/**
* \brief Select random coordinates for the new agent within a restricted birth area
*
* <p>Select random coordinates for the new agent within a restricted birth area. This restricted
* area is set within the protocol file, and defined as a ContinuousVector by the method
* defineSquareArea
*
* @param cc ContinuousVector that will hold the coordinates of this agent
* @param area Area within which these coordinates should be restricted
*/
public void shuffleCoordinates(ContinuousVector cc, ContinuousVector[] area) {
do {
cc.x = ExtraMath.getUniRandDbl(area[0].x, area[1].x);
cc.y = ExtraMath.getUniRandDbl(area[0].y, area[1].y);
cc.z = ExtraMath.getUniRandDbl(area[0].z, area[1].z);
} while (domain.testCrossedBoundary(cc) != null);
}
/**
* \brief Set the movement vector that states where to put a newly-created particle
*
* <p>Set the movement vector that states where to put a newly-created particle
*
* @param distance Distance between the this agent and the new agent
*/
public void setDivisionDirection(double distance) {
double phi, theta;
phi = 2 * Math.PI * ExtraMath.getUniRandDbl();
theta = 2 * Math.PI * ExtraMath.getUniRandDbl();
_divisionDirection.x = distance * Math.sin(phi) * Math.cos(theta);
_divisionDirection.y = distance * Math.sin(phi) * Math.sin(theta);
_divisionDirection.z = (_agentGrid.is3D ? distance * Math.cos(phi) : 0);
}
/**
* Called during the division of an EpiBac ; apply the segregation of plasmids, modify the number
* for the plasmid calling the method and sends the number for the other one.
*
* @param aPlasmid Episome
*/
public void segregation(Episome aPlasmid) {
if (ExtraMath.getUniRandDbl() > getSpeciesParam().lossProbability) {
_nCopy = 1;
aPlasmid._nCopy = 1;
} else {
_nCopy =
0; // jan: this introduces a bias, the 'old' cell always looses the plasmid. If the two
// daughter cells are not equal, then this is poor
aPlasmid._nCopy = 1;
}
}
public Boolean testProficiency() {
Double alea = ExtraMath.getUniRandDbl();
return (alea <= getSpeciesParam().transferProficiency);
}
/**
* \brief For self-attachment scenarios, determines whether a swimming agents move has taken it
* across a boundary, correcting the coordinate accordingly
*
* <p>For self-attachment scenarios, the agents are swimming through the domain, and we need to
* ensure that they perform the correct behaviour when the boundary is met. This method checks
* whether an agents move has taken it over the boundary and applies the relevant correction
* (either a bounce off the boundary or a reappearance on the other side). If the cell has hit the
* surface, the cell is deemed to have adhered to that surface and a relevant x coordinate
* generated to note that this is the case. The top of the domain is dealt with differently, as
* this is checked by the call to isNewCoordAboveBoundaryLayer, which determines if the agent has
* moved out of the boundary layer. If this is the case we assume this cell to have returned to
* the bulk and do no further action with that cell. An integer is returned noting the fate of
* this move - a 0 if the move is ok (after adjustment if required), a 1 if the agent has met the
* substratum and attached, and a 2 if the cell has returned to the bulk
*
* @param distanceMoving Distance the agent is moving (in microns) in this move
* @return Integer noting the fate of this move (0 move ok (after adjustment if required), 1 if
* attached to surface, 2 if returned to bulk
*/
public int agentMoveBorderCheck() {
// Simplest test to do first is to check if any boundaries have been crossed
AllBC boundaryCrossed = domain.testCrossedBoundary(swimmingAgentPosition);
// First is a simple test - has the cell returned to the bulk
// If this is the case, we can just forget this and have another go
// The cell will only have the capability to return to the bulk if the angle has it moving
// upwards or directly across
// (i.e 0-90 and 270-360 degrees)
if (isNewCoordAboveBoundaryLayer()) {
// The cell has returned into the bulk, and thus this try is over.
// Return 2 so the process starts with a new cell.
return 2;
} else {
// Now to see if the move takes the point outside any of the boundaries
if (boundaryCrossed == null) {
// No borders crossed, not back in the bulk.
return 0;
} else {
String boundaryCrossedName = boundaryCrossed.getSideName();
if (boundaryCrossedName.equals("y0z")) {
// Detected that the move has crossed the substratum, thus
// the cell has hit the biofilm. A return of 1 indicates
// that this is the case.
// Hit the biofilm, so set the species coordinates as required.
// We may have hit the biofilm but the Y and Z coordinates
// in this generated move may still be negative (as they
// may have gone over another boundary). So before we set
// the final x, we should check Y and Z.
// So firstly, set the X position onto the surface
swimmingAgentPosition.x = ExtraMath.getUniRandDbl();
// Now set the final X position.
// Do a new check on the boundary crossed.
boundaryCrossed = domain.testCrossedBoundarySelfAttach(swimmingAgentPosition);
if (boundaryCrossed != null) {
boundaryCrossedName = boundaryCrossed.getSideName();
if (boundaryCrossedName.equals("xNz") || boundaryCrossedName.equals("x0z"))
correctCrossedLeftRightBoundaries(boundaryCrossed);
else correctCrossedFrontBackBoundaries(boundaryCrossed);
}
return 1;
} else if (boundaryCrossedName.equals("xNz") || boundaryCrossedName.equals("x0z")) {
correctCrossedLeftRightBoundaries(boundaryCrossed);
return 0;
}
// Deal with 3D boundary too
else if (boundaryCrossedName.equals("x0y") || boundaryCrossedName.equals("xNy")) {
correctCrossedFrontBackBoundaries(boundaryCrossed);
return 0;
} else {
// This needs to be here so the function returns something.
// However this deals with the top boundary (yNz) and this
// has already been dealt with by the crossed bulk method.
// So it is highly doubtful we will ever end up here.
return 0;
}
}
}
}
/**
* \brief Set the angles an agent is to move in this tumble. If the domain is 3D, a move will
* involve calculation of
*
* <p>Set the angles an agent is to move in this tumble. If the domain is 3D, a move will involve
* calculation of two angles. This is done using a random number generator
*/
public void setAgentAngleOfMovement() {
angleOfMovingAgentXY = ExtraMath.getUniRandDbl(0.0, 2 * Math.PI);
if (domain.is3D) angleOfMovingAgentXZ = ExtraMath.getUniRandDbl(0.0, 2 * Math.PI);
else angleOfMovingAgentXZ = 0.0;
}
/**
* \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");
}