Mechano-circadian simulation results

Simulation results associated with the manuscript, "Computational modeling establishes mechanotransduction as a potent modulator of the mammalian circadian clock". See README file for descriptions of individual results files. All are stored as .m files for use in MATLAB. README reproduced below for easy access:

bayesianAnalysis.mat: This should be loaded after initializing UQLab and before running any of the scripts. It contains all the results from MCMC for Bayesian parameter estimation in a single variable, `myBayesianAnalysis`.

pSol_MAP.mat: This can be loaded for running simulations using only the maximum a posteriori parameters, contains a single variable `pSol`.

SobolAnalysis.mat: results of Sobol sensitivity analysis stored in single variable `SobolAnalysis` for use with UQLab.

circStored.mat: Contains variable `circStoreCell` to generate phase diagrams in CircadianAnalysis file.

BranchesStored.mat: Contains variable `BranchesStored` with the coordinates of Hopf bifurcation curves in the MRTF-YAP/TAZ phase plane. Generated by ddeBifCircadian.m, for use with CircadianAnalysis.m.

nMechCircStored.mat and nMechBranches.mat: Alterative versions of the above, corresponding to tests of different coupling Hill coefficients [1,1.5,2,3,4.5]

StiffnessTests.mat: results from population level simulations for Figure 4, with substrate stiffnesses [0.1, 0.3, 1, 3, 10, 30, 100, 300, 1e7]. Data stored in single variable `popSeq`, generated by MechanoCircadian_main.m

WTTests.mat: tests from Abenza et al for Figure 5, population level data in single variable `popSeq`, see MechanoCircadian_main.m for more details

StiffnessTestsYAPMutant.mat: same as stiffnessTests above, but for YAP mutant 5SA-YAP (see settings in MechanoCircadian_main.m)

StiffnessTestsLaminMutant.mat: same as stiffnessTests above, but for YAP mutant 5SA-YAP (see settings in MechanoCircadian_main.m)

AltMutantTests.mat: tests for Figure S5, all at substrate stiffness = 30 kPa. 6 populations, corresponding to 0.5x YAP mutant, 2x YAP mutant, 4x YAP mutant, 1.5x NPC opening (Lamin mutant), 3x NPC opening (Lamin mutant), 5x NPC opening (Lamin mutant) - all stored in `popSeq` as above