Example of a junction with N bonds

using CellAdhesion

Plots needs to be installed to run these examples and display plots of the data.

using Plots
using Statistics

Slip bond model

Example with constant force

Define the parameters for the Slip bond model for the junction
Generate a junction made of N bonds
Run the simulations for the junction subjected to a constant force within the range 2-10, 50 times for each level of force

Define the BondModel to compute the binding-unbinding rate

model = SlipBondModel((k_on_0=3e-3,), (k_off_0=3e-4, f_1e=0.055))

BondModel{Slip}((k_on = 0.003f0, k_off_0 = 0.0003f0, f_1e = 0.055f0))

Define the Cluster data structure parameters

N = 25;      # Number of bonds
l = 1.0;     # Distance between bonds

Define the range of constant forces to be applied

F = [2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0];

Run the Montecarlo simulations for different level of forces, n times each

n = 10;            # Number of simulations
n_f = length(F);    # Number of different forces to apply to the junction

time_break_F = zeros(n_f)  # Vector with mean rupture time for the different applied forces

p = plot()

# For loop on the applied Force (F)
for j = 1:1:n_f

    stress_break_v = zeros(n)
    time_break_v = zeros(n)

    # For loop on the different simulations for each scenario (n)
    for sim = 1:1:n

        # Initiate the junction (Cluster data structure)
        x = Cluster(N, l, model, :force_global)

        # Run the Montecarlo simulation until it breaks or it reaches the maximum number of iterations
        state, stress_break_v[sim], time_break_v[sim], step = runcluster(x, F[j], 0.01, max_steps = 500000)

    end

    # Plot all rupture time for all the simulations
    scatter!(p, repeat([F[j]],n), time_break_v, label = "", mc="#1E88E5", ms=4, ma=1)

    # Compute the mean rupture time
    time_break_F[j] = mean(time_break_v)
end

Plot the average rupture time as a function of the applied force

scatter!(p, F.+0.1, time_break_F, label="Mean", mc="#D81B60", ms=4, ma=1)
xlabel!("Force (N)")
ylabel!("Time (s)")

Example with varing force (linear force variation)

We define force ramps with different deformation rates (0.5%/s, 1%/s, 2%/s, 3%/s)

rates = [0.005, 0.01, 0.02, 0.03]
k = 1   # Spring stiffness

Run the Montecarlo simulations for different ramps, n times each

n = 20;            # Number of simulations
n_f = length(rates);    # Number of different forces to apply to the junction

time_break_F = zeros(n_f)  # Vector with mean rupture time for the different rates of application
stress_break_F = zeros(n_f)  # Vector with mean rupture stress for the different rates of application

p1 = plot()
p2 = plot()

# For loop on the applied Force (F)
for j = 1:1:n_f

    stress_break_v = zeros(n)
    time_break_v = zeros(n)

    # Generate the force vector
    t = collect(LinRange(0,6000,600001))
    ϵ = rates[j] .* t;

    f = k .* ϵ

    # For loop on the different simulations, for each scenario (n)
    for sim = 1:1:n

        # Initiate the junction (Cluster data structure)
        x = Cluster(N, l, model, :force_global)

        # Run the Montecarlo simulation until it breaks or it reaches the maximum number of iterations
        state, stress_break_v[sim], time_break_v[sim], step = runcluster(x, f, 0.01, max_steps = 500000)

    end

    # Plot all rupture time for all the simulations
    scatter!(p1, repeat([rates[j]*100],n), time_break_v, label = "", mc="#1E88E5", ms=4, ma=1)
    scatter!(p2, repeat([rates[j]*100],n), stress_break_v, label = "", mc="#1E88E5", ms=4, ma=1)

    # Compute the mean rupture time
    time_break_F[j] = mean(time_break_v)
    stress_break_F[j] = mean(stress_break_v)
end

Plot the average rupture time as a function of the applied force

scatter!(p1, (rates.+0.001)*100, time_break_F, label="Mean", mc="#D81B60", ms=4, ma=1)
xlabel!("Rate (%/s)")
ylabel!("Time (s)")

scatter!(p2, (rates.+0.001)*100, stress_break_F, label="Mean", mc="#D81B60", ms=4, ma=1)
xlabel!("Rate (%/s)")
ylabel!("Force (N)")

plot!(p1,p2)

Catch bond model

Example with constant force

Define the BondModel to compute the binding-unbinding rate

model = CatchBondModel((k_on_0 = 0.5,), (k_off_0s = 1e-4, f_1es = 1.0, k_off_0c = 1e-2, f_1ec = 1.0))

BondModel{Catch}((k_on = 0.5f0, k_off_0s = 0.0001f0, f_1es = 1.0f0, k_off_0c = 0.01f0, f_1ec = 1.0f0))

Define the Cluster data structure parameters

N = 20;      # Number of bonds
l = 1.0;     # Distance between bonds

Define the range of constant forces to be applied

F = collect(105.0:120.0);

Run the Montecarlo simulations for different level of forces, n times each

n = 10;            # Number of simulations
n_f = length(F);    # Number of different forces to apply to the junction

time_break_F = zeros(n_f)  # Vector with mean rupture time for the different applied forces

p = plot()

# For loop on the applied Force (F)
for j = 1:1:n_f

    stress_break_v = zeros(n)
    time_break_v = zeros(n)

    # For loop on the different simulations for each scenario (n)
    for sim = 1:1:n

        # Initiate the junction (Cluster data structure)
        x = Cluster(N, l, model, :force_global)

        # Run the Montecarlo simulation until it breaks or it reaches the maximum number of iterations
        state, stress_break_v[sim], time_break_v[sim], step = runcluster(x, F[j], 0.01, max_steps = 500000)

    end

    # Plot all rupture time for all the simulations
    scatter!(p, repeat([F[j]],n), time_break_v, label = "", mc="#1E88E5", ms=4, ma=1)

    # Compute the mean rupture time
    time_break_F[j] = mean(time_break_v)
end

Plot the average rupture time as a function of the applied force

scatter!(p, F.+0.1, time_break_F, label="Mean", mc="#D81B60", ms=4, ma=1)
xlabel!("Force (N)")
ylabel!("Time (s)")
title!("Catch bond model - constant force")

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