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Version 1.2 (June 2013)
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Version 1.2 (June 2013)
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Extends ActiveParam by adding location and behaviour parameters to a defined agent. More...
Public Member Functions | |
| LocatedParam () | |
| Create a new LocatedParam parameter storage object, calling the relevant extended class constructors. More... | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Assigns values to each of the location and behavioural specific parameters, reading these from the protocol file. More... | |
| double | getCellRunSpeed () |
| Return the cell run speed. Used in agent self-attachment scenarios. More... | |
| double | getStickinessRadius () |
| Return the cell stickiness radius. Used in agent self-attachment scenarios. More... | |
 Public Member Functions inherited from simulator.agent.ActiveParam | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Stores the reaction parameters for an active species and calculates the particle density of compounds involved in the reaction. More... | |
| Public Member Functions inherited from simulator.agent.SpeciesParam | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Read in specific parameters for this species, changing the default if required. More... | |
Public Attributes | |
| double | divRadius = .97 |
| double | divRadiusCV = .1 |
| double | babyMassFrac = .5 |
| double | babyMassFracCV = .1 |
| double | deathRadius = .2 |
| double | deathRadiusCV = .1 |
| double | shoveFactor = 1.15 |
| double | shoveLimit = 0 |
| double | cellRunSpeed |
| double | tumbleInterval |
| double | stickinessAddition |
| Public Attributes inherited from simulator.agent.ActiveParam | |
| double[] | particleDensity |
| double[][] | soluteYield |
| double[][] | particleYield |
| double[][] | reactionKinetic |
| double[] | lysisYield |
| Public Attributes inherited from simulator.agent.SpeciesParam | |
| double | initialMassCV = .1 |
Extends ActiveParam by adding location and behaviour parameters to a defined agent.
Extends ActiveParam by adding location and behaviour parameters to a defined agent. These parameters include the radius at which division occurs, the radius at which death occurs, and for self attach simulations, parameters involved in simulating a cells run and tumble motion
| simulator.agent.LocatedParam.LocatedParam | ( | ) |
Create a new LocatedParam parameter storage object, calling the relevant extended class constructors.
Create a new LocatedParam parameter storage object, calling the relevant extended class constructirs
| double simulator.agent.LocatedParam.getCellRunSpeed | ( | ) |
Return the cell run speed. Used in agent self-attachment scenarios.
Return the cell run speed. Used in agent self-attachment scenarios
| double simulator.agent.LocatedParam.getStickinessRadius | ( | ) |
Return the cell stickiness radius. Used in agent self-attachment scenarios.
Return the cell stickiness radius. Used in agent self-attachment scenarios. Captures the hypothesis that for some biological bacterial cells such as e-coli, there will be receptors on the outside of the cell that adhere to the biofilm or substratum surface, and thus this needs to be added to the cell radius
Assigns values to each of the location and behavioural specific parameters, reading these from the protocol file.
Assigns values to each of the location and behavioural specific parameters, reading these from the protocol file
| aSim | The simulation object used to simulate the conditions specified in the protocol file |
| aSpeciesRoot | A Species mark-up within the specified protocol file |
| double simulator.agent.LocatedParam.babyMassFrac = .5 |
Fraction of the mother's total mass that is given to the baby. Formerly called splitRatio
| double simulator.agent.LocatedParam.babyMassFracCV = .1 |
Degree of stochasticity used in determining cell mass distribution
| double simulator.agent.LocatedParam.cellRunSpeed |
For simulations that model self attachment to the substratum, the agents move from the boundary layer in a random walk. This parameter captures the speed of that move (KA 170513)
| double simulator.agent.LocatedParam.deathRadius = .2 |
Minimal radius before death (in m)
| double simulator.agent.LocatedParam.deathRadiusCV = .1 |
Degree of stochasticity used in determining cell death
| double simulator.agent.LocatedParam.divRadius = .97 |
Division radius (in µm)
| double simulator.agent.LocatedParam.divRadiusCV = .1 |
Degree of stochasticity used in determining cell division behaviour
| double simulator.agent.LocatedParam.shoveFactor = 1.15 |
Multiplier of the full radius to enhance distance between cells
| double simulator.agent.LocatedParam.shoveLimit = 0 |
Minimal distance between two cells (after shovingRadius computation)
| double simulator.agent.LocatedParam.stickinessAddition |
Some cells (e.g. some e-coli species) will express molecules on the surface that will stick to any other surface. For versions of the simulation where self-attachment is being modelled, this parameter captures the extra cell dimension that needs to be considered in collision detection (to see if the agent sticks) (KA 170513)
| double simulator.agent.LocatedParam.tumbleInterval |
For simulations that model self attachment to the substratum, the agents move from the boundary layer in a random walk. This parameter captures the interval at which the cell will 'tumble' and change direction (KA 170513)
1.8.3.1
