Kosiuk2015-Geometric analysis of the Goldbeter minimal model for the embryonic cell cycle

Model Identifier
BIOMD0000000933
Short description
A minimal model describing the embryonic cell division cycle at the molecular level in eukaryotes is analyzed mathematically. It is known from numerical simulations that the corresponding three-dimensional system of ODEs has periodic solutions in certain parameter regimes. We prove the existence of a stable limit cycle and provide a detailed description on how the limit cycle is generated. The limit cycle corresponds to a relaxation oscillation of an auxiliary system, which is singularly perturbed and has the same orbits as the original model. The singular perturbation character of the auxiliary problem is caused by the occurrence of small Michaelis constants in the model. Essential pieces of the limit cycle of the auxiliary problem consist of segments of slow motion close to several branches of a two dimensional critical manifold which are connected by fast jumps. In addition, a new phenomenon of exchange of stability occurs at lines, where the branches of the two-dimensional critical manifold intersect. This novel type of relaxation oscillations is studied by combining standard results from geometric singular perturbation with several suitable blow-up transformations.
Format
SBML
(L2V4)
Related Publication
-
Geometric analysis of the Goldbeter minimal model for the embryonic cell cycle.
- Kosiuk I, Szmolyan P
- Journal of mathematical biology , 4/ 2016 , Volume 72 , Issue 5 , pages: 1337-1368 , PubMed ID: 26100376
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany. ilona.kosiuk@mis.mpg.de.
- A minimal model describing the embryonic cell division cycle at the molecular level in eukaryotes is analyzed mathematically. It is known from numerical simulations that the corresponding three-dimensional system of ODEs has periodic solutions in certain parameter regimes. We prove the existence of a stable limit cycle and provide a detailed description on how the limit cycle is generated. The limit cycle corresponds to a relaxation oscillation of an auxiliary system, which is singularly perturbed and has the same orbits as the original model. The singular perturbation character of the auxiliary problem is caused by the occurrence of small Michaelis constants in the model. Essential pieces of the limit cycle of the auxiliary problem consist of segments of slow motion close to several branches of a two dimensional critical manifold which are connected by fast jumps. In addition, a new phenomenon of exchange of stability occurs at lines, where the branches of the two-dimensional critical manifold intersect. This novel type of relaxation oscillations is studied by combining standard results from geometric singular perturbation with several suitable blow-up transformations.
Contributors
Submitter of the first revision: Ahmad Zyoud
Submitter of this revision: Ahmad Zyoud
Modellers: Ahmad Zyoud
Submitter of this revision: Ahmad Zyoud
Modellers: Ahmad Zyoud
Metadata information
is (2 statements)
isDescribedBy (1 statement)
hasTaxon (1 statement)
hasProperty (4 statements)
isDerivedFrom (1 statement)
occursIn (1 statement)
isDescribedBy (1 statement)
hasTaxon (1 statement)
hasProperty (4 statements)
Mathematical Modelling Ontology
Ordinary differential equation model
Gene Ontology cell cycle
NCIt Enzyme Kinetics
NCIt Mitosis
Gene Ontology cell cycle
NCIt Enzyme Kinetics
NCIt Mitosis
isDerivedFrom (1 statement)
occursIn (1 statement)
Curation status
Curated
Modelling approach(es)
Tags
Connected external resources
Name | Description | Size | Actions |
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Model files |
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Kosiuk2015.xml | SBML L2V4 Kosiuk2015-Geometric analysis of the Goldbeter minimal model for the embryonic cell cycle | 33.66 KB | Preview | Download |
Additional files |
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Kosiuk2015.cps | COPASI version 4.27 (Build 217) Kosiuk2015-Geometric analysis of the Goldbeter minimal model for the embryonic cell cycle_Fig3_Curated | 58.55 KB | Preview | Download |
Kosiuk2015.sedml | sed-ml L1V2 Kosiuk2015-Geometric analysis of the Goldbeter minimal model for the embryonic cell cycle_Fig3_Curated | 2.66 KB | Preview | Download |
- Model originally submitted by : Ahmad Zyoud
- Submitted: Apr 24, 2020 1:09:29 PM
- Last Modified: Apr 24, 2020 1:09:29 PM
Revisions
Legends
: Variable used inside SBML models
: Variable used inside SBML models
Species
Reactions
Reactions | Rate | Parameters |
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=> M; C | compartment*(6*C/(1+2*C)*(1-M)/((epislon+1)-M)-3/2*M/(epislon+M)) | epislon = 0.001 |
=> X; M | compartment*(M*(1-X)/((epislon+1)-X)-7/10*X/(epislon+X)) | epislon = 0.001 |
=> C; X | compartment*1/4*((1-X)-C) | [] |
Curator's comment:
(added: 24 Apr 2020, 13:09:05, updated: 24 Apr 2020, 13:09:05)
(added: 24 Apr 2020, 13:09:05, updated: 24 Apr 2020, 13:09:05)
Figure 3 has been reproduced using Copasi 4.27 ( Build 217)