ActinRingsMC

Actin rings Monte Carlo simulation package

A Julia simulation package with functions for running adaptive umbrella sampling Monte Carlo simulations of crosslinked actin rings.

Repository

Documentation

This package implements the simulation protocol outlined in the Supplemental Material of Ref. 1.

Installation

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

add ActinRingsMC

to install from the General registry, or by running

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

to install directly from the development repository.

Running a simulation

In examples directory of the repository is a script for umbrella sampling. It has both an initial run and a continuation run. The commands can be run in the Julia REPL, or, when in the same directory as the script, it can be run with

julia run-umbrella-sampling.jl

To achieve good sampling, one should experiment with the number of steps per iteration and the number of iterations.

Analysis and visualization

The simulations output two data file types per simulation, or in the case of an umbrella sampling run, per iteration. The file type with an .ops extension contains order parameters saved at steps determined by the write interval and can be read in as a dataframe for analysis and plotting. Currently the order parameters include the energy, lattice height, and ring radius. The file type with a .vtf extension is able to be read by the molecular visualization program, VMD, such that the configurations of the simulations can be spatially visualized. When viewing in VMD, it is recommended to use "Chain" for "Coloring Method" and "VDW" for "Drawing Method". The simulations also output a file containing all the system and simulation parameters used in the run to a .parms file.

Umbrella sampling runs output additional file types. The output of these file is based on every step, not only those determined by the write frequency. The top row gives the lattice height (or bin, although binning has not been tested). Each subsequent row contains data from an iteration. .counts gives the number of times each lattice height was visited, .freqs gives a normalized version of this. .biases includes the biases that were used to for that iteration (in contrast to those that would be calculated from its data).

A related python package, actinrings, includes code for analyzing and plotting the output from these simulations, including free energies and ring constriction forces; see its documentation for details.

References

[1] A. Cumberworth and P. R. t. Wolde, Constriction of actin rings by passive crosslinkers.

Links

Julia programming language

Replication analysis package

VMD

• Lattice
• SimulationParams
• System
• SystemParams
• calc_Lf
• calc_lf
• calc_max_lattice_height
• calc_min_lattice_height
• calc_radius
• generate_starting_config
• run!
• run_us!
• update_occupancies!

Lattice(height::Int64, max_height::Int64, min_height::Int64) -> Lattice

2D lattice with periodic conditions on y.

The max and min heights should be calculated based on the number of scaffold filaments and the length of the filaments.

Simulation parameters.

• iters::Int64

  Number of iterations for US

• steps::Int64

  MC steps for a run or single iteration

• max_bias_diff::Float64

  Maximum change in bias energy (kbT)

• write_interval::Int64

  Number of steps between writing to output files

• radius_move_freq::Float64

  Frequency of radius moves (the remainder are filament translation moves)

• filebase::String

  Output filebase (include filepath)

• analytical_biases::Bool

  Use analytical model to generation starting biases

• read_biases::Bool

  Read starting biases from file

• biases_filename::String

  File to read biases from

• restart_iter::Int64

  Iteration to to start on

• binwidth::Int64

  Width of bins for lattice height bias (set to 1 for no binning)

System(parms::SystemParams, filaments::Vector{ActinRingsMC.Filament}, radius::Float64) -> System

System data, including parameters and positions of filaments.

The given radius should be that corresponding to the lattice height used to create the lattice and the starting configuration of the filaments.

System parameters.

• ks::Float64

  Dissociation constant for single crosslinker binding

• kd::Float64

  Dissociation constant for double crosslinker binding

• T::Float64

  Temperature (K)

• delta::Float64

  Lattice spacing (m)

• Xc::Float64

  Crosslinker concentration (M)

• EI::Float64

  Bending rigidity (N m^2)

• Lf::Float64

  Filament length (m)

• lf::Int64

  Binding sites per filament

• Nfil::Int64

  Total number of filaments

• Nsca::Int64

  Number of scaffold filaments

calc_Lf(lf::Int64, delta::Float64) -> Float64

Calculate the length of a filament.

calc_lf(Lf::Float64, delta::Float64) -> Int64

Calculate the number of sites per filament.

calc_max_lattice_height(Nsca::Int64, lf::Int64) -> Int64

Calculate the maximum allowable height of a lattice given Nsca.

calc_min_lattice_height(Nsca::Int64, lf::Int64) -> Int64

Calculate the minimum allowable height of a lattice given Nsca.

calc_radius(delta::Float64, height::Int64) -> Float64

Calculate the radius of a ring for a given lattice height.

generate_starting_config(lattice::Lattice, Nfil::Int64, Nsca::Int64, lf::Int64, overlap::Int64) -> Vector{ActinRingsMC.Filament}

Generate a starting configuration with uniform overlaps.

The number of scaffold filament Nsca and the number of lattices lf must be even.

run!(system::System, lattice::Lattice, simparms::SimulationParams, biases::ActinRingsMC.Biases, ops_file::IOStream, vtf_file::IOStream)

Run an MC simulation.

run!(system::System, lattice::Lattice, simparms::SimulationParams)

Run an MC simulation.

run_us!(system::System, lattice::Lattice, simparms::SimulationParams)

Run an umbrella sampling MC simulation.

update_occupancies!(filaments::Vector{ActinRingsMC.Filament}, lattice::Lattice)

Clear occupancies and fully update.