public class SingleFileChannelMembraneTransport extends ConcentrationBasedModule<UpdatableDeltaFunction>
Transporter proteins, so
called membrane channels. In the channels the cargo proteins move in a single file configuration.
The kinetics of the transport is guided by the osmotic pressure of solute molecules as well as the
OsmoticPermeability of the transporter.
The net flux of the cargo through the membrane is:
JC = pf * nt * (s1 - s2)where pf is the
OsmoticPermeability, nt is the number of transporters in the membrane and s1 and s2 are the
concentrations of the solute on both sides of the membrane, as in:
Finkelstein, Alan. "Water movement through membrane channels." Current Topics in Membranes and Transport. Vol. 21. Academic Press, 1984. 295-308.This concentration based module applies
IndependentUpdates and is UpdatableSpecific.
// get water from chebi
SmallMolecule water = ChEBIParserService.parse("CHEBI:15377", "water");
// define solutes as a single species
SmallMolecule solute = new SmallMolecule.Builder("solutes")
.name("solutes")
.build();
// aquaporin 2 as a transporter
Transporter aquaporin2 = UniProtParserService.parse("P41181", "aqp2").asTransporter();
aquaporin2.setFeature(new OsmoticPermeability(5.31e-14, BINESH2015));
// create module
SingleFileChannelMembraneTransport.inSimulation(simulation)
.transporter(aquaporin2)
.cargo(water)
.forSolute(solute)
.build(); | Modifier and Type | Class and Description |
|---|---|
static interface |
SingleFileChannelMembraneTransport.BuildStep |
static interface |
SingleFileChannelMembraneTransport.CargoStep |
static class |
SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder |
static interface |
SingleFileChannelMembraneTransport.SolutesStep |
static interface |
SingleFileChannelMembraneTransport.TransporterStep |
supplier| Constructor and Description |
|---|
SingleFileChannelMembraneTransport() |
| Modifier and Type | Method and Description |
|---|---|
static ModuleBuilder |
getBuilder(Simulation simulation) |
void |
initialize() |
static SingleFileChannelMembraneTransport.TransporterStep |
inSimulation(Simulation simulation) |
addDeltaFunction, addReferencedEntities, addReferencedEntity, calculateUpdates, checkFeatures, deltaIsValid, determineLargestLocalError, equals, getApplicationCondition, getDeltaCutoff, getErrorCutoff, getFeature, getFeatures, getIdentifier, getReferencedEntities, getRequiredFeatures, getScaledFeature, getScaledFeature, getScope, getSimulation, getSpecificity, getState, getSupplier, handleDelta, hashCode, onCompletion, onReset, optimizeTimeStep, resetState, run, setApplicationCondition, setDeltaCutoff, setErrorCutoff, setFeature, setIdentifier, setSimulation, toStringpublic static SingleFileChannelMembraneTransport.TransporterStep inSimulation(Simulation simulation)
public void initialize()
initialize in interface UpdateModuleinitialize in class ConcentrationBasedModule<UpdatableDeltaFunction>public static ModuleBuilder getBuilder(Simulation simulation)
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