Why do I receive an error when running this code?

I keep getting an error next to my Jk and IL under 2). I am unsure how to fix it.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%

% Template for Hodgkin Huxley model of action potential

% in a giant squid axon

% Complete the code by inserting appropriate expressions

% in the places marked

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Define constants here

Vrest = -60 ; % resting potential, mV

ENa = 52.4 ; % sodium Nernst potential, mV

gNa_max = 120 ; % sodium saturation conductance, mS/cm2

Cm = 1 ; % membrane capacitance, uF/cm^2

1) Define other constant related to IK and IL here

% Define other constants related to IK and IL here

Ek = -72.1 ; % potassium Nernst potential, mV

EL = -49.2 ; % leak Nernst potential, mV

% time stepping and stimulus related constants

deltaT = 0.01 ; % time step, millisec

tStart = -1.000 ; % start time, millisec

tEnd = 15.000 ; % end time, millisec

nStep = ceil((tEnd-tStart)/deltaT) ; % number of time steps

outputInterval = 20 ; % number of time steps between screen output

StimDur=2; % duration of the stimulus, millisec

Jstim=150; % strength of stimulus

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Set initial value of state variables

Vm = Vrest ; % membrane potential, mV

m = 0.05293 ; % initial value of m gate

2) similarly, declare initial values of h and n gates here

h = 0.59612 ; % h gate value

n = 0.31768 ; % n gate value

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Storage for variables to plot

plot_Vm = zeros(nStep,1) ;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Print a heading for the screen output

disp('Hodgkin-Huxley squid axon model')

fprintf('\t Time \t Vm \t n \t\t m \t\t h\n');

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Start the simulation

tNow = tStart ;

for iStep = 1:nStep

% Compute ion currents & stimulus current

JNa = gNa_max*m*m*m*h*(Vm-ENa) ;

Jk = gk_max*m*m*m*H*(Vm-Ek) ;

IL = gL_max*m*m*m*H*(Vm-EL) ;

3) write similar expressions for JK and IL here

if( 0<=tNow && tNow<StimDur ) % apply stimulus current at t=0

Jm = Jstim ;

else

Jm = 0 ;

end

% Compute gates' opening and closing rates

alpha_m = 0.1*(25-Vm)/(exp(0.1*(25-Vm))-1);

beta_m = 4*exp(-Vm/18);

m = m + deltaT*(alpha_m*(1-m)-beta_m*m);

4) Write similar expressions for n and h gates here

alpha_n = 0.1*(10-Vm)/(exp(0.1*(10-Vm))-1);

beta_n = 0.125*exp(-Vm/80);

n = n + deltaT*(alpha_n*(1-n)-beta_n*n);

alpha_h = 0.07*exp(-Vm/20);

beta_h = (exp((30-Vm)/10)+1)^-1;

h = h + deltaT*(alpha_h*(1-h)-beta_h*h);

% Compute change in state variables

deltaVm = -deltaT * (JNa + JK + JL - Jm)/Cm ;

% Record/display state variables & other values

plot_Vm(iStep) = Vm ;

plot_time(iStep) = tNow ;

if mod(iStep,outputInterval) == 0

fprintf('%8.2f %7.3f %7.5f %7.5f %7.5f\n', ...

tNow, Vm, n, m, h) ;

end % if mod(tNow)

% Update state variables

Vm = Vm + deltaVm ; % new Vm = current Vm + change in Vm

tNow = tStart + iStep*deltaT ; % increment the time

end % for iStep

% Plot the gates, probabilities, currents, Vm, etc

plot(plot_time, plot_Vm); grid on ;

5) Similarly plot gates n, m and h against time

end of file

[Cris LaPierre]

Consider sharing the complete error message (all the red text).

Answer 1

[David Hill]

You have not defined several variables: gk_max, gL_max, H, JK, JL. Once you define these variable the code will run.

gk_max=1;gL_max=1;H=1;JK=1;JL=1; %you need to define these variables.



Vrest = -60 ; % resting potential, mV
ENa = 52.4 ; % sodium Nernst potential, mV
gNa_max = 120 ; % sodium saturation conductance, mS/cm2
Cm = 1 ; % membrane capacitance, uF/cm^2
% Define other constants related to IK and IL here
Ek = -72.1 ; % potassium Nernst potential, mV
EL = -49.2 ; % leak Nernst potential, mV
% time stepping and stimulus related constants
deltaT = 0.01 ; % time step, millisec
tStart = -1.000 ; % start time, millisec
tEnd = 15.000 ; % end time, millisec
nStep = ceil((tEnd-tStart)/deltaT) ; % number of time steps
outputInterval = 20 ; % number of time steps between screen output
StimDur=2; % duration of the stimulus, millisec
Jstim=150; % strength of stimulus
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set initial value of state variables
Vm = Vrest ; % membrane potential, mV
m = 0.05293 ; % initial value of m gate
h = 0.59612 ; % h gate value
n = 0.31768 ; % n gate value
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Storage for variables to plot
plot_Vm = zeros(nStep,1) ;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Print a heading for the screen output
disp('Hodgkin-Huxley squid axon model')

Hodgkin-Huxley squid axon model

fprintf('\t Time \t Vm \t n \t\t m \t\t h\n');

	 Time 	 Vm 	 n 		 m 		 h

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Start the simulation
tNow = tStart ;
for iStep = 1:nStep
    % Compute ion currents & stimulus current
    JNa = gNa_max*m*m*m*h*(Vm-ENa) ;
    Jk = gk_max*m*m*m*H*(Vm-Ek) ;
    IL = gL_max*m*m*m*H*(Vm-EL) ;
    if( 0<=tNow && tNow<StimDur ) % apply stimulus current at t=0
        Jm = Jstim ;
    else
        Jm = 0 ;
    end
    
    % Compute gates' opening and closing rates
    
    alpha_m = 0.1*(25-Vm)/(exp(0.1*(25-Vm))-1);
    beta_m = 4*exp(-Vm/18);
    m = m + deltaT*(alpha_m*(1-m)-beta_m*m);
    alpha_n = 0.1*(10-Vm)/(exp(0.1*(10-Vm))-1);
    beta_n = 0.125*exp(-Vm/80);
    n = n + deltaT*(alpha_n*(1-n)-beta_n*n);
    alpha_h = 0.07*exp(-Vm/20);
    beta_h = (exp((30-Vm)/10)+1)^-1;
    h = h + deltaT*(alpha_h*(1-h)-beta_h*h);
    
    % Compute change in state variables
    deltaVm = -deltaT * (JNa + JK + JL - Jm)/Cm ;
    
    % Record/display state variables & other values
    plot_Vm(iStep) = Vm ;
    plot_time(iStep) = tNow ;
    if mod(iStep,outputInterval) == 0
        fprintf('%8.2f %7.3f %7.5f %7.5f %7.5f\n', ...
            tNow, Vm, n, m, h) ;
    end % if mod(tNow)
    
    % Update state variables
    Vm = Vm + deltaVm ; % new Vm = current Vm + change in Vm
    tNow = tStart + iStep*deltaT ; % increment the time
end % for iStep

   -0.81 -60.368 0.30209 0.00001 0.69649
   -0.61 -60.768 0.28723 0.00001 0.77324
   -0.41 -61.168 0.27305 0.00001 0.83157
   -0.21 -61.568 0.25953 0.00001 0.87565
   -0.01 -61.968 0.24664 0.00001 0.90876
    0.19 -33.868 0.23893 0.00043 0.92284
    0.39  -4.268 0.26219 0.00956 0.92372
    0.59  25.395 0.40576 0.09451 0.89478
    0.79  56.027 0.69205 0.39465 0.77357
    0.99  59.423 0.88685 0.70483 0.63841
    1.19  56.566 0.95011 0.83219 0.52891
    1.39  56.342 0.97303 0.89141 0.43886
    1.59  56.642 0.98174 0.92100 0.36423
    1.79  57.214 0.98518 0.93666 0.30225
    1.99  57.995 0.98665 0.94575 0.25072
    2.19  52.346 0.98597 0.94063 0.20943
    2.39  52.291 0.98544 0.93576 0.17545
    2.59  52.270 0.98522 0.93312 0.14713
    2.79  52.245 0.98513 0.93167 0.12355
    2.99  52.218 0.98508 0.93083 0.10390
    3.19  52.186 0.98505 0.93031 0.08754
    3.39  52.149 0.98503 0.92994 0.07390
    3.59  52.108 0.98501 0.92964 0.06255
    3.79  52.061 0.98498 0.92937 0.05309
    3.99  52.008 0.98496 0.92909 0.04521
    4.19  51.949 0.98493 0.92879 0.03865
    4.39  51.884 0.98490 0.92847 0.03318
    4.59  51.812 0.98487 0.92811 0.02863
    4.79  51.735 0.98483 0.92772 0.02485
    4.99  51.651 0.98479 0.92729 0.02170
    5.19  51.561 0.98475 0.92683 0.01907
    5.39  51.467 0.98470 0.92633 0.01689
    5.59  51.367 0.98465 0.92580 0.01508
    5.79  51.264 0.98460 0.92523 0.01358
    5.99  51.157 0.98455 0.92463 0.01233
    6.19  51.048 0.98449 0.92401 0.01130
    6.39  50.938 0.98443 0.92337 0.01044
    6.59  50.828 0.98437 0.92271 0.00973
    6.79  50.718 0.98431 0.92204 0.00915
    6.99  50.609 0.98425 0.92136 0.00867
    7.19  50.502 0.98419 0.92068 0.00828
    7.39  50.399 0.98413 0.92001 0.00795
    7.59  50.298 0.98408 0.91935 0.00769
    7.79  50.202 0.98402 0.91870 0.00748
    7.99  50.111 0.98397 0.91807 0.00730
    8.19  50.024 0.98392 0.91746 0.00717
    8.39  49.942 0.98387 0.91687 0.00706
    8.59  49.866 0.98382 0.91632 0.00697
    8.79  49.794 0.98378 0.91579 0.00690
    8.99  49.729 0.98374 0.91529 0.00685
    9.19  49.668 0.98370 0.91483 0.00681
    9.39  49.612 0.98366 0.91440 0.00678
    9.59  49.561 0.98363 0.91400 0.00676
    9.79  49.515 0.98360 0.91363 0.00674
    9.99  49.473 0.98357 0.91329 0.00673
   10.19  49.435 0.98355 0.91298 0.00673
   10.39  49.402 0.98353 0.91270 0.00673
   10.59  49.371 0.98351 0.91244 0.00673
   10.79  49.345 0.98349 0.91222 0.00673
   10.99  49.321 0.98347 0.91201 0.00674
   11.19  49.299 0.98346 0.91183 0.00674
   11.39  49.281 0.98344 0.91167 0.00675
   11.59  49.264 0.98343 0.91152 0.00675
   11.79  49.250 0.98342 0.91139 0.00676
   11.99  49.238 0.98341 0.91128 0.00676
   12.19  49.227 0.98341 0.91118 0.00677
   12.39  49.217 0.98340 0.91110 0.00677
   12.59  49.209 0.98339 0.91102 0.00678
   12.79  49.202 0.98339 0.91096 0.00678
   12.99  49.196 0.98339 0.91090 0.00679
   13.19  49.191 0.98338 0.91085 0.00679
   13.39  49.187 0.98338 0.91081 0.00680
   13.59  49.183 0.98338 0.91077 0.00680
   13.79  49.180 0.98337 0.91074 0.00680
   13.99  49.177 0.98337 0.91072 0.00681
   14.19  49.175 0.98337 0.91070 0.00681
   14.39  49.173 0.98337 0.91068 0.00681
   14.59  49.172 0.98337 0.91066 0.00681
   14.79  49.170 0.98337 0.91065 0.00681
   14.99  49.169 0.98337 0.91064 0.00682

% Plot the gates, probabilities, currents, Vm, etc
plot(plot_time, plot_Vm); grid on ;