Stortelder1997 - Thrombin Generation Amidolytic Activity
Mathematical modelling of a part of the blood coagulation mechanism.
This model is described in the article:
Abstract:
This paper describes the mathematical modelling of a part of the blood coagulation mechanism. The model includes the activation of factor X by a purified enzyme from Russel's Viper Venom (RVV), factor V and prothrombin, and also comprises the inactivation of the products formed. In this study we assume that in principle the mechanism of the process is known. However, the exact structure of the mechanism is unknown, and the process still can be described by different mathematical models. These models are put to test by measuring their capacity to explain the course of thrombin generation as observed in plasma after recalcification in presence of RVV. The mechanism studied is mathematically modelled as a system of differential-algebraic equations (DAEs). Each candidate model contains some freedom, which is expressed in the model equations by the presence of unknown parameters. For example, reaction constants or initial concentrations are unknown. The goal of parameter estimation is to determine these unknown parameters in such a way that the theoretical (i.e., computed) results fit the experimental data within measurement accuracy and to judge which modifications of the chemical reaction scheme allow the best fit. We present results on model discrimination and estimation of reaction constants, which are hard to obtain in another way.
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Mathematical modelling in blood coagulation ; Simulation and parameter estimation
- Stortelder W.J.H., Hemker P.W., Hemker H.C.
- CWI. Modelling, Analysis and Simulation [MAS], No. R 9720, p.1-11 1997 , Other Link (URL): http://www.narcis.nl/publication/RecordID/oai:cwi.nl:4725
- This paper describes the mathematical modelling of a part of the blood coagulation mechanism. The model includes the activation of factor X by a purified enzyme from Russel's Viper Venom (RVV), factor V and prothrombin, and also comprises the inactivation of the products formed. In this study we assume that in principle the mechanism of the process is known. However, the exact structure of the mechanism is unknown, and the process still can be described by different mathematical models. These models are put to test by measuring their capacity to explain the course of thrombin generation as observed in plasma after recalcification in presence of RVV. The mechanism studied is mathematically modelled as a system of differential-algebraic equations (DAEs). Each candidate model contains some freedom, which is expressed in the model equations by the presence of unknown parameters. For example, reaction constants or initial concentrations are unknown. The goal of parameter estimation is to determine these unknown parameters in such a way that the theoretical (i.e., computed) results fit the experimental data within measurement accuracy and to judge which modifications of the chemical reaction scheme allow the best fit. We present results on model discrimination and estimation of reaction constants, which are hard to obtain in another way.
Metadata information
BioModels Database BIOMD0000000358
Gene Ontology blood coagulation
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| BIOMD0000000358_url.xml | SBML L2V4 representation of Stortelder1997 - Thrombin Generation Amidolytic Activity | 21.26 KB | Preview | Download |
Additional files |
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| BIOMD0000000358-biopax2.owl | Auto-generated BioPAX (Level 2) | 14.17 KB | Preview | Download |
| BIOMD0000000358.sci | Auto-generated Scilab file | 3.56 KB | Preview | Download |
| BIOMD0000000358.png | Auto-generated Reaction graph (PNG) | 54.52 KB | Preview | Download |
| BIOMD0000000358_urn.xml | Auto-generated SBML file with URNs | 20.95 KB | Preview | Download |
| BIOMD0000000358.m | Auto-generated Octave file | 6.24 KB | Preview | Download |
| BIOMD0000000358.vcml | Auto-generated VCML file | 32.81 KB | Preview | Download |
| BIOMD0000000358.svg | Auto-generated Reaction graph (SVG) | 23.21 KB | Preview | Download |
| BIOMD0000000358.pdf | Auto-generated PDF file | 187.97 KB | Preview | Download |
| BIOMD0000000358-biopax3.owl | Auto-generated BioPAX (Level 3) | 22.05 KB | Preview | Download |
| BIOMD0000000358.xpp | Auto-generated XPP file | 4.03 KB | Preview | Download |
- Model originally submitted by : Michael Schubert
- Submitted: Aug 26, 2011 5:19:20 PM
- Last Modified: Oct 9, 2014 6:03:20 PM
Revisions
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Version: 2
- Submitted on: Oct 9, 2014 6:03:20 PM
- Submitted by: Michael Schubert
- With comment: Current version of Stortelder1997 - Thrombin Generation Amidolytic Activity
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Version: 1
- Submitted on: Aug 26, 2011 5:19:20 PM
- Submitted by: Michael Schubert
- With comment: Original import of Stortelder1997_ThrombinGeneration_AmidolyticActivity
(*) You might be seeing discontinuous
revisions as only public revisions are displayed here. Any private revisions
of this model will only be shown to the submitter and their collaborators.
: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| Xa Coagulation factor X |
0.0 nmol |
| PL | 9.999997 nmol |
| Va Coagulation factor V |
0.0 nmol |
| IIa Prothrombin |
0.0 nmol |
| II Prothrombin |
509.2998 nmol |
| IIa alpha2M Alpha-2-macroglobulin ; Prothrombin |
0.0 nmol |
| X Coagulation factor X |
81.24998 nmol |
| Xa ATIII Antithrombin-III ; Coagulation factor X |
0.0 nmol |
| PT | 0.0 nmol |
| Reactions | Rate | Parameters |
|---|---|---|
| compartment_1*kcat_X*RVV*X/(km_X+X) compartment_1*kcat_X*RVV*X/(km_X+X) |
kcat_X = 239.1; km_X = 23.65 | |
| compartment_1*(k_PT*Va*Xa*PL-k_PL*PT) compartment_1*(k_PT*Va*Xa*PL-k_PL*PT) |
k_PL = 801.4; k_PT = 122.9 | |
| compartment_1*kcat_2*Xa*II/(km_2+II) compartment_1*kcat_2*Xa*II/(km_2+II) |
kcat_2 = 12.4; km_2 = 0.06148 | |
| compartment_1*ki_IIaATIII*IIa compartment_1*ki_IIaATIII*IIa |
ki_IIaATIII = 0.7859 | |
| compartment_1*kcat_II*PT*II/(km_II+II) compartment_1*kcat_II*PT*II/(km_II+II) |
km_II = 62.25; kcat_II = 43.87 | |
| compartment_1*ki_IIaAlpha2M*IIa compartment_1*ki_IIaAlpha2M*IIa |
ki_IIaAlpha2M = 0.1762 | |
| compartment_1*ki_Xa*Xa compartment_1*ki_Xa*Xa |
ki_Xa = 4.531 | |
| compartment_1*kcat_V*IIa*V/(km_V+V) compartment_1*kcat_V*IIa*V/(km_V+V) |
km_V = 149.7; kcat_V = 7.844 |
(added: 26 Aug 2011, 17:23:37, updated: 26 Aug 2011, 17:23:37)