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Modeling action potentials
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Procedure:

 

Kindly go through the procedure of the experiment 'modeling resting potential of neurons' for general introduction to the simulator.

 

 

User Instructions:

 

The simulator consists of two sections: simulator window and variables menu.

 

The simulator window shows the membrane potential vs. time plots and the gating variables plots. This window is divided into two subplots. The upper subplot shows the membrane potential vs. time plot and the lower window shows the plots of the gating variables. The user has the ability to choose any 3 gating parameters provided at the bottom of the simulator window to visualize their dynamics.

 

  

The variables menu section allows a wide variety of options for the user to explore. The user can choose the type of clamp mode he/she wishes to test with, change the concentration of different ions like sodium, potassium and chlorine inside and outside, test with various passive parametric values for different voltage-gated channels and observe the behavior in the presence of pharmacological blockers such as tetrodotoxin(TTX) and tetraethylammonium(TEA).

 

 

In this exercise, we focus on action potential generation by giving certain stimulus inputs. The stimulus is set by the user using the buttons labeled as Stim1 and Stim2 under Stimuli section. Without clicking either of stimulus buttons, there will be no generation of the action potential, so the user has to choose either Stim1 or Stim2. After choosing one of the stimulus, the membrane potential starts to play against time in the upper sub-plot window. On the lower sub-plot window, the chosen gating parameters dynamics start to display. The user can choose which parameter dynamics he would like to observe by simply clicking on the checkboxes provided before the parameters.

 

 

 

 

From the stimuli section, the user can choose either Stim1 or Stim2. The duration of the stimulus of either Stim1 or Stim2 can be set by using the Set Stimulus section shown below. This section has Stim1 and Stim2 buttons.

 

 

On clicking either Stim1 button or Stim2 button, on the simulator window, the user can be able to set his/her required duration time of the stimulus given. The below figure shows that when Stim1 button is clicked the duration time of the Stim1 is displayed wherein the user could increase/decrease the duration of that stimulus. Same follows for Stim2 button.

 

 

 

The user can choose the desired duration value for either Stim1 or Stim2 by simply clicking and dragging with the mouse. The below screenshot shows how that happens.

 

 

Likewise for Stim2 also, the duration of the stimulus is increased. If you observe carefully, the current amplitude is also increased along with the duration for Stim2.

 

 

The user can also set the hyper-polarization state using the Stim1 and Stim2 button under the Set Stimuli section. After prolonged hyperpolarization, the sudden release from hyperpolarization leads to the generation of action potential which is termed as Anodal excitation or Rebound Spike. The below screenshot describes the phenomena for a single pulse.

 

 

The phenomena explained above, if done with two pulses is shown in the screenshot below. The user can set two different pulses with different duration and current amplitude for the same stimulus (either Stim1 or Stim2).

 

 

Under the stimuli section, there were other buttons like Stop and Reset. The user can stop the simulation after running for some particular duration of time or otherwise he can click on Reset button so that the simulator returns to its default state.

 

The user can also export the values for the variables which are chosen to get plotted on the graph using the Export Button. After clicking on this button, you can save your file at the specified location in .csv format and you can use later by importing these values into either MS-Excel sheet or MATLAB for high resolution images.

 

 

 

 

Help:

 

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• on Fedora - https://docs.fedoraproject.org/en-US/quick-docs/using-adobe-flash/

 

 

 

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