Laub-Loomis model

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.

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

Brief description of the model:

The governing equations for the seven variable are given by


[ACA]' = k1[CAR1]-k2[ACA]
[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[PKA][CAR1]

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