Polymer Folding Simulations from Hi-C Data

In the absence of a clear molecular understanding of the mechanism that stabilizes specific contacts in interphasic chromatin, we resort to the principle of maximum entropy to build a polymeric model based on the Hi-C data of the specific system one wants to study. The interactions are set by an iterative Monte Carlo algorithm to reproduce the average contacts summarized by the Hi-C map. The study of the ensemble of conformations generated by the algorithm can report a much richer set of information than the experimental map alone, including colocalization of multiple sites, fluctuations of the contacts, and kinetical properties.