mpacts.commands.misc. cellcycle

In order to be able to use this module import it like this:

import mpacts.commands.misc.cellcycle
#or assign it to a shorter name
import mpacts.commands.misc.cellcycle as cel

BinaryFissionCommand

class mpacts.commands.misc.cellcycle.BinaryFissionCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Binary Fission using a symmetrical dumb-bell description. The combined volume is kept constant during cytokinesis.
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • init_method — Method which should be used to initialize the cell division.
    • pc — Particle container on which the command is applied
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, init_method, [gate, predicate]
BinaryFissionCommand(name, parent, **kwargs)

CellDeathCommand

class mpacts.commands.misc.cellcycle.CellDeathCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Upon activation by a predicate, the cell will be flagged as dying and slowly become softer and less adhesive until it is removed from the simulation at a prescribed time ‘death_time’
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • death_time — Time it takes from initiating the cell death to deleting of the particle
    • pc — Particle container on which the command is applied
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, death_time, [gate, predicate]
CellDeathCommand(name, parent, **kwargs)

ChemModulatedGrowthCommand

class mpacts.commands.misc.cellcycle.ChemModulatedGrowthCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Growth model according to Qu et al 2005. During growth, cell volume increases linearly in time until a maximal radius ‘maxsize’ is reached. ‘maxsize’ is determined based upon the mean ‘radius_max’ and is standard deviation ‘radius_sd’. Moreover, the growth rate is modified based on the principal stress using a sigmoidal curve, with parameters ‘inflection_point’ and ‘steepness’
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • chem — Array containing the principal stresses of the cells. If not given, array ‘principal_stress’ is searched
    • density — Specific density of the cell (in absolute density)
    • growth_time — Time taken to grow from birth to maximum size
    • inflection_point — Inflection point (in [Pa]) of sigmoidal curve that modulates the growth rate
    • pc — Particle container on which the command is applied
    • radius_max — Mean maximum radius of the cell at which growth is stopped
    • radius_sd — Standard deviation on maximal radius to which the cell will grow using the growth model
    • steepness — Steepness (in [Pa^{-1}]) of the sigmoidal curve that modulates the growth rate
  • Optional keywords:
    • component (default value = -1) — Component of the principal stress vector (which is sorted from low - compressive - to high - tensile) to be used for modulating the growth rate. If not specified, the trace (s[0]+s[1]+s[2])/3 will be used
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • growth_const (default value = -1) — Growth constant used for calculating cell growth. Normally not given as parameter but calculated automatically
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
    • principal_stress (default value = None) — Array containing the principal stresses of the cells. If not given, array ‘principal_stress’ is searched
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, growth_time, radius_max, radius_sd, density, inflection_point, steepness, chem, [gate, predicate, growth_const, component, principal_stress]
ChemModulatedGrowthCommand(name, parent, **kwargs)

GrowthBudCommand

class mpacts.commands.misc.cellcycle.GrowthBudCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Calculates the radius of a bud that is growing on a mother cell.
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • init_method — Method which should be used to initialize the cell division.
    • pc — Particle container on which the command is applied
    • radius_init — Initial radius of a new bud
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, init_method, radius_init, [gate, predicate]
GrowthBudCommand(name, parent, **kwargs)

Growth_LinearCommand

class mpacts.commands.misc.cellcycle.Growth_LinearCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Growth model where the cell radius increases linearly in time until a maximal radius ‘maxsize’ is reached. ‘maxsize’ is determined based upon the mean ‘radius_max’ and is standard deviation ‘radius_sd’.
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • growth_time — Time taken to grow from birth to maximum size
    • pc — Particle container on which the command is applied
    • radius_max — Mean maximum radius of the cell at which growth is stopped
    • radius_sd — Standard deviation on maximal radius to which the cell will grow using the growth model
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • max_stress (default value = -1) — Maximum pressure (trace of the principal stress tensor), at which the cell still keeps growing
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, growth_time, radius_max, radius_sd, [gate, predicate, max_stress]
Growth_LinearCommand(name, parent, **kwargs)

Growth_QuCommand

class mpacts.commands.misc.cellcycle.Growth_QuCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Growth model according to Qu et al 2005. During growth, cell volume increases linearly in time until a maximal radius ‘maxsize’ is reached. ‘maxsize’ is determined based upon the mean ‘radius_max’ and is standard deviation ‘radius_sd’.
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • density — Specific density of the cell (in absolute density)
    • growth_time — Time taken to grow from birth to maximum size
    • pc — Particle container on which the command is applied
    • radius_max — Mean maximum radius of the cell at which growth is stopped
    • radius_sd — Standard deviation on maximal radius to which the cell will grow using the growth model
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • growth_const (default value = -1) — Growth constant used for calculating cell growth. Normally not given as parameter but calculated automatically
    • max_stress (default value = -1) — Maximum pressure (trace of the principal stress tensor), at which the cell still keeps growing
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, growth_time, radius_max, radius_sd, density, [gate, predicate, growth_const, max_stress]
Growth_QuCommand(name, parent, **kwargs)

LagTimeCommand

class mpacts.commands.misc.cellcycle.LagTimeCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

A timer will be activated upon activation by a given predicate. The child of this predicate should be a state predicate which signifies the ‘lagging’ state of the cell
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • lag_time — array which keeps the lag time.
    • pc — Particle container on which the command is applied
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, lag_time, [gate, predicate]
LagTimeCommand(name, parent, **kwargs)

QuiescenceCommand

class mpacts.commands.misc.cellcycle.QuiescenceCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Quiescent cells will be quiet and not grow nor divide until told otherwise
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • pc — Particle container on which the command is applied
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, [gate, predicate]
QuiescenceCommand(name, parent, **kwargs)

StressModulatedGrowthCommand

class mpacts.commands.misc.cellcycle.StressModulatedGrowthCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Growth model according to Qu et al 2005. During growth, cell volume increases linearly in time until a maximal radius ‘maxsize’ is reached. ‘maxsize’ is determined based upon the mean ‘radius_max’ and is standard deviation ‘radius_sd’. Moreover, the growth rate is modified based on the principal stress using a sigmoidal curve, with parameters ‘inflection_point’ and ‘steepness’
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • density — Specific density of the cell (in absolute density)
    • growth_time — Time taken to grow from birth to maximum size
    • inflection_point — Inflection point (in [Pa]) of sigmoidal curve that modulates the growth rate
    • pc — Particle container on which the command is applied
    • radius_max — Mean maximum radius of the cell at which growth is stopped
    • radius_sd — Standard deviation on maximal radius to which the cell will grow using the growth model
    • steepness — Steepness (in [Pa^{-1}]) of the sigmoidal curve that modulates the growth rate
  • Optional keywords:
    • component (default value = -1) — Component of the principal stress vector (which is sorted from low - compressive - to high - tensile) to be used for modulating the growth rate. If not specified, the trace (s[0]+s[1]+s[2])/3 will be used
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • growth_const (default value = -1) — Growth constant used for calculating cell growth. Normally not given as parameter but calculated automatically
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
    • principal_stress (default value = None) — Array containing the principal stresses of the cells. If not given, array ‘principal_stress’ is searched
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, growth_time, radius_max, radius_sd, density, inflection_point, steepness, [gate, predicate, growth_const, component, principal_stress]
StressModulatedGrowthCommand(name, parent, **kwargs)