API

Bond
Bond(state::{Bool}, f::{CellAdhesionFloat}, model)

`Bond` struct contains sate, force and model of a single bond

# Fields

- `state`: false (0)  = open, true (1) = closed
- `f`: force
- `t`: time
- `model`: BondModel describing the bond binding-unbinding dynamics

Cluster(u::Vector{Bond,Cluster}, state::{Bool}, f::{CellAdhesionFloat}, f_model::{Symbol}, n::{CellAdhesionInt}, l::{CellAdhesionFloat})

update!(v, dt)

Updates the state of an interface (that can be made of bonds or it can be a hierarchical structure).

Input parameters:

• v: interface (this can be a cluster or a bond)
• dt: time step of the simulation

runcluster(v, force, dt::Float64; max_steps::Integer = 1000, verbose::Bool = false)

Simulates a junction subjected to an external force using a Montecarlo algorithm.

Input paramters:

• v: structure of type Cluster
• force: it can either be an constant number (if the junction is subjected to a constant force), or a vector (if the junction is subjected to a varing force)
• dt: time step for the simulation
• max_steps: maximum number of iterations if the junction doesn't break

Output paramters:

• state of the whole Cluster
• force at which it breaks
• time at which it breaks
• number of steps after which it breaks

state!(v)

Updates the state field of a Cluster or a Bond. When all the subunits are open, then the state of the structure is set to open. Otherwise, it is close.

Input parameters:

• v: interface that can either be a Cluster or a Bond.

Output: State of the cluster/bond, false for broken, true otherwise.

bondstateforce(v; output=:flat, time=missing)

Return bond state/force information for a Bond, a Cluster{Bond}, or nested Cluster.

• output=:flat (default) returns tuples (states, forces) identical to previous API.
• output=:nested returns a Dict with keys "time", "states", "force", preserving hierarchy:
  • Bond -> Bool and scalar float
  • Cluster{Bond} -> Vector of Bool / Float
  • nested Cluster -> nested Vector structures

Closed bonds are assigned NaN in force output.

print_cluster(x)

Nice screen print of Cluster structure or Bond (x)

setforce!(v::Cluster{Bond{T}}, F::CellAdhesionFloat)

Input parameters:

• v: Cluster structure
• F: Force applied to the cluster

Output parameters:

• Updated the force applied to each Cluster structure (within the hierarchical structure)

force_global(v::Cluster)

Computer force distribution by equally dividing the force within the closed bonds

force_local(v::Cluster)

Computer force distribution by accounting for the distance of each link from its two closest neighbours

distance(v::BitVector, n::Integer)

Compute the distance of each from its two closest closed link on each side. Used to compute a "local" load distributions across closed bonds. Periodic bondary conditions for the edges.

Input parameters:

• v: vector with the state of each single bond
• n: number of bonds in the interface

Output parameters:

• l: vector of CellAdhesionFloat containing the distance for each closed bond