📂 Repository Structure

This repository contains two main folders:

• GUI/ → The graphical user interface for interactive simulations.
• manuscript/ → MATLAB scripts used to reproduce the results from the manuscript:
  "Emerging multidien cycles from partial circadian synchrony".

Emerging_multidien_cycles manuscript

This folder contains the necessary scripts to perform a large-scale parameter sweep of the model presented in the paper "Emerging multidien cycles from partial circadian synchrony." These simulations are intended to be run on a computing cluster. Otherwise skip the sl code and directly simulate the matlab codes for specific parameters.

Contents

• mainClusterChimerasAllparam.sl
  A Slurm batch script for submitting the simulation job to a computing cluster. It handles the job scheduling and execution environment.

• mainClusterChimerasAllparam.m
  The main MATLAB script that runs the full parameter exploration. It iterates over the desired range of model parameters and launches individual simulations using ChimerasSimAllParam.m.

• ChimerasSimAllParam.m
  This script contains the simulation logic for the Kuramoto-Sakaguchi model with local coupling. It returns time series data, the Kuramoto order parameter, and other metrics for each parameter configuration.

• WaveletTransform.m
  A utility function to compute the continuous wavelet transform (CWT) of the Kuramoto order parameter. Used to extract frequency content and identify multidien rhythms.

How to Run

To run the parameter sweep on a cluster:

1. Edit the Slurm script (mainClusterChimerasAllparam.sl) to match your environment (e.g., paths, modules, job time, etc.).
2. Submit the job using:

   sbatch mainClusterChimerasAllparam.sl
   
   
   

Kuramoto-Sakaguchi Model GUI

A MATLAB graphical user interface (GUI) for simulating the Kuramoto-Sakaguchi Model, which describes phase synchronization in a network of coupled oscillators. This tool allows users to interactively tune parameters and visualize oscillator dynamics in real time.

Equation

✨ Features

✅ Dynamic Polar Plot: Shows oscillators' phase positions with smooth animation.
✅ Kuramoto Order Parameter Plot: Tracks system-wide synchronization over time.
✅ Periodogram (Frequency Spectrum Analysis): Computed at the end of the simulation.
✅ Interactive Controls: Adjust model parameters in real-time:

• α (Phase Lag) – Controls phase shift in coupling.
• b (Broadness) – Defines the connectivity of the network of a squared kernel.
• ε (Zeitgeber Strength) – Strength of external forcing.
• p (Coupling Reduction) – Probability of randomly removing links.

🖥️ GUI Layout

• Left Panel → Polar Plot (oscillators' phase positions + mean vector arrow)
• Top-Right → Kuramoto Order Parameter (tracks synchronization over time)
• Bottom-Right → Periodogram (frequency spectrum at the end of the simulation)
• Right Panel → Parameter inputs & Start button

🚀 How to Run

1. Clone the repository:

   git clone https://github.com/MGrauLeguia/Emerging_multidien_cycles.git
   cd Emerging_multidien_cycles