Dataset: Connectivity and rigidity percolation of cytoskeletal networks.

Dataset containing information for "Connectivity and rigidity percolation of cytoskeletal networks."

File: Fig1A_MEDYAN_Unbranched_timeseries_motor_333_linker_1500_tmax_122.csv
Description:
Average MEDYAN simulations in a 1um3 box with 333 motors and 1500 linkers, no branchers.
Columns:
    Last_Timestep: Last time step of the simulations
    N_Motors: Total number of motors in the simulation
    N_Linkers: Total number of linkers in the simulation
    Simulation: Number of simulations
    M_p: Number of plus ends
    M_m: Number of minus ends
    M_c: Number of free binding sites
    M_M: Number of free motors
    M_L: Number of free linkers
    M_pm: Number of plus ends connected to minus ends (polymerized F-actin)
    M_cMc: Number of bound motors
    M_cLc: Number of bound linkers
    M_G: Number of free G-actin
    M_b: number of free branchers

File: Fig1A_ODE_Unbranched_timeseries_motor_333_linker_1500_tmax_10000.csv
Description:
Chemical kinetics calculations for transient concentrations of motor, linker and brancher for equivalent MEDYAN simulations of a 1um3 box with 333 motors and 1500 linkers, no branchers.
Columns:
    pm: Number of plus ends connected to minus ends (polymerized F-actin)
    L: Number of free linkers
    cMc: Number of bound motors
    cLc: Number of bound linkers
    c: Number of free binding sites
    m: Number of minus ends
    p: Number of plus ends
    G: Number of free G-actin
    M: Number of free motors

File: Fig1A_Unbranched_MEDYAN.csv
Description:
Species concentrations in MEDYAN simulations in a 1um3 box with 333 motors and 1500 linkers, no branchers.
The simulations can be found in the Simulations_Unbranched folder
Columns:
    Last_Timestep: Measured timestep
    N_Motors: Total number of motors in the simulation
    N_Linkers: Total number of linkers in the simulation
    chem_path: Path of the simulation
    AD: Number of unbound G-actins
    MD: Number of unbound motors
    LD: Number of unbound linkers
    FA: Number of bound F-actin monomers
    PA: Number of plus ends
    MA: Number of minus ends
    LA: Number of bound linkers
    MOA: Number of bound motors
    Simulation: Simulation ID

File: Fig1B_Branched_MEDYAN.csv
Description:
Species concentrations in MEDYAN simulations in a 1um3 box with 333 motors and 1500 linkers, 300 branchers.
The simulations can be found in the Simulations_Branched folder
Columns:
    Last_Timestep: Measured timestep
    N_Motors: Number of motors
    N_Linkers: Number of linkers
    chem_path: Path of the simulation
    AD: Number of unbound G-actins
    BD: Number of unbound branchers
    MD: Number of unbound motors
    LD: Number of unbound linkers
    FA: Number of bound F-actin monomers
    PA: Number of plus ends
    MA: Number of minus ends
    LA: Number of bound linkers
    MOA: Number of bound motors
    BA: Number of bound branchers
    Simulation: Simulation ID

File: Fig1B_MEDYAN_Branched_timeseries_motor_333_linker_1500_tmax_122.csv
Description:
Average MEDYAN simulations in a 1um3 box with 333 motors and 1500 linkers, 300 branchers.
Columns:
    Last_Timestep: Last time step of the simulations
    N_Motors: Total number of motors in the simulation
    N_Linkers: Total number of linkers in the simulation
    Simulation: Number of simulations
    M_p: Number of plus ends
    M_m: Number of minus ends
    M_c: Number of free binding sites
    M_M: Number of free motors
    M_L: Number of free linkers
    M_pm: Number of plus ends connected to minus ends (polymerized F-actin)
    M_cMc: Number of bound motors
    M_cLc: Number of bound linkers
    M_G: Number of free G-actin
    M_B: total number of branchers
    M_cBm: number of bound branchers
    M_b: number of free  branchers

File: Fig1B_ODE_Branched_timeseries_motor_333_linker_1500_tmax_10000_v2.csv
Description:
Chemical kinetics calculations for transient concentrations of motor, linker and brancher for equivalent MEDYAN simulations of a 1um3 box with 333 motors and 1500 linkers, and 300 branchers.
Columns:
    pm: Number of plus ends connected to minus ends (polymerized F-actin)
    L: Number of free linkers
    p: Number of plus ends
    cMc: Number of bound motors
    cBm: Number of bound branchers
    cLc: Number of bound linkers
    c: Number of free binding sites
    m: Number of minus ends
    M: Number of free motors
    G: Number of free G-actin
    B: Number of free branchers

File: Fig1C_Ps_timeseries_unbranched.csv
Description:
Flory-Stockmayer results for unbranched chemical kinetics calculations
Columns:
    pm: Number of plus ends connected to minus ends (polymerized F-actin)
    L: Number of free linkers
    cMc: Number of bound motors
    cLc: Number of bound linkers
    c: Number of free binding sites
    m: Number of free minus ends
    p: Number free of plus ends
    G: Number of free G-actin
    M: Number of free motors
    P0: Probability that an F-actin monomer is connected to another one on its plus end
    P1: Probability that an F-actin monomer is connected to another one on its minus end
    P2: Probability that an F-actin monomer is connected to another one on its binding site
    Ps: Probability that an F-actin monomer  is not connected to an infinite cluster
    Nb: Average number of bonds per F-actin monomer
    Nn: Mean cluster size
    Nw: Mean weighted cluster size
    Ratio: Nw/Nn Ratio

File: Fig1D_Ps_timeseries_branched.csv
Description:
Flory-Stockmayer results for branched chemical kinetics calculations
Columns:
    pm: Number of plus ends connected to minus ends (polymerized F-actin)
    L: Number of free linkers
    cMc: Number of bound motors
    cBm: Number of bound branchers
    cLc: Number of bound linkers
    c: Number of free binding sites
    m: Number of free minus ends
    p: Number free of plus ends
    G: Number of free G-actin
    M: Number of free motors
    B: Number of free branchers
    P0: Probability that an F-actin monomer is connected to another one on its plus end
    P1: Probability that an F-actin monomer is connected to another one on its minus end
    P2: Probability that an F-actin monomer is connected to another one on its binding site
    Ps: Probability that an F-actin monomer  is not connected to an infinite cluster
    Nb: Average number of bonds per F-actin monomer
    Nn: Mean cluster size
    Nw: Mean weighted cluster size
    Ratio: Nw/Nn Ratio
    Qm: Probability that an F-actin monomer  is not connected to an infinite cluster through the minus end
    Qp: Probability that an F-actin monomer  is not connected to an infinite cluster through the plus end
    Qc: Probability that an F-actin monomer  is not connected to an infinite cluster through the binding site

File: Fig2_Two-step.csv
Description:
Representative steady state concentrations for a non-cooperative two-step model of linker binding.
Columns:
    Fc: Concentration of free binding sites
    FcL: Concentration of linkers bound to a single binding site
    FcLFc: Concentration of linkers bound to a pair of binding sites
    L: Concentration of unbound linkers
    Fc0: Total concentration of binding sites
    L0: Total concentration of linkers

File: Fig3_two_step_heatmap.csv
Proportion of the concentration of crosslinks to the concentration of total binding sites as a function of the linker binding equilibrium constant
Description:
2D matrix, where the columns indicate the linker binding constant multiplied by the total concentration of binding sites, the rows indicate the total concentration of linkers per binding site , and the value corresponds to the total number of linkers bound to two binding sites divided by the total concentration of binding sites.

File: Fig5A_Ps_unbranched.csv
Description:
2D matrix, where the columns indicate the proportion of motors to actin, the rows indicate the proportion of linkers to actin , and the value corresponds to the probability that an F-actin monomer is in a finite cluster using the chemical kinetics model without brancher.

File: Fig5B Ps_branched.csv
Description:
2D matrix, where the columns indicate the proportion of motors to actin, the rows indicate the proportion of linkers to actin , and the value corresponds to the probability that an F-actin monomer is in a finite cluster using the chemical kinetics model with brancher.
    

File: Fig6_Ps_Branched_var.csv
Description:
2D matrix, where the columns indicate the proportion of branchers to actin, the rows indicate the proportion of linkers to actin , and the value corresponds to the probability that an F-actin monomer is in a finite cluster using the chemical kinetics model without brancher or motors.

File: Fig7B_Ps_unbranched_linkeronly.csv

Description:
2D matrix, where the columns indicate the proportion of motors to actin, the rows indicate the proportion of linkers to actin , and the value corresponds to the probability that an F-actin monomer is in a finite cluster using the chemical kinetics model without brancher. The clusters are defined here as F-actin monomers connected by linkers, and without including motor connections.

File: Fig7D_Ps_branched_linkeronly.csv

Description:
2D matrix, where the columns indicate the proportion of motors to actin, the rows indicate the proportion of linkers to actin , and the value corresponds to the probability that an F-actin monomer is in a finite cluster using the chemical kinetics model with brancher. The clusters are defined here as F-actin monomers connected by linkers or branchers, and without including motor connections.

File: Fig9_data.csv
Description:
Minimum motor concentration to reach rigidity percolation as a function of the linker concentration for systems with and without brancher, considering both linker and motor connections or just motor connections and for different values of linker rigidity. The motor and linker concentrations are measured as the proportion of linkers or motors to actin.
Columns:
    L: linker concentration 
    "M (unbranched, linkers and motors, bcLc=0)"
    "M (unbranched, linkers and motors, bcLc=1)"
    "M (unbranched, linkers and motors, bcLc=2)"
    "M (unbranched, linkers and motors, bcLc=3)"
    "M (unbranched, linkers and motors, bcLc=4)"
    "M (unbranched, linkers and motors, bcLc=5)"
    "M (unbranched, linkers and motors, bcLc=6)"
    "M (branched, linkers and motors, bcLc=0)"
    "M (branched, linkers and motors, bcLc=1)"
    "M (branched, linkers and motors, bcLc=2)"
    "M (branched, linkers and motors, bcLc=3)"
    "M (branched, linkers and motors, bcLc=4)"
    "M (branched, linkers and motors, bcLc=5)"
    "M (branched, linkers and motors, bcLc=6)"
    "M (unbranched, linkers only, bcLc=0)"
    "M (unbranched, linkers only, bcLc=1)"
    "M (unbranched, linkers only, bcLc=2)"
    "M (unbranched, linkers only, bcLc=3)"
    "M (unbranched, linkers only, bcLc=4)"
    "M (unbranched, linkers only, bcLc=5)"
    "M (unbranched, linkers only, bcLc=6)"
    "M (branched, linkers only, bcLc=0)"
    "M (branched, linkers only, bcLc=1)"
    "M (branched, linkers only, bcLc=2)"
    "M (branched, linkers only, bcLc=3)"
    "M (branched, linkers only, bcLc=4)"
    "M (branched, linkers only, bcLc=5)"
    "M (branched, linkers only, bcLc=6)"

File: FigS1_data.csv
Description:
Connectivity percolation as a function of the probabilities that an F-actin monomer site is bound to another F-actin.
Columns:
    ppm: probability that an F-actin monomer plus end is connected to another F-actin monomer minus end
    pcc: probability that an F-actin monomer binding site is connected to another F-actin monomer binding site
    Pcm: probability that an F-actin monomer binding site is connected to another F-actin monomer minus end
    Qp: Probability that an F-actin monomer  is not connected to an infinite cluster through the plus end
    Qm: Probability that an F-actin monomer  is not connected to an infinite cluster through the minus end
    Qc: Probability that an F-actin monomer  is not connected to an infinite cluster through the binding site
    Ps: Probability that an F-actin monomer  is not connected to an infinite cluster
Percolated: Whether the system is percolated or not.

File: simulations.tar.gz
Description: Contains the MEDYAN simulations used for figure 1. Each folder contains an individual simulation, with the following files:
systeminput.txt: Contains the input for the system conditions and settings
chemistryinput.txt: Contains the input for the chemical species
chemistry.traj: Output trajectory containing number of species in the simulations
snapshot.traj: Output trajectory containing the coordinates of the species.
For more information please reference the MEDYAN user guide and reference:
K Popov, JE Komianos and GA Papoian (2016) MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks. PLoS Comput Biol 12(4): e1004877. doi:10.1371/journal.pcbi.1004877