Sample simulation codes and data for Cell mechanics, environmental geometry, and cell polarity control cell-cell collision outcomes

These are the sample codes of numerical simulations and statistical data for the work presented in Yongtian Luo, Amrinder S. Nain, and Brian A. Camley, Cell mechanics, environmental geometry, and cell polarity control cell-cell collision outcomes, arXiv:2503.06239 and Soft Matter, 2025, DOI: 10.1039/D5SM00359H. The Jupyter Notebook YL_cell_collision.ipynb (in Python 3) contains all the necessary components for running a full cell-cell collision simulation cycle, generating phase-field images and determining the collision outcome. The whole simulation takes roughly 6-12 hours on typical desktop/laptop computers. In a parallel computing setting, one can use the code cell_collision.py in command line and sweep over parameter ranges (e.g. alpha, beta, and fiber spacing L) as inputs (such as "python cell_collision.py 90 0.1 10 1" for L=90, alpha=0.1, beta=10, and trajectory number 1), running multiple simulations for the same parameter set and saving the final collision outcomes ("training", "walk-past", or "reversing") as outputs to obtain a statistics of the probability of each possible collision outcome. The summary of our statistical results (numbers of different collision outcomes out of 96 simulation runs for each parameter set) is also included in the Excel file stat_data.xlsx.本数据集包含Yongtian Luo、Amrinder S. Nain与Brian A. Camley的研究工作配套的数值模拟与统计数据示例代码。该研究成果发表于《Soft Matter》2025年刊（DOI: 10.1039/D5SM00359H），预印本收录于arXiv:2503.06239，论文标题为《细胞力学、环境几何与细胞极性调控细胞-细胞碰撞结果》。 基于Python 3编写的Jupyter Notebook文件YL_cell_collision.ipynb，集成了完整细胞-细胞碰撞模拟循环所需的全部功能模块，可生成相场图像并判定碰撞结果。在常规台式机或笔记本电脑上运行整套模拟流程，耗时约6至12小时。 在并行计算环境下，可通过命令行调用cell_collision.py代码，遍历α、β与纤维间距L等参数范围作为输入。例如执行命令`python cell_collision.py 90 0.1 10 1`，对应参数为L=90、α=0.1、β=10，轨迹编号为1。对同一参数组合运行多次模拟后，将最终碰撞结果（"贴合附着"、"绕行通过"与"反向退却"）作为输出保存，即可统计各类可能碰撞结果的发生概率。 各参数组合下96次模拟运行得到的各类碰撞结果计数统计汇总，已收录于Excel文件stat_data.xlsx中。