de.bioforscher.singa.simulation.modules.diffusion

Class FreeDiffusion

java.lang.Object

de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion

All Implemented Interfaces:

Module, CumulativeUpdateBehavior, UpdateBehavior

public class FreeDiffusion
extends Object
implements Module, CumulativeUpdateBehavior

Diffusion is the net movement of molecules or atoms from a region of high concentration to a region of low concentration. This module defines the diffusion between BioNodes in a AutomatonGraph, as described by Fick's laws of diffusion.

Author:

cl

See Also:

Wikipedia: Fick's laws of diffusion

Constructor Summary

Constructors

Constructor and Description
FreeDiffusion()

Method Summary

Modifier and Type	Method and Description
void	applyTo(AutomatonGraph graph)
List<PotentialUpdate>	calculateUpdates(BioNode node)
Set<ChemicalEntity<?>>	collectAllReferencedEntities()
void	fixDiffusionCoefficientForEntity(ChemicalEntity entity, javax.measure.Quantity<Diffusivity> diffusivityQuantity)
ChemicalEntity	getEntityWithMaximalDiffusivity()
javax.measure.Quantity<Diffusivity>	getMaximalDiffusivity()
void	prepareDiffusionCoefficients(Set<ChemicalEntity<?>> entities)

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.bioforscher.singa.simulation.modules.model.updates.CumulativeUpdateBehavior

updateGraph

Constructor Detail

FreeDiffusion

public FreeDiffusion()

Method Detail

prepareDiffusionCoefficients

public void prepareDiffusionCoefficients(Set<ChemicalEntity<?>> entities)

applyTo

public void applyTo(AutomatonGraph graph)

Specified by:

applyTo in interface Module

calculateUpdates

public List<PotentialUpdate> calculateUpdates(BioNode node)

Specified by:

calculateUpdates in interface UpdateBehavior

collectAllReferencedEntities

public Set<ChemicalEntity<?>> collectAllReferencedEntities()

Specified by:

collectAllReferencedEntities in interface Module

getMaximalDiffusivity

public javax.measure.Quantity<Diffusivity> getMaximalDiffusivity()

getEntityWithMaximalDiffusivity

public ChemicalEntity getEntityWithMaximalDiffusivity()

fixDiffusionCoefficientForEntity

public void fixDiffusionCoefficientForEntity(ChemicalEntity entity,
                                             javax.measure.Quantity<Diffusivity> diffusivityQuantity)