DOI: 10.5281/zenodo.5645714
title: Dataset: Connectivity and rigidity percolation of cytoskeletal networks.

description: Dataset containing information for "Connectivity and rigidity percolation of cytoskeletal networks." File: Fig1A_MEDYAN_Unbranched_timeseries_motor_333_linker_1500_tmax_122.csv<br> Description:<br> Average MEDYAN simulations in a 1um3 box with 333 motors and 1500 linkers, no branchers.<br> Columns:<br> Last_Timestep: Last time step of the simulations<br> N_Motors: Total number of motors in the simulation<br> N_Linkers: Total number of linkers in the simulation<br> Simulation: Number of simulations<br> M_p: Number of plus ends<br> M_m: Number of minus ends<br> M_c: Number of free binding sites<br> M_M: Number of free motors<br> M_L: Number of free linkers<br> M_pm: Number of plus ends connected to minus ends (polymerized F-actin)<br> M_cMc: Number of bound motors<br> M_cLc: Number of bound linkers<br> M_G: Number of free G-actin<br> M_b: number of free branchers File: Fig1A_ODE_Unbranched_timeseries_motor_333_linker_1500_tmax_10000.csv<br> Description:<br> 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.<br> Columns:<br> pm: Number of plus ends connected to minus ends (polymerized F-actin)<br> L: Number of free linkers<br> cMc: Number of bound motors<br> cLc: Number of bound linkers<br> c: Number of free binding sites<br> m: Number of minus ends<br> p: Number of plus ends<br> G: Number of free G-actin<br> M: Number of free motors File: Fig1A_Unbranched_MEDYAN.csv<br> Description:<br> Species concentrations in MEDYAN simulations in a 1um3 box with 333 motors and 1500 linkers, no branchers.<br> The simulations can be found in the Simulations_Unbranched folder<br> Columns:<br> Last_Timestep: Measured timestep<br> N_Motors: Total number of motors in the simulation<br> N_Linkers: Total number of linkers in the simulation<br> chem_path: Path of the simulation<br> AD: Number of unbound G-actins<br> MD: Number of unbound motors<br> LD: Number of unbound linkers<br> FA: Number of bound F-actin monomers<br> PA: Number of plus ends<br> MA: Number of minus ends<br> LA: Number of bound linkers<br> MOA: Number of bound motors<br> Simulation: Simulation ID File: Fig1B_Branched_MEDYAN.csv<br> Description:<br> Species concentrations in MEDYAN simulations in a 1um3 box with 333 motors and 1500 linkers, 300 branchers.<br> The simulations can be found in the Simulations_Branched folder<br> Columns:<br> Last_Timestep: Measured timestep<br> N_Motors: Number of motors<br> N_Linkers: Number of linkers<br> chem_path: Path of the simulation<br> AD: Number of unbound G-actins<br> BD: Number of unbound branchers<br> MD: Number of unbound motors<br> LD: Number of unbound linkers<br> FA: Number of bound F-actin monomers<br> PA: Number of plus ends<br> MA: Number of minus ends<br> LA: Number of bound linkers<br> MOA: Number of bound motors<br> BA: Number of bound branchers<br> Simulation: Simulation ID File: Fig1B_MEDYAN_Branched_timeseries_motor_333_linker_1500_tmax_122.csv<br> Description:<br> Average MEDYAN simulations in a 1um3 box with 333 motors and 1500 linkers, 300 branchers.<br> Columns:<br> Last_Timestep: Last time step of the simulations<br> N_Motors: Total number of motors in the simulation<br> N_Linkers: Total number of linkers in the simulation<br> Simulation: Number of simulations<br> M_p: Number of plus ends<br> M_m: Number of minus ends<br> M_c: Number of free binding sites<br> M_M: Number of free motors<br> M_L: Number of free linkers<br> M_pm: Number of plus ends connected to minus ends (polymerized F-actin)<br> M_cMc: Number of bound motors<br> M_cLc: Number of bound linkers<br> M_G: Number of free G-actin<br> M_B: total number of branchers<br> M_cBm: number of bound branchers<br> M_b: number of free branchers File: Fig1B_ODE_Branched_timeseries_motor_333_linker_1500_tmax_10000_v2.csv<br> Description:<br> 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.<br> Columns:<br> pm: Number of plus ends connected to minus ends (polymerized F-actin)<br> L: Number of free linkers<br> p: Number of plus ends<br> cMc: Number of bound motors<br> cBm: Number of bound branchers<br> cLc: Number of bound linkers<br> c: Number of free binding sites<br> m: Number of minus ends<br> M: Number of free motors<br> G: Number of free G-actin<br> B: Number of free branchers File: Fig1C_Ps_timeseries_unbranched.csv<br> Description:<br> Flory-Stockmayer results for unbranched chemical kinetics calculations<br> Columns:<br> pm: Number of plus ends connected to minus ends (polymerized F-actin)<br> L: Number of free linkers<br> cMc: Number of bound motors<br> cLc: Number of bound linkers<br> c: Number of free binding sites<br> m: Number of free minus ends<br> p: Number free of plus ends<br> G: Number of free G-actin<br> M: Number of free motors<br> P0: Probability that an F-actin monomer is connected to another one on its plus end<br> P1: Probability that an F-actin monomer is connected to another one on its minus end<br> P2: Probability that an F-actin monomer is connected to another one on its binding site<br> Ps: Probability that an F-actin monomer is not connected to an infinite cluster<br> Nb: Average number of bonds per F-actin monomer<br> Nn: Mean cluster size<br> Nw: Mean weighted cluster size<br> Ratio: Nw/Nn Ratio File: Fig1D_Ps_timeseries_branched.csv<br> Description:<br> Flory-Stockmayer results for branched chemical kinetics calculations<br> Columns:<br> pm: Number of plus ends connected to minus ends (polymerized F-actin)<br> L: Number of free linkers<br> cMc: Number of bound motors<br> cBm: Number of bound branchers<br> cLc: Number of bound linkers<br> c: Number of free binding sites<br> m: Number of free minus ends<br> p: Number free of plus ends<br> G: Number of free G-actin<br> M: Number of free motors<br> B: Number of free branchers<br> P0: Probability that an F-actin monomer is connected to another one on its plus end<br> P1: Probability that an F-actin monomer is connected to another one on its minus end<br> P2: Probability that an F-actin monomer is connected to another one on its binding site<br> Ps: Probability that an F-actin monomer is not connected to an infinite cluster<br> Nb: Average number of bonds per F-actin monomer<br> Nn: Mean cluster size<br> Nw: Mean weighted cluster size<br> Ratio: Nw/Nn Ratio<br> Qm: Probability that an F-actin monomer is not connected to an infinite cluster through the minus end<br> Qp: Probability that an F-actin monomer is not connected to an infinite cluster through the plus end<br> Qc: Probability that an F-actin monomer is not connected to an infinite cluster through the binding site File: Fig2_Two-step.csv<br> Description:<br> Representative steady state concentrations for a non-cooperative two-step model of linker binding.<br> Columns:<br> Fc: Concentration of free binding sites<br> FcL: Concentration of linkers bound to a single binding site<br> FcLFc: Concentration of linkers bound to a pair of binding sites<br> L: Concentration of unbound linkers<br> Fc0: Total concentration of binding sites<br> L0: Total concentration of linkers File: Fig3_two_step_heatmap.csv<br> Proportion of the concentration of crosslinks to the concentration of total binding sites as a function of the linker binding equilibrium constant<br> Description:<br> 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<br> Description:<br> 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. <br> File: Fig5B Ps_branched.csv<br> Description:<br> 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.<br> File: Fig6_Ps_Branched_var.csv<br> Description:<br> 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. <br> File: Fig7B_Ps_unbranched_linkeronly.csv Description:<br> 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:<br> 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<br> Description:<br> 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.<br> Columns:<br> L: linker concentration <br> "M (unbranched, linkers and motors, bcLc=0)"<br> "M (unbranched, linkers and motors, bcLc=1)"<br> "M (unbranched, linkers and motors, bcLc=2)"<br> "M (unbranched, linkers and motors, bcLc=3)"<br> "M (unbranched, linkers and motors, bcLc=4)"<br> "M (unbranched, linkers and motors, bcLc=5)"<br> "M (unbranched, linkers and motors, bcLc=6)"<br> "M (branched, linkers and motors, bcLc=0)"<br> "M (branched, linkers and motors, bcLc=1)"<br> "M (branched, linkers and motors, bcLc=2)"<br> "M (branched, linkers and motors, bcLc=3)"<br> "M (branched, linkers and motors, bcLc=4)"<br> "M (branched, linkers and motors, bcLc=5)"<br> "M (branched, linkers and motors, bcLc=6)"<br> "M (unbranched, linkers only, bcLc=0)"<br> "M (unbranched, linkers only, bcLc=1)"<br> "M (unbranched, linkers only, bcLc=2)"<br> "M (unbranched, linkers only, bcLc=3)"<br> "M (unbranched, linkers only, bcLc=4)"<br> "M (unbranched, linkers only, bcLc=5)"<br> "M (unbranched, linkers only, bcLc=6)"<br> "M (branched, linkers only, bcLc=0)"<br> "M (branched, linkers only, bcLc=1)"<br> "M (branched, linkers only, bcLc=2)"<br> "M (branched, linkers only, bcLc=3)"<br> "M (branched, linkers only, bcLc=4)"<br> "M (branched, linkers only, bcLc=5)"<br> "M (branched, linkers only, bcLc=6)" File: FigS1_data.csv<br> Description:<br> Connectivity percolation as a function of the probabilities that an F-actin monomer site is bound to another F-actin.<br> Columns:<br> ppm: probability that an F-actin monomer plus end is connected to another F-actin monomer minus end<br> pcc: probability that an F-actin monomer binding site is connected to another F-actin monomer binding site<br> Pcm: probability that an F-actin monomer binding site is connected to another F-actin monomer minus end<br> Qp: Probability that an F-actin monomer is not connected to an infinite cluster through the plus end<br> Qm: Probability that an F-actin monomer is not connected to an infinite cluster through the minus end<br> Qc: Probability that an F-actin monomer is not connected to an infinite cluster through the binding site<br> Ps: Probability that an F-actin monomer is not connected to an infinite cluster<br> Percolated: Whether the system is percolated or not. File: simulations.tar.gz<br> Description: Contains the MEDYAN simulations used for figure 1. Each folder contains an individual simulation, with the following files:<br> systeminput.txt: Contains the input for the system conditions and settings<br> chemistryinput.txt: Contains the input for the chemical species<br> chemistry.traj: Output trajectory containing number of species in the simulations<br> snapshot.traj: Output trajectory containing the coordinates of the species.<br> For more information please reference the MEDYAN user guide and reference:<br> 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
description: Figure 4 data boundaries were obtained using the data from Figure 3 as an input. Figure7A uses the same data as Figure5A