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

Class Diffusion

java.lang.Object

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

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

All Implemented Interfaces:

UpdateModule, Runnable

public class Diffusion
extends ConcentrationBasedModule<EntityDeltaFunction>

Diffusion is the fundamental force governing the random movement of molecules in cells. As a ConcentrationBasedModule it has the DependentUpdate scope and is EntitySpecific. The module is only applied for automaton nodes for the entities specified during the build process (via Diffusion.DiffusionBuilder). Diffusion is parametrized by the Diffusivity Feature, therefore Diffusivity must be assigned to each entity or a FeatureProvider will try to resolve it.

  // define the feature to parametrize the diffusion
  Diffusivity diffusivity = new Diffusivity(Quantities.getValue(2.28E-05, SQUARE_CENTIMETRE_PER_SECOND),
         Evidence.MANUALLY_ANNOTATED);
  // assign it to the chemical entity
  SmallMolecule ammonia = new SmallMolecule.Builder("ammonia")
         .name("ammonia")
         .assignFeature(diffusivity)
         .build();
  // create the module
  Diffusion diffusion = Diffusion.inSimulation(simulation)
         .identifier("ammonia diffusion")
         .onlyFor(ammonia)
         .build(); 

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	Diffusion.BuildStep
static class	Diffusion.DiffusionBuilder
static interface	Diffusion.SelectionStep

Field Summary

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

supplier

Constructor Summary

Constructors

Constructor and Description
Diffusion()

Method Summary

Modifier and Type	Method and Description
void	checkFeatures()
static ModuleBuilder	getBuilder(Simulation simulation)
static Diffusion.SelectionStep	inSimulation(Simulation simulation)

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

addDeltaFunction, addReferencedEntities, addReferencedEntity, calculateUpdates, deltaIsValid, determineLargestLocalError, equals, getApplicationCondition, getDeltaCutoff, getErrorCutoff, getFeature, getFeatures, getIdentifier, getReferencedEntities, getRequiredFeatures, getScaledFeature, getScaledFeature, getScope, getSimulation, getSpecificity, getState, getSupplier, handleDelta, hashCode, initialize, onCompletion, onReset, optimizeTimeStep, resetState, run, setApplicationCondition, setDeltaCutoff, setErrorCutoff, setFeature, setIdentifier, setSimulation, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Diffusion

public Diffusion()

Method Detail

inSimulation

public static Diffusion.SelectionStep inSimulation(Simulation simulation)

checkFeatures

public void checkFeatures()

Specified by:

checkFeatures in interface UpdateModule

Overrides:

checkFeatures in class ConcentrationBasedModule<EntityDeltaFunction>

getBuilder

public static ModuleBuilder getBuilder(Simulation simulation)