80..788aee0 100644 --- a/examples/kinetics_fad_semmiclassical.py +++ b/examples/kinetics_fad_semmiclassical.py @@ -7,7 +7,7 @@ def main(): - # Kinetic simulation of FAD at pH 2.3. + # Kinetic simulation of FAD at pH 2.1. # For FAD quenching: uncomment the three quenching kinetic parameters. # FAD kinetic parameters @@ -31,22 +31,29 @@ def main(): Q = Rate(0, "Q") # 1e-3 # quencher concentration # Rate equations + S0, S1, T1p, T10, T1m, FR = "S0", "S1", "T1+", "T10", "T1-", "FR" + SS, STp, ST0, STm = "SS", "ST+", "ST0", "ST-" + TpS, TpTp, TpT0, TpTm = "T+S", "T+T+", "T+T0", "T+T-" + T0S, T0Tp, T0T0, T0Tm = "T0S", "T0T+", "T0T0", "T0T-" + TmS, TmTp, TmT0, TmTm = "T-S", "T-T+", "T-T0", "T-T-" + base = {} - base["S0"] = { - "S0": -kex, - "T+/-": kd, - "T0": kd, - "S": kbet, - "S*": kfl + kic, - "Quencher": kp, + base[S0] = { + S0: -kex, + S1: kfl + kic, + T1p: kd, + T10: kd, + T1m: kd, + SS: kbet, + FR: kp, } - base["S*"] = { - "S*": -(kfl + kic + 3 * kisc), - "S0": kex, + base[S1] = { + S1: -(kfl + kic + 3 * kisc), + S0: kex, } - base["T*+/-"] = { - "T*+/-": -(kd + k1 + krt), - "T+/-": km1 * Hp, + base[T1p] = { + T1p: -(kd + k1 + krt), + Tp: km1 * Hp, "T*0": 2 * krt, "S*": 2 * kisc, } @@ -116,10 +123,6 @@ def main(): field_on = fac * result_on[keys] delta_delta_A = field_on - field_off - fluor_off = result_off["S0"] - fluor_on = result_on["S0"] - fluor_del_A = fluor_on - fluor_off - plt.clf() fig = plt.figure() scale = 1e6 @@ -140,26 +143,6 @@ def main(): path = __file__[:-3] + f"_{0}.png" plt.savefig(path) - plt.clf() - fig = plt.figure() - scale = 1e6 - gs = fig.add_gridspec(2, hspace=0) - axs = gs.subplots(sharex=True) - fig.suptitle("FAD (pH 2.3) Fluorescence", size=18) - axs[0].plot(time * scale, fluor_off, color="blue", linewidth=2) - axs[0].plot(time * scale, fluor_on, color="green", linewidth=2) - axs[1].plot(time * scale, fluor_del_A, color="orange", linewidth=2) - plt.xscale("linear") - axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"]) - axs[1].set_xlabel("Time ($\mu s$)", size=14) - axs[0].set_ylabel("$F$", size=14) - axs[1].set_ylabel("$\Delta F$", size=14) - axs[0].tick_params(labelsize=14) - axs[1].tick_params(labelsize=14) - fig.set_size_inches(10, 5) - path = __file__[:-3] + f"_{1}.png" - plt.savefig(path) - if __name__ == "__main__": main()