Loop Extrusion Model with Peripheral Adsorption and Topological Constraints

This model employs coarse-grained molecular dynamics to simulate a chromatin system featuring phase-separated compartments and dynamic loop extrusion. Within this framework, loop extruders, represented as sliding bonds, bi-directionally expand chromatin loops, a process governed by spatial constraints, mutual collisions, and directional CTCF barriers. Additionally, the model incorporates LBR complexes tethered to the nuclear envelope to mimic chromatin anchoring at the periphery. By varying whether LBR presents a steric hindrance to extruder progression, the model enables the investigation of two distinct mechanisms through which the nuclear lamina can influence chromatin architecture and loop extrusion dynamics.