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java.lang.Object org.simBio.core.Component org.simBio.core.Parameter org.simBio.core.Composite org.simBio.core.Reactor org.simBio.bio.matsuoka_et_al_2004.function.MassConservation2 org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationPi
public class ConcentrationPi
calculation of iorganic phosphate concentration (conformed to mass conservation law)
Pitotal = 3*[ATP]cell + 2*[ADP]cell + [AMP] + [PhosphoCreatine] + [Pi]cell + (3*[ATP]mito + 2*[ADP]mito + [Pi]mito) / Rcm [Pi]cell = Pitotal - (3*[ATP]cell + 2*[ADP]cell + [AMP] + [PhosphoCreatine] + (3*[ATP]mito + 2*[ADP]mito + [Pi]mito) / Rcm)
Field Summary | |
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Node |
ADPtcell
total ADP concentration in cytosol |
Node |
ADPtmit
total ADP concentration in mitochondria |
Node |
AMP
AMP concentration in cytosol |
Node |
ATPtcell
total ATP concentration in cytosol |
Node |
ATPtmit
total ATP concentration in mitochondria |
Node |
PCr
phosphocreatine concentration in cytosol |
Node |
Pimit
iorganic phosphate concentration in mitochondria |
double |
PiTotal
total iorganic phosphate concentration in whole cell |
Node |
Rcm
volume ratio between cytosol and mitochondrial matrix |
Fields inherited from class org.simBio.bio.matsuoka_et_al_2004.function.MassConservation2 |
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other1, other2, total |
Fields inherited from class org.simBio.core.Parameter |
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value |
Constructor Summary | |
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ConcentrationPi()
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Method Summary | |
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protected void |
calculate(double t)
write equations here, and calculate dy over dt. |
Methods inherited from class org.simBio.core.Composite |
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accept, getLink, getNode, getNodesIterator, getNodesSize |
Methods inherited from class org.simBio.core.Parameter |
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addValue, getValue, getValueString, prepare, setInitializer, setValue, setValueString, setValueToField |
Methods inherited from class org.simBio.core.Component |
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addDydt, end, getIndent, getIndentedShortName, getName, getName, getParent, getRoot, getShortName, getUnits, isNamed, isPrefixed, logIndented, quit, setLinks |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.simBio.core.Node |
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addDydt, addValue, getValue, setValue |
Field Detail |
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public Node ATPtcell
public Node ADPtcell
public Node AMP
public Node PCr
public Node ATPtmit
public Node ADPtmit
public Node Pimit
public Node Rcm
public double PiTotal
Constructor Detail |
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public ConcentrationPi()
Method Detail |
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protected void calculate(double t)
Reactor
calculate
in class MassConservation2
t
- elapsed time (ms)
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