neurord.numeric.grid

Class NextEventQueue.NextDiffusion

java.lang.Object

neurord.numeric.grid.NextEventQueue.NextEvent

neurord.numeric.grid.NextEventQueue.NextDiffusion

All Implemented Interfaces:

IGridCalc.Event, NextEventQueue.Node

Enclosing class:

NextEventQueue

public class NextEventQueue.NextDiffusion
extends NextEventQueue.NextEvent

Field Summary

Fields inherited from class neurord.numeric.grid.NextEventQueue.NextEvent

extent, leap, original_wait, reverse, reverse_is_leaping, scoeff_ki, time

Method Summary

Modifier and Type	Method and Description
void	addRelations(HashMap<Integer,ArrayList<NextEventQueue.NextEvent>> map, String[] species, boolean verbose)
double	calcPropensity() Calculate propensity of this event.
int	element2() "target" voxel number (different from source only for diffusion)
IGridCalc.EventType	event_type()
int	leap_count(double current, double time, boolean bidirectional) Calculate the (randomized) extent of the reaction based in the time given.
double	leap_time(double current) Calculate leap_time based on the limit on variance and expected extents.
int[]	substrate_stoichiometry() Stoichiometries of species, negative on the lhs, positive on the rhs
Map<Integer,int[][]>	substrates_by_voxel()
int[]	substrates() Indices of species on both sides of the reaction
String	toString()

Methods inherited from class neurord.numeric.grid.NextEventQueue.NextEvent

addDependent, addReverse, dependent, description, element, event_number, index, reactant_stoichiometry, reactantPopulation, reactants, setEvent, setIndex, stat_index_description, stat_index, time, updateStatistics

Methods inherited from class java.lang.Object

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

Method Detail

event_type

public IGridCalc.EventType event_type()

Specified by:

event_type in interface IGridCalc.Event

Specified by:

event_type in class NextEventQueue.NextEvent

calcPropensity

public double calcPropensity()

Description copied from class: NextEventQueue.NextEvent

Calculate propensity of this event.

substrates

public int[] substrates()

Description copied from interface: IGridCalc.Event

Indices of species on both sides of the reaction

Specified by:

substrates in interface IGridCalc.Event

Specified by:

substrates in class NextEventQueue.NextEvent

substrate_stoichiometry

public int[] substrate_stoichiometry()

Description copied from interface: IGridCalc.Event

Stoichiometries of species, negative on the lhs, positive on the rhs

Specified by:

substrate_stoichiometry in interface IGridCalc.Event

Specified by:

substrate_stoichiometry in class NextEventQueue.NextEvent

element2

public int element2()

Description copied from interface: IGridCalc.Event

"target" voxel number (different from source only for diffusion)

substrates_by_voxel

public Map<Integer,int[][]> substrates_by_voxel()

Specified by:

substrates_by_voxel in class NextEventQueue.NextEvent

leap_time

public double leap_time(double current)

Calculate leap_time based on the limit on variance and expected extents. As a temporary workaround for problem of updating deterministic solutions for large times, use the following formulas: y = (N/2 - Xm) p V = V1 + V2 = = X1 p1 (1-p1) + X2 p2 (1-p2) p1 = 1 - r1/(r1+r2) (1 - exp[-(r1+r2)t]) p2 = 1 - r2/(r1+r2) (1 - exp[-(r1+r2)t]) But assume linearity in y: y' = (N/2 - Xm) 2rt This gives: y' ≤ ε Xm t ≤ ε/2r Xm/(N/2 - Xm) V ≤ ε^2 Xm^2 p ≤ ε^2 Xm^2 / (X1 + ρX2) (in linear approximation for the square root) ρ = r2/r1 t ≤ - log (1-p1 (1+ρ)) / (r1 + r2)

leap_count

public int leap_count(double current,
                      double time,
                      boolean bidirectional)

Description copied from class: NextEventQueue.NextEvent

Calculate the (randomized) extent of the reaction based in the time given.

addRelations

public void addRelations(HashMap<Integer,ArrayList<NextEventQueue.NextEvent>> map,
                         String[] species,
                         boolean verbose)

Specified by:

addRelations in class NextEventQueue.NextEvent

Parameters:

map - contains, for every voxel, a list of events which depend on the state of that voxel. Subsequently, if this event should look at events attached to any voxel it modifies, and maybe add them as its relation.

toString

public String toString()

Overrides:

toString in class Object