Model of Synchronized Oscillations in the Choroid Plexus

This is a model for the 24-hour synchronized rhythms of the clock gene expression in the choroid plexus (CP), used in

Myung J, Schmal C, Hong S, Tsukizawa Y, Rose P, Zhang Y, Holtzman MJ, De Schutter E, Herzel H (2018) The Choroid Plexus is an Important Circadian Clock Component. Nat Commun, in press.

Here we present three example models for two distinct configurations, contained in the following directories:

1. 2D_Poincare_Simulation

This is a model used for Fig. S11c, implemented in Python. The main file of this simulation 2DPoincareSimulation.py and requires packages,

• numpy,
• scipy,
• matplotlib.

The simulation is self-contained and generates Fig. S11c of the paper.

2. Simulation_Fig_S13

This is a model for Fig. S13 and written in MATLAB. The main program is Simulation_Fig_S13.m, and running this generates an output fig_s13_data.mat. To generate Fig. S13 from this data, use Plot_Fig_S13.ipynb that is a Jupyter notebook written in Julia language.

3. CP_TwistChain_Simulation

This is a smaller, one-dimensional chain model implemented in Mathematica, which is used for Fig. 3 in the paper.

Written by Sungho Hong, Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Japan.

February 9, 2018

Correspondence: Jihwan Myung (jhmyung@gmail.com), Graduate Institute of Humanities in Medicine, Taipei Medical University, Taiwan.