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.