bier2

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000254) Biomodels notes: The model reproduces figure 3 of the reference publication. The model was integrated and simulated using Copasi v4.5.31. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment.

  • M Bier
  • Barbara M Bakker
  • Hans V Westerhoff
Biophys. J. 2000; 78 (3): 1087-1093
Abstract
Of all the lifeforms that obtain their energy from glycolysis, yeast cells are among the most basic. Under certain conditions the concentrations of the glycolytic intermediates in yeast cells can oscillate. Individual yeast cells in a suspension can synchronize their oscillations to get in phase with each other. Although the glycolytic oscillations originate in the upper part of the glycolytic chain, the signaling agent in this synchronization appears to be acetaldehyde, a membrane-permeating metabolite at the bottom of the anaerobic part of the glycolytic chain. Here we address the issue of how a metabolite remote from the pacemaking origin of the oscillation may nevertheless control the synchronization. We present a quantitative model for glycolytic oscillations and their synchronization in terms of chemical kinetics. We show that, in essence, the common acetaldehyde concentration can be modeled as a small perturbation on the "pacemaker" whose effect on the period of the oscillations of cells in the same suspension is indeed such that a synchronization develops.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
Id Name Spatial dimensions Size
compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
G1 Glucose_1 6.6 compartment
G2 Glucose_2 10.3 compartment
T1 ATP_1 7.6 compartment
T2 ATP_2 0.41 compartment

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
vG1toT1 G1 = {2.0}T1

k1 * G1 * T1
vG2toT2 G2 = {2.0}T2

k1 * G2 * T2
vIn vIn ∅ = G1 + G2

V_in
vOut1T1 T1 = ∅

kp * T1 / (km + T1)
vOut1T2 T2 = ∅

kp * T2 / (km + T2)
vT2toT1 vT2toT1 T2 = T1

epsilon * (T2 - T1)

Global parameters

Id Value
Tdiff 0.0
Tsum 0.0
V_in 0.36
epsilon 0.01
k1 0.02
km 13.0
kp 6.0

Local parameters

Id Value Reaction

Assignment rules

Definition
Tsum = T2 + T1
Tdiff = T2 - T1

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments