bio.singa.simulation.model.modules.concentration.imlementations

Class MembraneDiffusion

java.lang.Object

bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<UpdatableDeltaFunction>

bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion

All Implemented Interfaces:

UpdateModule

public class MembraneDiffusion
extends ConcentrationBasedModule<UpdatableDeltaFunction>

The membrane diffusion module describes the movement of chemical entities across Membranes driven by the MembranePermeability of the cargo. The cargo molecules are crossing a membrane from one side to the other side. The flux of concentration is determined by terms of

  JM = Pd * A * (c1 - c2)

where Pd is the MembranePermeability, A is the area of the membrane, and c1 and c2 are the concentrations on both sides of the membrane; as in:

  Stein, Wilfred. Transport and diffusion across cell membranes. Elsevier, 2012.

This concentration based module applies SemiDependentUpdates and is UpdatableSpecific.

  // define the feature to parametrize the diffusion
  MembranePermeability membranePermeability = new MembranePermeability(Quantities.getQuantity(3.5E-03, CENTIMETRE_PER_SECOND),
         FeatureOrigin.MANUALLY_ANNOTATED);

  // assign it to the chemical entity
  SmallMolecule water = new SmallMolecule.Builder("water")
         .assignFeature(membranePermeability)
         .build();

  // create the module
  MembraneDiffusion.inSimulation(simulation)
         .cargo(water)
         .build();

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	MembraneDiffusion.BuildStep
static interface	MembraneDiffusion.CargoStep
static class	MembraneDiffusion.MembraneDiffusionBuilder

Field Summary

Fields inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

supplier

Constructor Summary

Constructors

Constructor and Description
MembraneDiffusion()

Method Summary

Modifier and Type	Method and Description
void	initialize()
static MembraneDiffusion.CargoStep	inSimulation(Simulation simulation)
String	toString()

Methods inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

addDeltaFunction, addModuleToSimulation, addReferencedEntities, addReferencedEntity, calculateUpdates, checkFeatures, deltaIsValid, determineLargestLocalError, getApplicationCondition, getDeltaCutoff, getErrorCutoff, getFeature, getFeatures, getIdentifier, getReferencedEntities, getRequiredFeatures, getScaledFeature, getScaledFeature, getScope, getSimulation, getSpecificity, getState, getStringForProtocol, getSupplier, handleDelta, listFeatures, onCompletion, onReset, optimizeTimeStep, resetState, scaleScalableFeatures, setApplicationCondition, setDeltaCutoff, setErrorCutoff, setFeature, setIdentifier, setSimulation

Methods inherited from class java.lang.Object

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

Constructor Detail

MembraneDiffusion

public MembraneDiffusion()

Method Detail

inSimulation

public static MembraneDiffusion.CargoStep inSimulation(Simulation simulation)

initialize

public void initialize()

toString

public String toString()

Overrides:

toString in class ConcentrationBasedModule<UpdatableDeltaFunction>