<b>Modeling phase separation of biomolecular condensates with data-driven mass-conserving reaction-diffusion systems</b>

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.<b>Fig1:</b>Response function fit and BIC with R code.<b>Fig2:</b><code>Fig2b_code</code>: Contains the numerical simulation codes for Figure 2b.<code>Fig2c_code</code>: Contains the numerical simulation codes for Figure 2c.These codes can be run directly with Jupyter Notebook.<b>Fig3:</b><code>Code</code> folder: Includes the model simulation and data analysis codes using Matlab. It covers structure factor analysis, experimental data, and simulation output.<b>Fig4:</b><code>fig3code</code>, <code>fig4data</code>, and <code>fig4figs</code> folders: Include the code, data, and output results, respectively.<b>Fig5:</b>Stores the code and data within different subfolders, respectively.<b>Fig6:</b>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.

本开源仓库提供了复现论文《Modeling phase separation of biomolecular condensates with data-driven mass-conserving reaction-diffusion systems》（作者Cheng Li、Man-Ting Guo、Xiaoqing He、Quan-Xing Liu、Zhi Qi，2025年发表于《Structure》，DOI待公布）中相分离模型(1)的OpenCL与Matlab代码。
代码使用说明
本文件夹包含5个子文件夹，分别对应图2至图6。
<b>图1：</b>采用R代码完成响应函数拟合与贝叶斯信息准则（BIC, Bayesian Information Criterion）计算。
<b>图2：</b><code>Fig2b_code</code>：包含图2b的数值模拟代码；<code>Fig2c_code</code>：包含图2c的数值模拟代码。上述代码可直接通过Jupyter Notebook运行。
<b>图3：</b><code>Code</code>文件夹：收录了基于Matlab编写的模型模拟与数据分析代码，涵盖结构因子分析、实验数据及模拟输出相关内容。
<b>图4：</b><code>fig3code</code>、<code>fig4data</code>与<code>fig4figs</code>子文件夹：分别存放对应代码、实验数据与输出结果。
<b>图5：</b>在不同子文件夹中分别存放代码与实验数据。
<b>图6：</b>包含来自Ping Lv、Clément Narteau等人2021年发表于《美国国家科学院院刊》（PNAS, Proceedings of the National Academy of Sciences）第118卷第17期（文章编号e2024105118）的已发表文献中的波纹演化数据，数据取自该文献图5(B)。
疑问咨询：若对本代码有任何疑问，请联系Quan-Xing Liu，邮箱：[e-mail]。