ABSTRACT
This chapter focuses on the task of reconstructing the conformational ensemble of the chromatin fiber across a cell population, at the level of single topologically associating domains, starting from population-averaged 5C or Hi–C contact maps, without making any mechanistic assumption on the specific forces that drive chromosomal structures. The chapter discusses a coarse-grained polymer model of a sub-Mb chromosomal region, whose equilibrium ensemble reproduces experimental 3C-based data. The core of the modeling strategy consists in finding interaction potentials between beads such that the equilibrium contact map of the model is as close as possible to the experimental data. The chapter aims to develop a Monte Carlo implementation which is suitable for studying coarse-grained models of most types of biopolymers. An additional problem is that the Monte Carlo algorithm does not provide an intrinsic time scale for the motion of the model, but measures time in terms of the number of steps of unknown time duration.
