/**
* \brief Examines all the agents within a voxel of the agent-grid, to determine if a swimming
* agent is in contact with an agent in the biofilm
*
* <p>To determine if a swimming cell is near contact with the biofilm surface, the agent checks
* the status of the agent grid voxel it resides within. If this is 1, this is noted as having
* agents within it that are within the biofilm structure. The agent now examines how close it is
* to each of these agents. If within a certain distance (radius + stickiness constant), then the
* agent is deemed to have adhered to the structure. Any overlap will be addressed during shoving
* analysis. If not, the agent will perform another move.
*
* @author Kieran Alden
* @param gridIndex The index of the agent grid to be checked
* @param distanceSeekingAgent The distance within which two cells are deemed to be in contact
* @return Boolean noting whether the agent is in contact with an agent in the biofilm
*/
public Boolean isAgentInContactWithAgentInBiofilm(int gridIndex, double distanceSeekingAgent) {
LocatedGroup agentsInGrid = currentSimulator.agentGrid.returnGroupInVoxel(gridIndex);
Double dist = 0.0;
// Now iterate through each one. If we're close enough, move done.
// Shoving can then sort out distance between the two cells.
for (LocatedAgent aLoc : agentsInGrid.group)
dist = aLoc.getLocation().distance(swimmingAgentPosition);
if (dist <= distanceSeekingAgent) return true;
// If not, we'll do another move.
return false;
}
/**
* \brief On agent division, divides the mass between the old and new agent, at a specified
* fraction
*
* <p>On agent division, divides the mass between the old and new agent, at a specified fraction
*
* @param baby The new agent, which is inheriting mass
* @param babyMassFrac The fraction of this agents mass that should be transferred to the new
* agent
*/
public void divideCompounds(LocatedAgent baby, double babyMassFrac) {
// Choose the division plan and apply position modifications
for (int i = 0; i < particleMass.length; i++) {
baby.particleMass[i] *= babyMassFrac;
this.particleMass[i] *= 1 - babyMassFrac;
}
// Update radius, mass, volumes and growth rates
updateSize();
baby.updateSize();
updateGrowthRates();
baby.updateGrowthRates();
}
/**
* \brief Create a new agent in a specified position
*
* <p>Create a new agent in a specified position
*
* @param position Vector stating where this agent should be located
*/
public void createNewAgent(ContinuousVector position) {
try {
// Get a clone of the progenitor
LocatedAgent baby = (LocatedAgent) sendNewAgent();
baby.giveName();
// randomize its mass
baby.mutatePop();
baby.updateSize();
this._myDivRadius = getDivRadius();
baby._myDivRadius = getDivRadius();
baby._myDeathRadius = getDeathRadius();
// Just to avoid to be in the carrier
position.x += this._totalRadius;
baby.setLocation(position);
baby.registerBirth();
} catch (CloneNotSupportedException e) {
utils.LogFile.writeLog("Error met in LocAgent:createNewAgent()");
}
}
/**
* \brief Pulling : The movement of agents by a shrinking biofilm. Move calculated and added to
* the agents movement vector.
*
* <p>The movement of agents by a shrinking biofilm. Move calculated and added to the agents
* movement vector.
*
* @param aNeighbor Reference to the potentially shoving neighbour
* @param isMutual Whether movement is shared between two agents or applied only to this one
* @param gain Double noting change in position
* @return Boolean stating whether pulling is detected (true) or not (false)
*/
public boolean addSpringMovement(LocatedAgent aNeighbor, boolean isMutual, double gain) {
double d, distance, delta;
if (aNeighbor == this) return false;
// Build the escape vector and find the distance between you and your
// neighbourhood
d = computeDifferenceVector(_location, aNeighbor._location);
_diff.normalizeVector();
distance = getShoveRadius() + aNeighbor.getShoveRadius();
distance += getSpeciesParam().shoveLimit;
delta = d - distance;
double lMax = _totalRadius;
if (delta > 0) gain *= Math.exp(-delta * 5 / (lMax));
if (delta > lMax) gain = 0;
/* Apply shoving _________________________________________________ */
if (isMutual) {
_diff.times(-0.5 * delta * gain);
this._movement.add(_diff);
aNeighbor._movement.subtract(_diff);
} else {
_diff.times(-delta * gain);
this._movement.add(_diff);
}
return (_movement.norm() > _radius * gain);
}
/**
* \brief Mutual shoving : The movement by shoving of an agent is calculated based on the cell
* overlap and added to the agents movement vector.
*
* <p>Mutual shoving : The movement by shoving of an agent is calculated based on the cell overlap
* and added to the agents movement vector. Both agents are moved of half the overlapping distance
* in opposite directions.
*
* @param aNeighbour Reference to the potentially shoving neighbour
* @param isMutual Whether movement is shared between two agents or applied only to this one
* @param gain Double noting change in position
* @return Boolean stating whether shoving is detected (true) or not (false)
*/
public boolean addPushMovement(LocatedAgent aNeighbour, boolean isMutual, double gain) {
double d, distance;
if (aNeighbour == this) return false;
// Build the escape vector and find the distance between you and your
// neighbourhood
d = computeDifferenceVector(_location, aNeighbour._location);
_diff.normalizeVector();
// Compute effective cell-cell distance
distance = getShoveRadius() + aNeighbour.getShoveRadius();
distance += getSpeciesParam().shoveLimit;
distance = d - distance;
/* Apply shoving _________________________________________________ */
// Compute shoving distance for the current agent
if (distance <= 0) {
if (isMutual) {
_diff.times(gain * 0.5 * Math.abs(distance));
this._movement.add(_diff);
aNeighbour._movement.subtract(_diff);
} else {
_diff.times(Math.abs(gain * distance));
this._movement.add(_diff);
}
return true;
} else {
return false;
}
}
/**
* \brief Used in 'one-time' attachment scenarios, where clones of the progenitor are created in
* the birth area of the substratum.
*
* @param spRoot The XML mark-up group for a particular species being created.
*/
public void createPop(XMLParser spRoot) {
int howMany = spRoot.getAttributeInt("number");
if (howMany <= 0) return;
// Define the birth area - this is taken from the coordinates tags in the protocol file
// (Nov13) OR if an initial area is not declared, this is the whole Y and Z of the domain with a
// height of 1.
ContinuousVector[] _initArea = defineSquareArea(spRoot);
// Create all the required agents
ContinuousVector cc = new ContinuousVector();
for (int i = 0; i < howMany; i++)
if (_progenitor instanceof LocatedAgent) {
// Set coordinates within the birth area - randomly
if (!Simulator.isChemostat) shuffleCoordinates(cc, _initArea);
// Create the agent at these coordinates
((LocatedAgent) _progenitor).createNewAgent(cc);
} else _progenitor.createNewAgent();
LogFile.writeLog(
howMany
+ " agents of species "
+ speciesName
+ " for one-time attachment successfully created");
}
/**
* \brief Find a sibling of this agent
*
* <p>Find a sibling of this agent
*
* @param indexSpecies The index used to reference this species in the simulation dictionary
*/
public void findCloseSiblings(int indexSpecies) {
int nNb;
boolean test;
double shoveDist;
LocatedAgent aNb;
getPotentialShovers(getInteractDistance());
nNb = _myNeighbors.size();
for (int iNb = 0; iNb < nNb; iNb++) {
aNb = _myNeighbors.removeFirst();
// test EPS-species
test = (indexSpecies == aNb.speciesIndex);
// Test distance
shoveDist = 2 * (getShoveRadius() + aNb.getShoveRadius());
test = test && computeDifferenceVector(_location, aNb.getLocation()) <= shoveDist;
if (test & aNb != this) _myNeighbors.addLast(aNb);
}
}
/**
* \brief With it determined that cell division will occur, create a new agent from the existing
* one
*
* <p>With it determined that cell division will occur, create a new agent from the existing one
*
* @throws CloneNotSupportedException Thrown if the agent cannot be cloned
*/
public void makeKid() throws CloneNotSupportedException {
// Create the new instance
LocatedAgent baby = (LocatedAgent) sendNewAgent();
// Note that mutateAgent() does nothing yet
baby.mutateAgent();
this._myDivRadius = getDivRadius();
baby._myDivRadius = getDivRadius();
baby._myDeathRadius = getDeathRadius();
// Update the lineage
recordGenealogy(baby);
// Share mass of all compounds between two daughter cells and compute
// new size
divideCompounds(baby, getBabyMassFrac());
// sonia:chemostat
if (Simulator.isChemostat) {
// upon division the daughter cells remain with the coordinates of their progenitor
} else {
// Compute movement to apply to both cells
setDivisionDirection(getInteractDistance(baby) / 2);
// move both daughter cells
baby._movement.subtract(_divisionDirection);
_movement.add(_divisionDirection);
}
// Now register the agent inside the guilds and the agent grid
baby.registerBirth();
baby._netVolumeRate = 0;
}
/**
* \brief On agent division, transfers EPS between the old and new agent, at a specified ratio
*
* <p>On agent division, transfers EPS between the old and new agent, at a specified ratio
*
* @param baby The new agent, which is inheriting mass
* @param splitRatio The ratio of the EPS that should be transferred to the new agent
*/
public void transferCompounds(LocatedAgent baby, double splitRatio) {
// Choose the division plan and apply position modifications
double m;
for (int i = 0; i < particleMass.length; i++) {
m = this.particleMass[i] * splitRatio;
baby.particleMass[i] += m;
this.particleMass[i] = this.particleMass[i] - m;
}
// Update radius, mass and volumes
updateSize();
baby.updateSize();
}
@SuppressWarnings("unchecked")
/**
* \brief Creates a daughter Located Agent by cloning this agent and parameter objects
*
* <p>Creates a daughter Located Agent by cloning this agent and parameter objects
*
* @throws CloneNotSupportedException Thrown if the agent cannot be cloned
*/
public Object clone() throws CloneNotSupportedException {
LocatedAgent o = (LocatedAgent) super.clone();
o._location = (ContinuousVector) this._location.clone();
o._movement = (ContinuousVector) this._movement.clone();
o._divisionDirection = (ContinuousVector) this._divisionDirection.clone();
o._myNeighbors = (LinkedList<LocatedAgent>) this._myNeighbors.clone();
o._agentGridIndex = this._agentGridIndex;
return (Object) o;
}
/**
* \brief Return the shoving interaction distance to be used in shoving against a specified agent
*
* <p>Return the shoving interaction distance to be used in shoving against a specified agent
*
* @return Double specifying the shoving interaction distance that will be applied
*/
public double getInteractDistance(LocatedAgent baby) {
return getShoveRadius() + baby.getShoveRadius() + ((LocatedParam) _speciesParam).shoveLimit;
}
/**
* \brief For self-attachment scenarios, initialises agents on the boundary layer rather than
* substrarum, and models their swim to the surface or biofilm
*
* <p>For self-attachment scenarios, the agents are initialised at the top of the boundary layer
* rather than on the substratum. These agents then perform a 'run and tumble' motion until they
* either attach to the substratum or forming biofilm. This method captures this behaviour for
* cells that are created for a time step. Once this swimming action has been performed, the agent
* is created at its final position. Note that input of agents onto the boundary layer is decided
* by a parameter set in the protocol file, cellAttachmentFrequency, measured in hours. The number
* of cells is adjusted to suit the global time step that is being used. Also note that this
* injection of cells can be for a set period (specified in the protocol file as parameter
* cellInjectionPeriod), or can be stopped and started (modelling a 'settling' period) using
* parameters cellInjectionOffPeriod and cellInjectionStopHour. This is explained in detail in the
* tutorial for version 1.2 of iDynoMiCS.
*
* @param spRoot The Species markup from the protocol file for one particular species being
* initialised
* @param numberAttachedInjectedAgents The number of agents of this type that need to be created
* in this global timestep
*/
public void createBoundaryLayerPop(XMLParser spRoot, int numberAttachedInjectedAgents) {
LogFile.writeLog(
"\t\tAttempting to create "
+ numberAttachedInjectedAgents
+ " agents of "
+ speciesName
+ " in the boundary layer");
// Create all the required agents
// Note that this continues UNTIL THE DESIRED NUMBER OF CELLS HAVE ATTACHED SOMEWHERE
// Just out of interest, I've decided to keep a count of how many cells are required for this to
// happen
int totalNumberOfInjectedAgents = 0;
int agentsReturnedToBulk = 0;
int requiredNumAttachedAgents = numberAttachedInjectedAgents;
// Temporary DiscreteVector to make finding the boundary layer tidier.
DiscreteVector dV = new DiscreteVector();
while (numberAttachedInjectedAgents > 0) {
totalNumberOfInjectedAgents++;
if (_progenitor instanceof LocatedAgent) {
swimmingAgentPosition.reset();
// Now to choose coordinates for this particular agent
while (true) {
// This cell needs to take a random location in the Z and Y
// directions. The X will come from the position of the
// boundary layer on those axes. Generate these randomly.
swimmingAgentPosition.y = ExtraMath.getUniRandDbl() * domain.length_Y;
if (domain.is3D) {
swimmingAgentPosition.z = ExtraMath.getUniRandDbl() * domain.length_Z;
}
// Now to work out the X coordinate. This is based on where
// the top of the boundary layer is when this agent is
// created. The top of the boundary layer is calculated in
// Domain at each step. Now the resolution differs (this is
// in nI x nJ x nK rather than microns - so this will need
// to be converted accordingly. Method to calculate this:
// - get the value from the top of the boundary layer
// - reduce by 1 (such that the micron value will be the
// top of the layer)
// - multiply by resolution of this domain.
dV.set(swimmingAgentPosition, domain._resolution);
if (!domain.is3D) dV.k = 1;
swimmingAgentPosition.x = domain._topOfBoundaryLayer[dV.j][dV.k] - 1.0;
swimmingAgentPosition.x *= domain._resolution;
// Check this is ok.
// System.out.println("Trying starting position "+dV.toString()+" =>
// "+this.swimmingAgentPosition.toString());
if (domain.testCrossedBoundary(swimmingAgentPosition) == null) break;
}
// Now we can do the run and tumble motion of these cells
int cellRunResult = performRunAndTumble(spRoot);
// If increment the relevant counters, as these may be useful
switch (cellRunResult) {
case 1: // Successfully Attached
numberAttachedInjectedAgents--;
// Create the agent at these coordinates
((LocatedAgent) _progenitor).createNewAgent(this.swimmingAgentPosition);
// System.out.println("Cell "+swimmingAgentPosition.toString()+" attached");
break;
case 2:
// System.out.println("Cell at "+swimmingAgentPosition.toString()+" returned to bulk");
agentsReturnedToBulk++;
break;
}
} else {
// If this isn't a located species, just create a new agent.
_progenitor.createNewAgent();
}
}
// Write the stats to the log file incase of interest
LogFile.writeLog(
requiredNumAttachedAgents
+ " agents of species "
+ speciesName
+ " for self-attachment successfully created");
LogFile.writeLog(
totalNumberOfInjectedAgents + " agents of species " + speciesName + " attempted to attach");
LogFile.writeLog(
agentsReturnedToBulk + " agents of species " + speciesName + " returned to the bulk");
}