org.simBio.bio.oka_et_al_2006.function.kinetics
Class RateConstantCaGate

java.lang.Object
  org.simBio.core.Component
      org.simBio.core.Parameter
          org.simBio.core.Composite
              org.simBio.core.Reactor
                  org.simBio.bio.function.Function
                      org.simBio.bio.oka_et_al_2006.function.kinetics.RateConstantCaGate

All Implemented Interfaces:

Node

public class RateConstantCaGate
extends Function

Calculate the forward and backward rate constans of two-state model by using time constant, pKd and Hill coefficient

Version:

$Revision: 1.1 $

Author:

Chiaki Oka

See Also:

RateConstantCaGate.ja.doc (Japanese, WORD doc)

Field Summary

Node	k_backward backward rate constant
Node	k_forward forward rate constant
double	Kx half-maximum concentration (mM)
double	nHill hill coefficient (dimensionless)
Node	pX p[X].
double	timeconstant time constant at a given pX (ms)

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

RateConstantCaGate()

Method Summary

protected void	calculate(double t) Nothing performed
protected void	prepare() Calculate forward and backward rate constants

Methods inherited from class org.simBio.core.Composite

accept, getLink, getNode, getNodesIterator, getNodesSize

Methods inherited from class org.simBio.core.Parameter

addValue, getValue, getValueString, setInitializer, setValue, setValueString, setValueToField

Methods inherited from class org.simBio.core.Component

addDydt, end, getIndent, getIndentedShortName, getName, getName, getParent, getRoot, getShortName, getUnits, isNamed, isPrefixed, logIndented, quit, setLinks

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.simBio.core.Node

addDydt, addValue, getValue, setValue

Field Detail

k_forward

public Node k_forward

forward rate constant

k_backward

public Node k_backward

backward rate constant

pX

public Node pX

p[X]. [X] represents the ligand concentration.

timeconstant

public double timeconstant

time constant at a given pX (ms)

Kx

public double Kx

half-maximum concentration (mM)

nHill

public double nHill

hill coefficient (dimensionless)

Constructor Detail

RateConstantCaGate

public RateConstantCaGate()

Method Detail

calculate

protected void calculate(double t)

Nothing performed

Specified by:

calculate in class Reactor

Parameters:

t - elapsed time (ms)

See Also:

Reactor.calculate(double)

prepare

protected void prepare()

Calculate forward and backward rate constants

Overrides:

prepare in class Parameter

See Also:

Component.prepare()