 |  |  CaM |
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Parameters for PKM (Pathway Number 917) Pathway Layout
Pathway Basic Parameters | Pathway Name | PKM | | Pathway Entry Number | 917 | | Accession Number | 83 | | Accession Name | Ajay_Bhalla_2007_ReacDiff2 | | Species | Rat | | Tissue | Hippocampal CA1 | | CellCompartment | Dendrite | | Related Pathways | 328,
346,
374,
380,
387,
393,
399,
406,
412,
419,
424,
429,
435,
441,
447,
453,
459,
465,
471,
477,
483,
489,
495,
501,
507,
513,
519,
525,
531,
538,
544,
550,
556,
562,
569,
574,
580,
586,
592,
598,
604,
610,
616,
622,
628,
634,
640,
646,
652,
658,
664,
670,
676,
682,
689,
696,
702,
707,
713,
719,
725,
731,
737,
743,
749,
755,
761,
767,
773,
779,
785,
791,
797,
803,
809,
815,
821,
827,
833,
839,
845,
851,
857,
863,
869,
875,
881,
887,
893,
899,
905,
911
| | Notes | This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
| Statistics Conversion formatThis pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway. |
Pathway Detail Molecule List Enzyme List Reaction List
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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