ActinFriction

Actin rings dynamics simulation package

A Julia package for simulating the dynamics of passively crosslinked actin rings.

Repository

Documentation

This package allows the SDEs described in Ref. 1 to be solved, and provides methods for directly calculating the friction coefficients described in the same paper.

Installation

The package can be installed by starting the Julia REPL, typing ] to enter package mode, and running

add ActinFriction

to install from the General registry, or by running

add https://github.com/cumberworth/ActinFriction.jl

to install directly from the development repository.

A related python package, actinfrictionpy, includes code for analyzing and plotting the output from these ...

References

[1] A. Cumberworth and P. R. ten Wolde, Constriction of actin rings by passive crosslinkers, arXiv:2203.04260 [physics.bio-ph].

Links

Julia programming language

Plotting package

Replication package Ref. 1

• R_to_lambda
• RingParams
• bending_force
• condensation_force
• entropic_force
• equilibrium_occupancy
• equilibrium_ring_radius
• force_L_to_R
• free_energy_barrier_Nd_exact
• free_energy_barrier_Nd_exp
• free_energy_barrier_cX
• friction_coefficient_Nd_exact
• friction_coefficient_Nd_exp
• friction_coefficient_cX
• kramers_r0
• l_to_lambda
• lambda_to_R
• lambda_to_l
• savename
• solve_and_write_ring_Nd_contin_exp
• solve_and_write_ring_Nd_contin_exp_noise
• solve_and_write_ring_Nd_discrete_exact
• solve_and_write_ring_Nd_discrete_exact_noise
• solve_and_write_ring_Nd_discrete_exp
• solve_and_write_ring_Nd_discrete_exp_noise
• solve_and_write_ring_cX
• solve_and_write_ring_cX_noise

• k01::Float64: Per site rate constant of initial crosslinker binding (s^-1)

• r01::Float64: Per site rate of initial crosslinker binding (M^-1 s^-1)

• r10::Float64: Per site rate (constant) of singly bound crosslinker unbinding (s^-1)

• r12::Float64: Per site rate (constant) of singly bound crosslinker doubly binding (s^-1)

• r21::Float64: Per site rate (constant) of doubly bound crosslinker unbinding one head (s^-1)

• deltas::Float64: Spacing between binding sites on a filament (m)

• deltad::Float64: Spacing for doubly bound crosslinkers (m)

• k::Float64: Spring constant of crosslinker (N m^-1)

• T::Float64: Temperature (K)

• Nf::Int64: Number of filaments

• Nsca::Int64: Number of scaffold filaments

• EI::Float64: Bending rigidity (N m^2)

• Lf::Float64: Filament length (m)

• r0::Float64: Jump rate prefactor

• Df::Float64: Actin filament diameter (m)

• eta::Float64: Viscosity of fluid (kg m^-1 s^-1)

• Ds::Float64: Diffusion coefficient of singly bound crosslinkers on filament (m^2 s^-1)

• KsD::Float64: Dissociation constant for single crosslinker binding from solution (M)

• KdD::Float64: Dissociation constant for double crosslinker binding from solution (M)

• cX::Float64: Crosslinker concentration (M)

• n::Float64: Number of overlaps moving collectively during constriction

• tend::Float64: Duration of dynamics (s)

• lambda0::Float64: Initial lambda

• Ndtot0::Float64: Initial total doubly-bound crosslinkers

• interval::Float64: Write inteval for mean and variance of stochastic simulations

• zeta::Float64: Friction coefficient

Parameters for actin-anillin ring system.

R_to_lambda(R, p::RingParams) -> Any

Convert from ring radius to lambda.

bending_force(lambda, p::RingParams) -> Any

Calculate current bending force on L in a ring.

condensation_force(p::RingParams) -> Float64

Calculate condenstation force on L in a ring.

Since the condenstation force only depends on the total number of overlaps, it is constant as the ring constricts.

entropic_force(lambda, Ndtot, p::RingParams) -> Any

Calculate current entropic force on L for a ring.

equilibrium_occupancy(p::RingParams) -> Float64

Calculate the equilibrium occupancy.

equilibrium_ring_radius(p::RingParams) -> Float64

Calculate the equilibrium radius of a ring.

force_L_to_R(force, p::RingParams) -> Any

Convert from force on L to force on R.

free_energy_barrier_Nd_exact(Nd, p::RingParams) -> Any

Calculate free-energy barrier for the explicit-binding regime with exact friction.

free_energy_barrier_Nd_exp(Nd, p::RingParams) -> Any

Calculate free-energy barrier for the explicit-binding regime with approximate friction.

The barrier to sliding a distance of deltas, in units of kbT.

free_energy_barrier_cX(l, p::RingParams) -> Any

Calculate free-energy barrier for the fast-binding regime.

The barrier to sliding a distance of deltas, in units of kbT.

friction_coefficient_Nd_exact(
    Nd,
    p::RingParams
) -> Vector{Any}

Calculate friction coefficient in the explicit-binding regime with exact friction.

friction_coefficient_Nd_exp(Nd, p::RingParams) -> Any

Calculate friction coefficient in the explicit-binding regime with approximate friction.

friction_coefficient_cX(lambda, p::RingParams) -> Any

Calculate friction coefficient in the fast-binding regime.

kramers_r0(Nd, p::RingParams) -> Any

Calculate jump rate prefactor from Kramers' theory.

l_to_lambda(l, p::RingParams) -> Any

Convert from continuous number of sites in an overlap to lambda.

lambda_to_R(lambda, p::RingParams) -> Any

Convert from lambda to ring radius.

lambda_to_l(lambda, p::RingParams) -> Any

Convert from lambda to continuous number of sites in an overlap.

savename(
    prefix,
    params;
    digits,
    suffix,
    ignored_fields
) -> String

Generate file name from a set of parameters.

This is a replacement for the DrWatson function that has better handling of rounding and trailing zeros.

solve_and_write_ring_Nd_contin_exp(
    u0,
    tspan,
    p,
    ifields,
    filebase
)

Solve ring dynamics in the continuous explicit-binding regime with approximate friction.

solve_and_write_ring_Nd_contin_exp_noise(
    u0,
    tspan,
    trajs,
    p,
    ifields,
    filebase
)

Solve ring dynamics in the continuous explicit-binding regime with approximate friction and noise.

solve_and_write_ring_Nd_discrete_exact(
    u0,
    tspan,
    trajs,
    p,
    ifields,
    filebase
)

Solve ring dynamics in the discrete explicit-binding regime with exact friction.

solve_and_write_ring_Nd_discrete_exact_noise(
    u0,
    tspan,
    trajs,
    p,
    ifields,
    filebase
)

Solve ring dynamics in the discrete explicit-binding regime with exact friction and noise.

solve_and_write_ring_Nd_discrete_exp(
    u0,
    tspan,
    trajs,
    p,
    ifields,
    filebase
)

Solve ring dynamics in the discrete explicit-binding regime with approximate friction.

solve_and_write_ring_Nd_discrete_exp_noise(
    u0,
    tspan,
    trajs,
    p,
    ifields,
    filebase
)

Solve ring dynamics in the discrete explicit-binding regime with approximate friction and noise.

solve_and_write_ring_cX(u0, tspan, p, ifields, filebase)

Solve ring dynamics in the fast-binding regime.

solve_and_write_ring_cX_noise(
    u0,
    tspan,
    trajs,
    p,
    ifields,
    filebase
)

Solve ring dynamics in the fast-binding regime with noise.