/** * \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"); }