DOI: 10.5061/dryad.sj3tx96dg
title: Dataset of phototactic response kinetics of Chlamydomonas reinhardtii

description: The directed movement of microorganisms towards light is called
 phototaxis-a fundamental process shown by many uni- and multi-cellular
 photosynthetic microorganisms for their survival and growth. Here, we
 determine the time-dependent response of a population of model phototactic
 single-celled algae Chlamydomonas reinhardtii to changing light
 conditions. When the condition changes from dark to light, we show that
 the response of a dark-adapted isotropic population depends on not just
 the light intensity but also on the cell number density. On the other
 hand, when conditions change from light to dark, the time dependence of
 the recovery from an aligned state to an isotropic state is independent of
 cell density and light intensity. We find that such kinetics emerge from
 the coupling between flagellar dynamics, cell speed, and incident photon
 flux. We further show that existing minimal non-interacting models, that
 robustly describe the steady state properties of populations of
 Chlamydomonas under given light conditions, capture this time-dependent
 phenomenon only for dilute suspensions.
description: All experimental data presented here are obtained by
 quantitatively analysing microscopy images using MATLAB. Data analysis and
 numerical calculations are performed in MATLAB and Mathematica.
description: # Dataset of phototactic response kinetics of *Chlamydomonas reinhardtii*
 [https://doi.org/10.5061/dryad.sj3tx96dg](https://doi.org/10.5061/dryad.sj3tx96dg) ## Description of the data and file structure This dataset corresponds to experimental data and associated theoretical modelling for dynamics during phototaxis of *Chlamydmonas reinhardtii* algal cells. ### Files and variables #### File: CR\_Phototactic\_Response\_Kinetics\_Data.zip *Contents:*  1. Math-formatted detailed README file Data_Information.pdf 2. Folders titled (a) Response (b) Recovery (c) Numerical (d) Matlab Scripts (e) Mathematica Script MATLAB codes provided are written in MATLAB R2022a version. Mathematica codes provided are written in Mathematica, Version 14.0 (2021). **Brief description of the contents in the folders** **Folder Name: Response** * Sub Folder: Polarization * This folder contains data on average polarization during response. * Sub Folder: Speed_Res * This folder contains data on average speed (in micrometers/seconds) as a function of time and the standard deviation during response. * Sub Folder: Speed Dark_Indv * This folder contains contains average cell speed (in micrometers/seconds) in the dark and standard deviation during response. * Sub Folder: ExpFit_IndvPol_TimeConstant * This folder contains data on the exponential fit to the polarization during response. * Sub Folder: Sorted Response time IndvFit * This folder presents data from ExpFit_IndvPol_TimeConstant subfolder sorted and arranged intensity and concentration-wise.  * Sub Folder: ExpFit_AvgPol_TimeConst * This folder contains the Average response time (in seconds) from the average polarization of all repeats at a given cell concentration and light intensity. * Sub Folder: Probability Distribution * This folder contains the averaged probability distribution of orientation during response. Refer to the math-formatted README file Data_Information.pdf for detailed data categorization in all of the above subfolders. **Folder Name: Recovery** * Sub Folder: Polarization * This folder contains data on polarization during recovery. * Sub Folder: Speed * This folder contains data on speed (in micrometers/seconds) during recovery. * Sub Folder: ExpFit_IndvPol_TimeConst * This folder contains data for recovery time (in seconds) obtained by fitting exponential decay to polarization corresponding to each repeat at a given cell concentration and light intensity. * Sub Folder: Probability distribution * This folder contains data on the probability density of orientation during recovery. Refer to the math formatted readme file Data_Information.pdf for detailed data categorization in all of the above subfolders. **Folder Name: Numerical** The folder has an Excel sheet “output.csv”. It contains the following data column-wise. (1st column) Light [in terms of current [mA] provided to laser source] (2nd column) OPIndex [running index to categorize folders] (3rd column) PolarTimeConstNum [in seconds] (4th column) PolarTimeConstNumSmall [in seconds] (5th column) PolarTimeConstNumBig [in seconds] (6th column) PolarTimeConstExp [in seconds] (7th column) kTimeConstNum [in seconds]   (8th column) kTimeConstNumSmall [in seconds] (9th column) kTimeConstNumBig [in seconds] (10th column) kTimeConstExp [in seconds] (11th column) PolarWakeTime [in seconds] (12th column) kWakeTime [in seconds]   (13th column) GammaSteadyExp [radians/seconds]   (14th column) ThetaShiftSteadyExp [radians]   (15th column) GammaErrorSteadyExp [radians/seconds]   (16th column) PolarSteadyExp   (17th column) PolarTimeConstErrorExp [in seconds]   (18th column) kTimeConstErrorExp [in seconds] For details refer to the example and comments provided in the folder named "Mathematica Script". **Folder Name: Mathematica Script** This folder contains Mathematica code used for numerical calculations and part of data analysis. The data in the file “output.csv” are generated through analysis in Mathematica.  **Folder Name: Matlab Scripts** This folder contains Matlab codes used to generate figures in the manuscript. Refer to the math formatted readme file Data_Information.pdf for details of the mapping of codes to the data in the manuscript.