Array indices must be positive integers or logical values.

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Jonathan Louie
Jonathan Louie 2022-6-5
评论： Image Analyst 2022-6-6
clearvars
% Setup
t_max= 1200; % in s
k=0.01; % in s^-1
g_nr=2; % in molecules/s
t_nr=0; % in s
x_nr=5; % in molecules
time_log=0;
% Simulation of the non-regulated construct
t=0;
prod_rate=g_nr;
deg_rate=k*x_nr;
while t<t_max
wait_time=-log(rand)/(prod_rate+(deg_rate*x_nr(t_nr)));
prob_prod=prod_rate/(prod_rate+deg_rate*x_nr(t_nr)); % Propensity of production
t=t+wait_time; % Update current time
t_nr=t_nr+1; % Update the number of steps (reactions) associated with the experiment.
time_log(t_nr)=t; % Add the current time to the time log
if rand < prob_prod % Defines whether production takes place based on Monte Carlo method.
x_nr(t_nr)=x_nr(t_nr-1)+1; % Implements production
else
x_nr(t_nr)=x_nr(t_nr-1)-1; % Implements degradation
end
end
if t>t_max
t_nr(end)=[];
x_nr(end)=[];
end
close all
plot(time_log,t_nr,'r','LineWidth',2)
hold on
plot(time_log,x_nr,'r','LineWidth',2)
I get the error Array indices must be positive integers or logical values in line 24:
wait_time=-log(rand)/(prod_rate+(deg_rate*x_nr(t_nr)));
Does anyone know why this is?
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Jonathan Louie
Jonathan Louie 2022-6-6
I checked the units and I understand that the deg rate should be 1/s molecules/s. But the instructions given for my assignment is:
the degradation rate of both models will be given by: deg(x(t)) = kx(t) where x(t) stands for the number of repressor molecules in the system. k is given as 0.01s^-1, but what I'm unsure of is if the statement below is referring to the variable for number of repressor molecules.
Define a variable (x_nr) with the number of molecules of the non-regulated system and initialize it with value 5 molecules. As for tnr &, xnr will be a vector that contains the changes in number of molecules corresponding to the different time points of vector tnr.
Because that's why I plugged in x_nr for x(t) for the deg rate equation.
Also for reference, I'm trying to plot the dynamics of the non-regulated construct and the auto-regulated construct by running the Gillespie algorithm until we reach the maximum time, t_max. To do this, set up a while loop so that the state of the system’s dynamics – its transitions – is simulated from 0 s up to time t_max, then drawing a wait time dt from an Negative exponential distribution (Poisson process).
Thank you so much for any help I really appreciate it.
Image Analyst
Image Analyst 2022-6-6
And what about the help you got below, you know, in the official Answers section of this page? Did you see it? If not, scroll down.

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回答（2 个）

Image Analyst
Image Analyst 2022-6-5
Since this is one of the most common FAQs, see the FAQ for a thorough discussion:
https://matlab.fandom.com/wiki/FAQ#.22Subscript_indices_must_either_be_real_positive_integers_or_logicals..22
Torsten
Torsten 2022-6-6
if rand < prob_prod % Defines whether production takes place based on Monte Carlo method.
x_nr(t_nr)=x_nr(t_nr-1)+1; % Implements production
else
x_nr(t_nr)=x_nr(t_nr-1)-1; % Implements degradation
end
The first time you enter this if-clause, t_nr = 1.
Thus you address x_nr(t_nr-1) = x_nr(0).
This throws an error in MATLAB since array indices start with index 1, not 0.

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