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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.molecule.RespiratoryChain.ATPsynthase
public class ATPsynthase
Mitochondrial F1/F0 ATP Synthase.
vSN = kSN * (gamma - 1) / (gamma + 1) gamma = 10^(dGSN / Zett) dGSN = nA * dP - dGp dGp = dGp0 / F + Zett * log(1000*[ATP]total_mito/[ADP]total_mito/[Pi]mito) (concentrations expressed in mM)
Field Summary | |
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Node |
ADPtmito
total ADP concentration in mitochondrial matrix |
double |
Amp
amplifying factor described in Kuzumoto et al, 2007. |
Node |
ATPtmito
total ATP concentration in mitochondrial matrix |
double |
dGp0
standard free-energy change of ATP synthase |
Node |
dP
proton driving force on mitochondrial inner membrane |
double |
F
Faraday constant |
Node |
Hcell
proton concentration in cytosol |
Node |
Hmito
proton concentration in mitochondrial matrix |
double |
kSN
rata constant of ATP synthase |
double |
nA
phenomenological H+/ATP stoichiometry of ATP synthase |
Node |
Pitmito
inorganic phosphate concentration in mitochondrial matrix |
Node |
rbuffermito
buffering capacity for proton in mitochondrial matrix |
Node |
Rcm
ratio of cytosol volume and mitochondria volume |
double |
Zvalue
Z = 2.303 * R * T / F |
Fields inherited from class org.simBio.core.Parameter |
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value |
Constructor Summary | |
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ATPsynthase()
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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 dP
public Node Hcell
public Node Hmito
public Node ATPtmito
public Node ADPtmito
public Node Pitmito
public Node Rcm
public Node rbuffermito
public double Zvalue
public double dGp0
public double kSN
public double nA
public double F
public double Amp
Constructor Detail |
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public ATPsynthase()
Method Detail |
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protected void calculate(double t)
Reactor
calculate
in class Reactor
t
- elapsed time (ms)
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