Single Channel Simulation

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Contents

Features

QuB can simulate the current generated by a Model. You can customize the simulation to:

  • start from equilibrium or from given entry probabilities
  • generate multiple data segments with the same entry probabilities
  • generate the response to a constant or time-varying stimulus
  • combine the current from multiple models
  • re-simulate automatically when anything in the model changes

Options

Model options

class amp, Std deviation
For conductance class (black:closed, red:open), set its mean current and noise profile in State Properties
entry probabilities
A state's entry probability is called "Starting prob" in State Properties. The default of all zeros makes it equally likely to start in any state. You can edit these numbers yourself -- they will be normalized to sum to 1.0 -- or set them to equilibrium using "Equilibrium P -> Calculate and assign" from the model's right-click menu.
ligand/voltage dependence
make a rate sensitive to ligand concentration or voltage by checking "P" or "Q" in Rate Properties and naming the variable. In simulation properties you can set a variable to a constant value or assign it to a stimulus protocol.
channel count
how many identical ion channels together in the simulated patch

Simulation options

To simulate, use the "Sim" or "Simulate" action button on the right. Like most action buttons in QuB, it is configured by right-clicking it, while left-clicking just runs it. Here are some relevant options; the full list is at Simulation:Simulate#Properties.

new/append/replace
When you repeat a simulation, the default is to replace the data from the previous simulation
model(s)
The current model in the Model window is the default. You can choose a different (open) model, or control-click to multi-select. All selected models will be simulated together.
parameters
If one or more rates in your model are ligand- or voltage-dependent, set the concentration or voltage here
microscopic or macroscopic
microscopic: sums the activity of each of n channels
macroscopic: scales the ideal ensemble current by n
A/D channel count
(for new data files) always 1 unless you're simulating with an #Acquisition Protocol (then it's the number of stimulus channels + 1)
scaling
(for new data files) determines the smallest and largest data values that can be represented in the file. See Data Theory#Choosing a Scaling value.

Acquisition Protocol

To simulate the response to a time-varying stimulus, you first build the stimulus in the Acquisition Protocol window. Then in simulation properties, set stimulation:file and choose your protocol. Multiple stimuli are possible; assign each variable to an a/d channel under "Parameters".

Tutorials

In the simulation tutorial we generate several data files which will be used for the analysis tutorials.


Prev: Single Channel Analysis Outline Next: Tutorial:Simulation
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