PorousDiffusion (singa-simulation 0.7.0 API)

java.lang.Object
- bio.singa.simulation.model.modules.AbstractUpdateModule
- - bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<UpdatableDeltaFunction>
  - - bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion

All Implemented Interfaces:

UpdateModule, Runnable
```
public class PorousDiffusion
extends ConcentrationBasedModule<UpdatableDeltaFunction>
```
Calculates diffusion through large pores (pore significantly larger than the cargo) in the membrane. J_s = -(D_w)*(A_p/A_m)*DC/l J_S id th flux, D_W is the diffusivity of the cargo, A_p is the area of the pore, A_m is the area of the membrane, DC is the difference in concentration between both sites of the membrane, l is the membrane thickness

Author:

cl

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static interface`	`PorousDiffusion.BuildStep`
`static interface`	`PorousDiffusion.FeatureStep`
`static class`	`PorousDiffusion.PorousDiffusionBuilder`

Field Summary
- Fields inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
  supplier

Constructor Summary

Constructors
Constructor Description

PorousDiffusion()

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static ModuleBuilder`	`getBuilder(Simulation simulation)`
`static PorousDiffusion.FeatureStep`	`inSimulation(Simulation simulation)`

Methods inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
addDeltaFunction, calculateUpdates, deltaIsValid, determineLargestLocalError, getApplicationCondition, getRestrictedSubsection, getScaledFeature, getScaledFeature, getScope, getSpecificity, getSupplier, handleDelta, inBetweenHalfSteps, initialize, onCompletion, onReset, optimizeTimeStep, restrictApplication, setApplicationCondition, setRestrictedSubsection

Methods inherited from class bio.singa.simulation.model.modules.AbstractUpdateModule
addEvidence, addReferencedEntities, addReferencedEntity, checkFeatures, equals, getEvidence, getFeature, getFeatureManager, getFeatures, getIdentifier, getReferencedChemicalEntities, getRequiredFeatures, getSimulation, getState, hashCode, reset, run, setEvidence, setFeature, setFeatureManager, setIdentifier, setSimulation, setState, toString

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail
- PorousDiffusion
```
public PorousDiffusion()
```

Method Detail

inSimulation

public static PorousDiffusion.FeatureStep inSimulation(Simulation simulation)

getBuilder

public static ModuleBuilder getBuilder(Simulation simulation)