In-silico Hi-C simulations: data and code

This record contains the data and analysis code supporting the manuscript:“Understanding the physical processes behind DNA–DNA proximity ligation assays.”

The repository includes curated, post-aggregation outputs from in-silico Hi-C simulations, together with analysis scripts and documentation required to reproduce the reported results and figures. The dataset contains ligation-derived observables, contact probability curves, time-resolved structural observables, and selected representative contact and distance maps.

All simulation and analysis code is provided, including routines for molecular dynamics simulations with crosslinking and digestion, ligation analysis, data aggregation, and plotting.

Raw molecular dynamics trajectories and intermediate per-trajectory analysis files (multiple terabytes) are not included due to their size. The repository instead provides final processed datasets sufficient to reproduce all figures.

Input chromatin structures were generated using the NuChrom model (Harris et al., Nature Communications 14, 3303 (2023)). A small subset of representative structures is included for inspection. The full ensemble is not redistributed here and is available at:https://github.com/DiPierroLab/NuChroM

The in-silico Hi-C protocol implemented in this work models crosslinking, enzymatic digestion, and proximity ligation explicitly within a molecular dynamics framework, enabling direct comparison between simulated ligation signals and underlying chromatin structure.

Processed datasets are also available as a downloadable archive; see repository README for directory structure and file descriptions.

本数据集包含支撑下述学术论文的实验数据与分析代码：《DNA-DNA邻近连接测定背后的物理过程》（Understanding the physical processes behind DNA–DNA proximity ligation assays）。

本仓库收录经整理的计算机模拟（in-silico）Hi-C实验的聚合后输出文件，以及复现论文中报告结果与图表所需的分析脚本与说明文档。本数据集涵盖连接反应衍生可观测数据、接触概率曲线、时间分辨结构可观测数据，以及精选的代表性接触图谱与距离图谱。

本仓库提供全部模拟与分析代码，包括带有交联与酶切步骤的分子动力学模拟程序、连接反应分析程序、数据聚合程序与绘图脚本。

由于文件体积过大，原始分子动力学轨迹文件与单轨迹中间分析文件（总容量达数太字节）未被纳入本仓库。本仓库仅提供足以复现全部图表的最终处理后数据集。

输入的染色质结构通过NuChrom模型（NuChrom model）生成（Harris等人，《自然-通讯》，14卷，3303页，2023年）。本仓库包含一小部分代表性结构供用户检视，完整结构集合未在此处分发，可通过以下链接获取：https://github.com/DiPierroLab/NuChroM

本研究实现的计算机模拟Hi-C实验方案，在分子动力学框架内显式建模了交联反应、酶切反应与邻近连接过程，可实现模拟连接信号与底层染色质结构之间的直接比对。

处理后的数据集也可作为可下载归档文件获取；如需了解目录结构与文件说明，请参阅本仓库的README文档。