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 differentialalgebraic 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.111 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 differentialalgebraic 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 

BIOMD0000000358_url.xml  SBML L2V4 representation of Stortelder1997  Thrombin Generation Amidolytic Activity  21.26 KB  Preview  Download 
Additional files 

BIOMD0000000358biopax2.owl  Autogenerated BioPAX (Level 2)  14.17 KB  Preview  Download 
BIOMD0000000358.sci  Autogenerated Scilab file  3.56 KB  Preview  Download 
BIOMD0000000358.png  Autogenerated Reaction graph (PNG)  54.52 KB  Preview  Download 
BIOMD0000000358_urn.xml  Autogenerated SBML file with URNs  20.95 KB  Preview  Download 
BIOMD0000000358.m  Autogenerated Octave file  6.24 KB  Preview  Download 
BIOMD0000000358.vcml  Autogenerated VCML file  32.81 KB  Preview  Download 
BIOMD0000000358.svg  Autogenerated Reaction graph (SVG)  23.21 KB  Preview  Download 
BIOMD0000000358.pdf  Autogenerated PDF file  187.97 KB  Preview  Download 
BIOMD0000000358biopax3.owl  Autogenerated BioPAX (Level 3)  22.05 KB  Preview  Download 
BIOMD0000000358.xpp  Autogenerated 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

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

Version: 1
 Submitted on: Aug 26, 2011 5:19:20 PM
 Submitted by: Michael Schubert
 With comment: Original import of Stortelder1997_ThrombinGeneration_AmidolyticActivity
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: 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 Alpha2macroglobulin ; Prothrombin 
0.0 nmol 
X Coagulation factor X 
81.24998 nmol 
Xa ATIII AntithrombinIII ; 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*PLk_PL*PT) compartment_1*(k_PT*Va*Xa*PLk_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)