Understanding and Simulating the Dynamics of a Polymer-Like Chromatin

Chromatin modeling enables the characterization of chromatin architecture at a resolution so far unachievable with experimental techniques. Polymer models fill our knowledge gap on a wide range of structures, from chromatin loops to nuclear compartments. Many physical properties already known for polymers can thus explain the dynamics of chromatin. With molecular simulations, it is possible to probe an ensemble of conformations, which attest to the variability observed in individual cells and the general behavior of a population of cells. In this review, we describe universal characteristics of polymers that chromatin carries. We introduce how these characteristics can be assessed with polymer simulations while also addressing specific aspects of chromatin and its environment. Finally, we give examples of plant chromatin models that, despite their paucity, augur well for the future of polymer simulations to plant chromosome biology.