The data and codes are used for modeling and generating figures in the paper entitleed "The younger flagellum sets the beat for Chlamydomonas reinhardtii" and published with eLife (https://doi.org/10.7554/eLife.86102)
Matlab scripts included are:
1.PhaseDynamicsAtDifferentDetuning_model.m
2.SyncProfiles_model.m
3.ArnoldTongue_model.m
Dependent customized functions are:
segmentBooleanSig.m
markSync.m
Dataset is inlcuded in:
Data.zip
Detailed information for these files are given in the following
** Description of the scripts
This script is the model corresponding to equation 2 in the paper. It simulates the phase interaction between external flow and the two flagella. Variables are named in the same way as used in the paper (for a complete summary of the notations see Appendix1-table1 in the paper).
This script directly outputs the phase dynamics of flow entrainment at varyiing detunings (Fig.5B).
The only abbreviations used in the codes are:
_eff_ : effective
eps_: epsilon
Fs: sampling frequency
This script models entrainment profiles under varying flagellar-asymmetry, which is underlying Fig.5E-H. The custom function that measures the synchronized/entrainment fraction from a time series (markSync.m) is used.
This script scans flow entrainment (described by the model) for varying flow-flagella detuning and varying flow amplitude. The resultant landscape of flow entrainment/flagellar synchronization is what underlies Fig.5CD and Appendix1-figure3.
** functions
This function takes a time series of phase difference, and mark the fractions whose temporal variation is slower than a threshold (can be specified by an input argument 'ThresholdSlope') as synchronized/entrained. Detailed description can be found in the Doc at the beginning of the file.
This function parses a binary array (the only input), returns the starting/ending indices of consecutive elements of '1's and '0's. It is used in the function markSync.m.
** Data specific information
Datasets underlying each panel of Figure1-4 are included. The spreadsheet file maps each folder/mat file to each figure panel.
The variables 'ThPh1_unwrapped' and 'ThPh2_unwrapped' are the variable-independent phase of two flagella. 'fps' is the frame rate.
In this folder, each file named as '180703c1_axial_#freq.mat' includes the phase dynamics of the cells beating under the frontal flows of the frequency indicated.
In the file named '180703c1_axial_synchronization.mat', relevant data for the same cell under N=14 different tested flow frequencies are included. The variables 'slope_d_*' are respectively the local slope of phase differences (i.e. frequency mismatch). The suffices '_Ph1', '_Ph2' or'_PhFlag' describe if the phase difference is between the cis and the flow (_Ph1), the trans and the flow (_Ph2), or between the cis and trans (_PhFlag).
The \tau values reported in the paper are in the array 'TSync*Ratio_list'. The flows' frequencies is recorded in the variable 'freqList'.
In this folder, the hydrodynamic computations that combines Boundary Element Method and Slender Body Theory are included. The data underlies Figure 1E-G and Appendix1-figure1.
Due to historical reasons, the uploaded file include all variables our computation generates hitherto, and most relevant ones are described below:
Cell size [micron] and other modeling settings are
a = 5.14;
b = 4.45;
flag_length = 12.68;
fps = 801.42 [Hz]
eta = 0.9544e-3; [Pa S]
The forces can be computed from the included variables as:
DragX1 = eta * D1(:,1) * 1e-12 ; % [N]
DragY1 = eta * D1(:,2) * 1e-12 ;
DragX2 = eta * D2(:,1) * 1e-12 ;
DragY2 = eta * D2(:,2) * 1e-12 ;
DragTot1 = sqrt(DragX1.^2 + DragY1.^2);
DragTot2 = sqrt(DragX2.^2 + DragY2.^2);
P_visc_1 = eta * phi1 * 1e-18;
P_visc_2 = eta * phi2 * 1e-18;
P_visc_tot = P_visc_1 + P_visc_2;
Where the suffix 1/2 denotes flagella; X/Y denotes the direction of vector component, _tot means total, _visc means viscous. The variables 'D*' and 'phi*' are the core part of load computation.
The field that reads 'FlowON'/'FlowOff' in the filenames (e.g., BEMsolution_c02BEM_01XY_FlowOn.mat) means whether the background flow is switched on or off. The other field that reads '01XY','02MinXY','03Axial', and '04Cross' correspond to the cis-flows, trans-flows, frontal-flows, and the flow that oscillates perpendicular to the axis of pipette (\theta=0, Appendix1-figure1-GH).
The flagellar shapes therein are manually marked by mouse clicking (a Logitech mouse was worn out, may it rest in peace); they are represented by the x and y coordinates of the collocation points along the flagellar centerline, see the variables 'xflag' and 'yflag'. The dimensions of 'xflag' correspond to: the frame, cis_or_trans, and # out of the 26 collocation points.
The last file in the folder, , stores the time points where the flagella display the most forward-reaching shape in a beat (~mark the beginning of a power stroke).
Data underlying the experimentally meausred Arnold tongues for wt and ptx1 cells, Figure 2B-C. Each mat file correspond to a scan in frequency. The synchronized time fraction is stored in 'TSync*Ratio_IP_list'. The file is in the same format as '180703c1_axial_synchronization.mat', which was described above.
Data underlying the experimentally measured flow entrainment profiles, Figure 3A and 4A. In the file, 'xi_' represents the entrained time fraction, which reads '\tau' in the paper. The suffices _c,t,a represent respective cis-flow, trans-flow, and frontal flow.
Data underlying the measured flow entrainment strength \varepsilon (or entrained time fraction \tau) for wt (or ptx1) cells, Figure 3B-C and Figure 4B-C.