mpacts.commands.force.constraints. changevolume

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

import mpacts.commands.force.constraints.changevolume
#or assign it to a shorter name
import mpacts.commands.force.constraints.changevolume as cha

ComputeActiveIonTransportCommand

class mpacts.commands.force.constraints.changevolume.ComputeActiveIonTransportCommand

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

Computes the net flow rate of ions due to active (ion) pumps [mol/s]. The pumps work as long as the osmotic pressure in the cell is lower than the critical pump pressure. This command should be used for volume regulation at long time scales.
Default location: ‘loop_cmds/pre_integration_cmds’
  • Required keywords:
    • KActive (s^3 . mol . kg^-2 . m^-2) — Rescaled ion permeability constant of active ion pumps: J_a = KActive * (Pi_a - (Pi_{in} - Pi_{out}).
    • MCrit (kg . m^-1 . s^-2) — Critical pumping pressure in Pa: PCrit=Pi_{out}*delta G_A/(R*T)``with ``delta G_A as the free energy gain upon hydrolysis of ATP in physiological conditions in J/mol
    • 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, KActive, MCrit, [gate, predicate]
ComputeActiveIonTransportCommand(name, parent, **kwargs)

ComputePassiveIonTransportCommand

class mpacts.commands.force.constraints.changevolume.ComputePassiveIonTransportCommand

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

Computes the net flow rate of ions due to passive mechanosensitive membrane channels [mol/s]. The channels are membrane proteins that can open a pore in response to mechanical stimuli and act as emergency valves. The channels only open if a certain threshold is surpassed. This command should be used for volume regulation at long time scales.
Default location: ‘loop_cmds/pre_integration_cmds’
  • Required keywords:
    • KPassive (s^3 . mol . m^-1 . kg^-2) — Ion permeability of passive mechanosensitive channels: J_p = -KPassive * (P - P_c) * (Pi_{in} - Pi_{out})..
    • pCrit (kg . s^-2) — Critical pressure for opening the passive ion channels``J_p = -KPassive * (P - P_c) * (Pi_{in} - Pi_{out})``.
    • 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, KPassive, pCrit, [gate, predicate]
ComputePassiveIonTransportCommand(name, parent, **kwargs)

ComputeVolumeRegulationCommand

class mpacts.commands.force.constraints.changevolume.ComputeVolumeRegulationCommand

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

This command updates the equilibrium volume and amount of ions in the cells based on the net flows.
Default location: ‘loop_cmds/integration_cmds’
  • Required keywords:
    • MOut (kg . m^-1 . s^-2) — Osmotic pressure of medium
    • T (K) — Temperature in K
    • 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, MOut, T, [gate, predicate]
ComputeVolumeRegulationCommand(name, parent, **kwargs)

ComputeWaterFluxCommand

class mpacts.commands.force.constraints.changevolume.ComputeWaterFluxCommand

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

Computes the flow rate of water due to membrane permeability and pores [m^3/s].The permeability coefficient can be altered to include aquaporins ect. This command should be used for volume regulation at long time scales. The waterflux has hydrostatic and osmotic pressure contributions.
Default location: ‘loop_cmds/pre_integration_cmds’
  • Required keywords:
    • KWater (kg . s^-3) — cell membrane water permeability: dV_0/dt = -KWater * Area * J_{H_2O}.
    • 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, KWater, [gate, predicate]
ComputeWaterFluxCommand(name, parent, **kwargs)