Modigliani  2.0
A stochastic simulator for axons, neurons, and networks
Public Member Functions | List of all members
modigliani_core::Lua_based_stochastic_voltage_gated_channel Class Reference

Stochastic ion channel with transition probabilities read from a lua script. More...

+ Inheritance diagram for modigliani_core::Lua_based_stochastic_voltage_gated_channel:

Public Member Functions

 Lua_based_stochastic_voltage_gated_channel (modigliani_base::Real newArea, modigliani_base::Real newDensity, modigliani_base::Real newConductivity, modigliani_base::Real reversalPotential, modigliani_base::Real newTimeStep, modigliani_base::Real newTemperature, string fileName)
 Loads transition probabilities by running a lua script. More...
 
virtual modigliani_base::Real ComputeTimeConstant () const
 Returns channels time constant. More...
 
virtual modigliani_base::Real ComputeConductance () override
 Sets the conductance of the membrane current to the value given by the number of open channels. More...
 
virtual modigliani_base::ReturnEnum StepCurrent () override
 Calculates all transitions in ion channels. More...
 
virtual modigliani_base::Real OpenChannels () const override
 Returns number of open ionic channels. More...
 
- Public Member Functions inherited from modigliani_core::Voltage_gated_ion_channel_current
 Voltage_gated_ion_channel_current (modigliani_base::Real reversalPotential, modigliani_base::Real density, modigliani_base::Real area, modigliani_base::Real conductivity)
 Constructor. More...
 
modigliani_base::Real density () const
 Returns channel density. More...
 
modigliani_base::Real area () const
 Returns membrane surface area. More...
 
modigliani_base::Real conductivity () const
 Returns conductivity per channel. More...
 
modigliani_base::Real MaxConductivity () const
 Conductivity if all channels open. More...
 
void UpdateNumChannels ()
 Sets the number of channels to agree with the membrane area and the density of channels.
 
modigliani_base::Real num_channels () const
 Returns number of ionic channels. More...
 
modigliani_base::Real OpenChannelsRatio () const
 Returns ratio of open channels over total number of channels. More...
 
- Public Member Functions inherited from modigliani_core::Membrane_current
 Membrane_current (modigliani_base::Real reversalPotential)
 Constructs a current. More...
 
modigliani_base::Real conductance () const
 Returns momentary conductance. More...
 
void set_reversal_potential (modigliani_base::Real eRev)
 Sets the reversal potential. More...
 
modigliani_base::Real reversal_potential () const
 Returns the reversal potential. More...
 
modigliani_base::Real temperature () const
 Returns the temperature. More...
 
modigliani_base::ReturnEnum set_temperature (modigliani_base::Real newTemp)
 Sets the temperature. More...
 
modigliani_base::Real q10 () const
 Returns the Q10 factor. More...
 
virtual modigliani_base::ReturnEnum set_q10 (modigliani_base::Real newQ10)
 Sets the Q10 factor. More...
 
enum StochasticType simulation_mode () const
 Returns the simulation mode. More...
 
virtual void set_simulation_mode (enum StochasticType newMode)
 Sets simulation mode. More...
 
void set_voltage (modigliani_base::Real newVoltage)
 Sets the membrane potential. More...
 
modigliani_base::ReturnEnum Step (modigliani_base::Real newVm)
 Runs one step of the simulation, updates the conductance and the current flowing through. More...
 
modigliani_base::Real ComputeCurrent (modigliani_base::Real vM)
 Computes, sets and returns the current going through. More...
 
virtual modigliani_base::Real ComputeTimeConstant ()
 Computes and returns the rate constants. More...
 
modigliani_base::Real current () const
 Returns the current. More...
 
- Public Member Functions inherited from modigliani_core::Object
modigliani_base::Real timestep () const
 Returns simulation timestep. More...
 
void set_timestep (modigliani_base::Real newTimeStep)
 Sets simulation timestep. More...
 

Additional Inherited Members

- Protected Member Functions inherited from modigliani_core::Membrane_current
modigliani_base::Real set_current (modigliani_base::Real newVal)
 Sets the current. More...
 
modigliani_base::Real set_conductance (modigliani_base::Real newVal)
 Sets the conductance. More...
 
- Protected Attributes inherited from modigliani_core::Membrane_current
modigliani_base::Real voltage_
 Membrane potential in [ $\si{\milli\volt}$].
 
modigliani_base::Real temperature_
 Temperature in [ $\si{\celsius}$].
 

Detailed Description

Stochastic ion channel with transition probabilities read from a lua script.

Transition probabilities are read for a range of membrane potentials by calling a lua script. The actual simulations are carried inside the program.

Constructor & Destructor Documentation

modigliani_core::Lua_based_stochastic_voltage_gated_channel::Lua_based_stochastic_voltage_gated_channel ( modigliani_base::Real  newArea,
modigliani_base::Real  newDensity,
modigliani_base::Real  newConductivity,
modigliani_base::Real  reversalPotential,
modigliani_base::Real  newTimeStep,
modigliani_base::Real  newTemperature,
string  fileName 
)

Loads transition probabilities by running a lua script.

Parameters
newAreaMembrane area in [ $\si{\micro\meter\squared}$]
newDensityChannel density [ $\si{\per\micro\meter\squared}$]
newConductivityMax conductivity [ $\si{\milli\siemens}$] per channel
reversalPotentialCurrent reversal potential [ $\si{\milli\volt}$]
newTimeStepSimulation time step [ $\si{\milli\second}$]
newTemperatureSimulation temperature [ $\si{\celsius}$]
fileNameLua script

The lua script must define the following variables :

  • float base_temp
  • uint number_states
  • array(uint) open_states
  • float minV
  • float maxV
  • float step

The lua script must define the following functions :

  • get_probability(uint, uint, float)
  • get_q10(uint, uint)

See SGA_sodium.lua for an example of such a lua script.

Member Function Documentation

modigliani_base::Real modigliani_core::Lua_based_stochastic_voltage_gated_channel::ComputeConductance ( )
inlineoverridevirtual

Sets the conductance of the membrane current to the value given by the number of open channels.

Returns
Conductance in [ $\si{\milli\siemens}$]

Implements modigliani_core::Membrane_current.

modigliani_base::Real modigliani_core::Lua_based_stochastic_voltage_gated_channel::ComputeTimeConstant ( ) const
inlinevirtual

Returns channels time constant.

Returns
Time constant in [ $\si{\per\second}$]
modigliani_base::Real modigliani_core::Lua_based_stochastic_voltage_gated_channel::OpenChannels ( ) const
inlineoverridevirtual

Returns number of open ionic channels.

Returns
Number of open channels

Implements modigliani_core::Voltage_gated_ion_channel_current.

modigliani_base::ReturnEnum modigliani_core::Lua_based_stochastic_voltage_gated_channel::StepCurrent ( )
inlineoverridevirtual

Calculates all transitions in ion channels.

Returns
Status
Warning
Does not update conductance

Implements modigliani_core::Membrane_current.


The documentation for this class was generated from the following files: