Laub-Loomis model

To run the simulation, click on "start". Integration can be continued by clicking on "integrate". The coefficients k1 through k14 and the starting values of [CAR1] etc. can be chosen by typing them in the appropriate box. All seven variables can be plotted by selecting them (click on the little box that appears to the left of their definition). The results can be plotted either normalized (i.e. the values are rescaled so that the maximum value is 1) or not. Peak values are given. The integration time in minutes can be chosen in the box "integration time=" in the upper right hand corner.

Brief description of the model:

The network is shown on the right. The governing equations for the seven variables are given by

[ACA]' = k1[CAR1]-k2[ACA][PKA]
[PKA]' = k3[cAMPi]-k4[PKA]
[ERK2]' = k5[CAR1]-k6[PKA][ERK2]
[RegA]' = k7-k8[ERK2][RegA]
[cAMPi]' = k9[ACA]-k10[RegA][cAMPi]
[cAMPe]' = k11[ACA]-k12[cAMPe]
[CAR1]' = k13[cAMPe]-k14[CAR1]

Where ' stands for differentiation with respect to time and where

  • k1 affects activation of ACA (adenylyl cyclase)
  • k2 affects inactivation of ACA
  • k3 affects activation of PKA (protein kinase)
  • k4 affects inactivation of PKA
  • k5 affects activation of ERK2 (protein kinase)
  • k6 affects inactivation of ERK2
  • k7 affects activation of RegA (internal phosphodiesterase)
  • k8 affects inactivation of RegA
  • k9 is the proportion of cAMP not secreted
  • k10 affects the breakdown of internal cAMP
  • k11 is the proportion of cAMP secreted
  • k12 is the activity of PdsA (extracellular phosphodiesterase)
  • k13 affects activation of CAR1 (cAMP receptor)
  • k14 affects inactivation of CAR1

    The equations are integrated using the explicit Euler's method with a time step of dt=0.005 min.

    This applet simulates a modified version of a model for spontaneous oscillations during the aggregation stage of Dictyostelium (Laub, M.T., and Loomis, W. F. (1998) A molecular network that produces spontaneous oscillations in excitable cells of Dictyostelium. Mol. Biol. Cell 9, 3521-3532.)
    This page was built by Wouter-Jan Rappel. We thank Flavio Fenton who kindly provided us the Java applet.