Modeling phase separation of biomolecular condensates with data-driven mass-conserving reaction-diffusion systems

This repository provides the OpenCL and Matlab codes that simulate the phase separation model (1) from our manuscript, “Modeling phase separation of biomolecular condensates with data-driven mass-conserving reaction-diffusion systems” by Cheng Li, Man-Ting Guo, Xiaoqing He, Quan-Xing Liu, and Zhi Qi, 2025, Stucture, DOI: will come soon.Guide for CodeThis folder includes five subfolders, from Fig. 2 to Fig. 6.Fig1:Response function fit and BIC with R code.Fig2:Fig2b_code: Contains the numerical simulation codes for Figure 2b.Fig2c_code: Contains the numerical simulation codes for Figure 2c.These codes can be run directly with Jupyter Notebook.Fig3:Code folder: Includes the model simulation and data analysis codes using Matlab. It covers structure factor analysis, experimental data, and simulation output.Fig4:fig3code, fig4data, and fig4figs folders: Include the code, data, and output results, respectively.Fig5:Stores the code and data within different subfolders, respectively.Fig6:Contains the data on ripple development from the previously published literature by Ping Lv, Clément Narteau, et al., 2021, PNAS. Vol. 118 No. 17 e2024105118. Data is taken from Figure 5(B).Questions:Please contact Quan-Xing Liu ([e-mail]) for any questions on the code.