Effects of Extruder Dynamics and Noise on Simulated Chromatin Contact Probability Curves

Loop extrusion by SMC complexes is a key mechanism underlying chromatin folding during both interphase and mitosis. Despite this shared mechanism, computational models of loop extrusion often rely on fundamentally different assumptions: interphase models typically use dynamic extruders with finite lifetimes, while mitotic models employ static extruders placed according to loop size distributions. In this work, we investigate whether these modeling paradigms are interchangeable or yield intrinsically incompatible results. Using publicly available Hi-C data from mitotic chicken cells, we systematically compare dynamic and static loop extrusion models implemented in the Polychrom framework. We evaluate how key parameters—such as extruder lifetime, extrusion velocity, and spatial noise—affect simulated contact probability curves P(s) and loop size distributions. Our results reveal that while both model types can be tuned to approximate the general shape of P(s), they produce distinct internal structures and divergent relationships between loop size and contact decay. We also show that increased extruder lifetimes lead to excessive nested loop formation, which alters both loop statistics and P(s) derivatives. Introducing spatial exclusion constraints between extruders partially restores consistency with static models. These findings highlight that differences in extruder behavior and polymer noise levels can significantly impact chromatin model outcomes and must be carefully accounted for when interpreting or comparing simulation results across biological conditions.