Hi,
The main modification is to reflect the integrins that hit the boundary. To do this, I added a nested for loop right after the initial for loop that updates the position of the integrins. In the new loop, I checked if the x or y coordinate of an integrin has gone out of bounds (less than 0 or greater than L), and if so, I reflected its position to the opposite side of the boundary.
Also the code you provided has some errors that need to be corrected. Kindly find the corrected code along with the modifications to reflect the integrins at the boundary given below:
N = 10; % number of integrins
L = 100; % size of the domain in nm
D = 0.01; % diffusion coefficient in nm^2/s
dt = 1; % time step in s
F = randi([1, 10], 1); % force on the bond with a random number of 1 to 10 pN
P_a = rand(1); % binding rate of a random number from 0 to 1
P_ub = 1 / (1.5 * F); % unbinding rate based on our previous values
Tmax = 500; % max time
% Initialize our integrins
x = randi([0, 360], N, 1); % initial x-coordinates randomly distributed
y = randi([0, 50], N, 1); % initial y-coordinates randomly distributed
state = ones(N, 1); % Each integrin is set to an inactive state at 0
colors = repmat([1 0 0], N, 1); % red for inactive state
colors(state == 1, :, :) = repmat([0 1 0], sum(state == 1), 1); % green for active state
% Create the figure
figure;
axis([0 L 0 L]);
set(gca, 'nextplot', 'replacechildren');
% Main time loop
for t = 0:dt:Tmax
% Update the positions of the integrins
for i = 1:N
if state(i) == 1
dx = sqrt(2 * D * dt) * randn(1); % Random displacement in x
dy = sqrt(2 * D * dt) * randn(1); % Random displacement in y
x(i) = x(i) + dx; % Update x-coordinate
y(i) = y(i) + dy; % Update y-coordinate
end
end
% Reflect integrins at the boundary
for i = 1:N
if x(i) < 0
x(i) = -x(i);
elseif x(i) > L
x(i) = 2 * L - x(i);
end
if y(i) < 0
y(i) = -y(i);
elseif y(i) > L
y(i) = 2 * L - y(i);
end
end
% Update integrin states
for i = 1:N
if state(i) == 1
if rand(1) < P_a % Probability of activation
state(i) = 2; % Turn integrin active
colors(i, :, :) = repmat([0 1 0], 1, 1, 3); % Update color to green
end
elseif rand(1) < P_ub % Probability of unbinding
state(i) = 1; % Return integrin to inactive state
colors(i, :, :) = repmat([1 0 0], 1, 1, 3); % Update color to red
end
end
% Plot the integrins
scatter(x, y, 100, colors, 'filled');
title(sprintf('Time: %.2f s', t));
drawnow;
end
Hope this helps.
Thankyou
