BioModels Database logo

BioModels Database

spacer

BIOMD0000000358 - Stortelder1997 - Thrombin Generation Amidolytic Activity

 

 |   |   |  Send feedback
Reference Publication
Publication ID: http://www.narcis.nl...
Stortelder, W.J.H.; Hemker, P.W.; Hemker, H.C.
Mathematical modelling in blood coagulation ; Simulation and parameter estimation
CWI. Modelling, Analysis and Simulation [MAS], No. R 9720, p.1-11
  [more]
Model
Original Model: BIOMD0000000358.origin
Submitter: Michael Schubert
Submission ID: MODEL1108260009
Submission Date: 26 Aug 2011 16:19:20 UTC
Last Modification Date: 09 Oct 2014 17:03:20 UTC
Creation Date: 26 Aug 2011 16:35:29 UTC
Encoders:  Michael Schubert
set #1
bqmodel:is Gene Ontology blood coagulation
set #2
bqbiol:occursIn Taxonomy Eukaryota
bqmodel:isDescribedBy NARCIS oai:cwi.nl:4725
Notes
Stortelder1997 - Thrombin Generation Amidolytic Activity

Mathematical modelling of a part of the blood coagulation mechanism.

This model is described in the article:

Stortelder W.J.H., Hemker P.W., Hemker, H.C.
CWI. Modelling, Analysis and Simulation, No. R 9720, p.1-11.

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.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: http://www.narcis.nl... Submission Date: 26 Aug 2011 16:19:20 UTC Last Modification Date: 09 Oct 2014 17:03:20 UTC Creation Date: 26 Aug 2011 16:35:29 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6 R7 R8
Rules
Assignment Rule (variable: AmAct)      
Physical entities
Compartments Species
compartment_1 X Xa Xa_ATIII
PL PT Va
IIa V II
IIa_alpha2M IIa_ATIII RVV
Global parameters
kcat_X km_X ki_Xa k_PT
k_PL kcat_V km_V kcat_II
km_II kcat_2 km_2 ki_IIaAlpha2M
ki_IIaATIII AmAct    
Reactions (8)
 
 R1 [X] → [Xa];   {RVV}
 
 R2 [Xa] → [Xa_ATIII];  
 
 R3 [Va] + [Xa] + [PL] ↔ [PT];  
 
 R4 [V] → [Va];   {IIa}
 
 R5 [II] → [IIa];   {PT}
 
 R6 [II] → [IIa];   {Xa}
 
 R7 [IIa] → [IIa_alpha2M];  
 
 R8 [IIa] → [IIa_ATIII];  
 
Rules (1)
 
 Assignment Rule (name: AmAct) AmAct = IIa+0.556*IIa_alpha2M
 
Functions (1)
 
 Henri-Michaelis-Menten (irreversible) kcat lambda(kcat, enzyme, substrate, Km, kcat*enzyme*substrate/(Km+substrate))
 
   compartment_1 Spatial dimensions: 3.0  Compartment size: 1.0
 
 X
Compartment: compartment_1
Initial concentration: 81.24998
 
 Xa
Compartment: compartment_1
Initial concentration: 0.0
 
 Xa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
   PL
Compartment: compartment_1
Initial concentration: 9.999997
 
   PT
Compartment: compartment_1
Initial concentration: 0.0
 
 Va
Compartment: compartment_1
Initial concentration: 0.0
 
 IIa
Compartment: compartment_1
Initial concentration: 0.0
 
 V
Compartment: compartment_1
Initial concentration: 6.711998
 
 II
Compartment: compartment_1
Initial concentration: 509.2998
 
 IIa_alpha2M
Compartment: compartment_1
Initial concentration: 0.0
 
 IIa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
   RVV
Compartment: compartment_1
Initial concentration: 0.3349999
 
Global Parameters (14)
 
 kcat_X
Value: 239.1
Constant
 
 km_X
Value: 23.65
Constant
 
 ki_Xa
Value: 4.531
Constant
 
 k_PT
Value: 122.9
Constant
 
 k_PL
Value: 801.4
Constant
 
 kcat_V
Value: 7.844
Constant
 
 km_V
Value: 149.7
Constant
 
 kcat_II
Value: 43.87
Constant
 
 km_II
Value: 62.25
Constant
 
 kcat_2
Value: 12.4
Constant
 
 km_2
Value: 0.06148
Constant
 
 ki_IIaAlpha2M
Value: 0.1762
Constant
 
 ki_IIaATIII
Value: 0.7859
Constant
 
   AmAct  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000358

Curator's comment: (updated: 26 Aug 2011 17:23:37 BST)

Reproduction of figure 5 of the article.

Model integrated using PySCeS and plotted with Matplotlib.

spacer
spacer