# 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.*