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