MEDYAN.FilamentMechParams

Union{}

FilamentMechParams(; kwargs...)

Mechanical parameters shared by all filaments of a type.

Elastic constants are specified at the monomer scale. With n = numpercylinder and a = spacing, a full cylinder has rest length L0 = n*a; mechanics uses klength/n, kangle/n, and ktwist/n. Keep these monomer-scale constants fixed when changing cylinder resolution.

The bending parameter is named kangle. Its continuum bending rigidity is EI = kangle*spacing (pN·nm²). For a three-dimensional wormlike chain, the bending persistence length is

lp = EI/(kB*T) = kangle*spacing/(kB*T)
kangle = kB*T*lp/spacing

Here lp and spacing are in nm and kB*T is in pN·nm. For example, at 310 K, spacing = 2.7 and kangle = 16_000 give lp ≈ 10_093 nm (10.1 μm).

The NaN and -1 defaults are placeholders, not a complete physical parameter set. Supply geometry, elastic and collision constants, cylinder size, and the tip limit. Leave twist_per_monomer = NaN to disable twist; otherwise supply both twist_per_monomer and ktwist.

  • radius::Float64: Cylinder radius (nm), used for excluded-volume contact distances and filament geometry.
  • spacing::Float64: Axial rest-length increment per monomer (nm). A full cylinder spans numpercylinder*spacing.
  • klength::Float64: Monomer-scale stretching spring constant (pN/nm). A cylinder contributes E = (klength/numpercylinder)*(L-L0)^2/2, where L and L0 are its current and rest lengths. The corresponding axial rigidity is EA = klength*spacing (pN).
  • kangle::Float64: Monomer-scale bending constant (pN·nm/rad²). Each joint contributes E = (kangle/numpercylinder)*(1-cos(θ)), where θ = 0 is straight. For small bends this is (kangle/numpercylinder)*θ^2/2. Set kangle = kB*T*lp/spacing for the desired continuum bending persistence length lp.
  • ktwist::Float64: Monomer-scale torsional constant (pN·nm/rad²), used only when twist is enabled. For excess twist Δφ relative to the relaxed twist, a joint contributes E = 2*(ktwist/numpercylinder)*tan(Δφ/2)^2, approximately (ktwist/numpercylinder)*Δφ^2/2 near equilibrium. The continuum torsional rigidity is C = ktwist*spacing (pN·nm²).
  • twist_per_monomer::Float64: Signed relaxed rotation of the material direction per monomer (rad). The reference twist between neighboring cylinders is numpercylinder*twist_per_monomer. NaN disables twist degrees of freedom; 0 enables twist with an untwisted reference state.
  • numpercylinder::Int32: Number of monomers represented by a full cylinder; must be positive. Controls mechanical discretization and the division of the monomer-scale elastic constants. End cylinders can be shorter.
  • kcollide::Float64: Excluded-volume repulsion stiffness (pN/nm) supplied to the collision model. Larger values penalize overlap more strongly. This is separate from stretching stiffness and is not divided by numpercylinder.
  • collision_layers::UInt32: Bitmask of collision layers occupied by this filament type; default UInt32(1) selects the first layer. Multiple bits may be set.
  • no_collide_mask::UInt32: Bitmask of layers this filament type ignores. A pair is excluded if either object’s mask intersects the other’s layers. Default UInt32(0) excludes no layers.
  • max_num_unmin_end::Int32: Maximum number of newly added, mechanically unminimized monomers allowed at each tip. Tip reactions that would exceed this limit are disabled until mechanical relaxation. Choose a nonnegative limit smaller than (radius + minimum_other_filament_radius)/spacing so unrelaxed growth remains shorter than the filament contact distance.