Neuron Simulator is an online simulating platform for a section of excitable neuronal membrane of squid axon. Simulator uses Hodgkin and Huxley equation and it provides full accesses to HH parameters, membrane parameters, various ionic concentrations, pharmacological effects, stimulus parameters and Vclamp protocol. Loading Neuron simulator by clicking on the tab called “simulator” (see the below sample screen shot (Fig.1.) of the simulator).
Fig 1. Screen shot of the Neuron Simulator
The simulator consists of two main sections: simulator window and variables menu. The simulator window shows the membrane potential plot and plots of various parameters. The upper plot shows the membrane potential vs. time plots (red), stimuli just below the Vm(blue) and lower plot displays a variety of parameters including HH-parameters, various currents and conductance any three variables at a time can be plotted in this window, by default I_leak,Ina,IK was plotted.
Click on the Stim1/Stim2 buttons to inject depolarization / hyperpolarization current to neuronal membrane.One can midify simulation parameters can be mo in Membrane window, Channels window, Drugs window, Stimuli windows (see the figure (Fig.2) below).
Fig 2. Variables menu
Simulation control window
Simulation control menu is used to simulate the experiments. The functionalities includes, Run button (will continuously simulate the neuronal membrane, without giving any input stimuli), Stop button (will help to stop the simulation at any point of time), Stim1 and Stim2 buttons (are two are used to inject an external stimulus as some nA of current to the neuronal membrane, user can modify this by clicking Stim1 and Stim2 window). Simulation runs for around 30ms when a stimulus (Stim1/Stim2) is applied, Export button (this functionality of this simulator will give user to the freedom of accessing/exporting the simulated models data to an excel sheet, by using these data user can make high resolution pictures) and finally the Reset button (helps to reset the whole simulator).
Fig 3 . Simulation control menu
Membrane window provides accesses to internal and external ionic concentration and membrane properties.
Fig 4 . Membrane tab
Channel window provides accesses to various parameters of passive as well as active channel types. Individual channel can be disabled by making the conductance of that channel to zero.
Passive channels conductance can be varied in the channel window. Voltage gated channels parameters can be accessed by clicking on channel details. Channel details will display a new detailed window with channel properties of fast sodium, delayed rectifier and user defined channels. The figure given below shows the detailed channel properties of fast sodium channel.
Fig 5. Channel tab
Stimuli window consists of two external stimuli (Stim1 and Stim2) which can be set by user, each of which consists of either single pulse or a sequence of two independent adjustable pulses.
Fig 6 . Stimuli tab
Drug window allows to study the pharmacological effect in neuronal membrane by the application of three drugs TTX (Inhibit Na current), TEX (Inhibit K current), Pronase (eliminate Na+ inactivation). These drugs can inject using Drugs window.
Fig 7 . Drugs tab
Procedure for Current clamp experiments:
By default the simulator will be in current clamp mode, for every reset the simulator the mode will reset to current clamp.
In this exercise we are studying how the action potential is initiated and propagated along the axon and the importance of passive membrane properties such as capacitance and conductance in the process of initiation and propagation of action potential. This exercise will also help to study different response from a nerve cell such as action potential, excitatory and inhibitory post synaptic potentials and the effect of drugs.
The simulator tab will directly take in to the simulator interface (as shown fig 8).
Fig .8 Simulator interface
Effect of capacitance can be studied by modifying Cm in the membrane tab, default value is 1. Capacitance property of neuronal membrane is directly proportional to the first spike amplitude and latency . This property of HH neuron can be simulated by varying, Cm in the membrane tab to 1.5 nF from its default value 1 nF. Fig 7. is the simulated plot from the simulator, shows when the capacitance of neuronal membrane increases noted there is a significant reduction in spike amplitude , width of the signal and increase in spike latency.
Fig. 9 . Show the effect of capacitance in spike amplitude , width of the signal and the latency.
Effect of conductance can be studied by modifying gNa or gK (conductance of sodium and potassium). These variable in the simulator can be access under channel tab channel details sub-window (as shown in the figure 10 and 11).
Fig. 10 . Show the effect of conductance of sodium channel in spike amplitude, width of the signal and the latency.
Fig. 11 . Show the effect of conductance of potassium channel in spike amplitude , width of the signal and the latency.
Effect of drugs TTX and TEA (Tetredotoxin and Tetraethylammonium) on action potential generation and propagation can also be studied by accessing the drug tab. Here the student will be studying the effect of TTX and TEA clicking on the respective percentage graph. This effect of drugs in our simulator is simulated by accessing conductance of sodium for TTX and the conductance of potassium for TEA ( see Fig 7 ).
Fig 12. Drugs tab for studying the effect of drugs, applying TEA by 50% and TEA by 17%.
NOTE: Hit the reset button at the right corner of the simulation control window, to reset all parameters to its initial/default values.
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