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java.lang.Object org.primordion.xholon.base.Xholon org.primordion.xholon.base.XholonWithPorts org.primordion.cellontro.app.XhAbstractSbml org.primordion.cellontro.app.sbml.XhDimericMWCstiff
Example of very stiff biochemical model
This is a model of an allosteric enzyme following the MWC dimeric model, in which the substrate S interacts only with the enzyme species in the R-state. The system of ODEs of this model is very stiff, and correct results can only be obtained with a stiff ODE solver.
This example comes from Hayashi, K. and Sakamoto, N. (1986) Dynamic Analysis of Enzyme Systems, Japan Scientific Societies Press, Tokyo.
Example for: Time course simulation, plotting
Actions:
Field Summary | |
static int |
P_SM_PRD1
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static int |
P_SM_PRD2
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static int |
P_SM_SUB1
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static int |
P_SM_SUB2
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static int |
timeStepMultiplier
|
Fields inherited from class org.primordion.cellontro.app.XhAbstractSbml |
pheneVal, roleName, securityException |
Fields inherited from class org.primordion.xholon.base.XholonWithPorts |
port |
Fields inherited from class org.primordion.xholon.base.Xholon |
DEFAULT_LEVEL, interaction, interactionsEnabled |
Fields inherited from interface org.primordion.xholon.base.IXholon |
DEFAULT_SIZE_MSG_Q, NINCLUDE_PSC, NINCLUDE_PSx, NINCLUDE_PxC, NINCLUDE_Pxx, NINCLUDE_xSC, NINCLUDE_xSx, NINCLUDE_xxC, NINCLUDE_xxx |
Constructor Summary | |
XhDimericMWCstiff()
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Method Summary | |
void |
act()
Do some action during this time step. |
int |
getNumModifiers()
Get maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model. |
int |
getNumProducts()
Get maximum number of products that any xholon instance may have in this model. |
int |
getNumReactants()
Get maximum number of reactants (substrates) that any xholon instance may have in this model. |
int |
getTimeStepMultiplier()
Get the time step multiplier, needed for numerical integration. |
void |
setNumModifiers(int numM)
Set maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model. |
void |
setNumProducts(int numP)
Set maximum number of products that any xholon instance may have in this model. |
void |
setNumReactants(int numR)
Set maximum number of reactants (substrates) that any xholon instance may have in this model. |
static void |
setTimeStepMultiplier(int tms)
Set the time step multiplier, needed for numerical integration. |
Methods inherited from class org.primordion.cellontro.app.XhAbstractSbml |
configure, decPheneVal, getPheneVal, getRoleName, getVal, incPheneVal, initialize, preAct, setRoleName, toString |
Methods inherited from class org.primordion.xholon.base.XholonWithPorts |
getMaxPorts, getPort, isActiveObject, isBound, isContainer, isPassiveObject, postConfigure, setMaxPorts, setPorts, terminate |
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
public static final int P_SM_SUB1
public static final int P_SM_SUB2
public static final int P_SM_PRD1
public static final int P_SM_PRD2
public static int timeStepMultiplier
Constructor Detail |
public XhDimericMWCstiff()
Method Detail |
public int getNumReactants()
IBioXholon
getNumReactants
in interface IBioXholon
getNumReactants
in class XhAbstractSbml
public void setNumReactants(int numR)
IBioXholon
setNumReactants
in interface IBioXholon
setNumReactants
in class XhAbstractSbml
public int getNumProducts()
IBioXholon
getNumProducts
in interface IBioXholon
getNumProducts
in class XhAbstractSbml
public void setNumProducts(int numP)
IBioXholon
setNumProducts
in interface IBioXholon
setNumProducts
in class XhAbstractSbml
public int getNumModifiers()
IBioXholon
getNumModifiers
in interface IBioXholon
getNumModifiers
in class XhAbstractSbml
public void setNumModifiers(int numM)
IBioXholon
setNumModifiers
in interface IBioXholon
setNumModifiers
in class XhAbstractSbml
public int getTimeStepMultiplier()
XhAbstractSbml
getTimeStepMultiplier
in class XhAbstractSbml
public static void setTimeStepMultiplier(int tms)
XhAbstractSbml
public void act()
IXholon
act
in interface IXholon
act
in class Xholon
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