Nuclear molecules control the functional properties of the chromatin fiber by shaping its morphological properties. The biophysical mechanisms controlling how bridging molecules compactify the chromatin are a matter of debate. On the one side, bridging molecules could cross-link faraway sites and fold the fiber through the formation of loops. Interacting bridging molecules could also mediate long-range attractions by first tagging different locations of the fiber and then undergoing microphase separation. Using a coarse-grained model and Monte Carlo simulations, we study the conditions leading to compact configurations both for interacting and non-interacting bridging molecules. In the second case, we report on an unfolding transition at high densities of the bridging molecules. We clarify how this transition, which disappears for interacting bridging molecules, is universal and controlled by entropic terms. In general, chains are more compact in the case of interacting bridging molecules since, in this case, interactions are not valence-limited. However, this result is conditional on the ability of our simulation methodology to relax the system towards its ground state. In particular, we clarify how, unless using reaction dynamics that change the length of a loop in a single step, the system is prone to remain trapped in metastable, compact configurations featuring long loops.

中文翻译：

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桥接因子过表达驱动染色质纤维的展开

核分子通过塑造染色质纤维的形态特性来控制其功能特性。控制桥接分子如何压缩染色质的生物物理机制尚有争议。一方面，桥接分子可以交联较远的位点，并通过形成环将纤维折叠起来。相互作用的桥接分子还可以通过先标记纤维的不同位置然后进行微相分离来介导长距离吸引力。使用粗粒度模型和蒙特卡洛模拟，我们研究了导致相互作用和非相互作用桥联分子的紧凑构型的条件。在第二种情况下，我们报道了桥联分子在高密度下发生的过渡转变。我们阐明了这种过渡，由于相互作用的桥联分子而消失，它是普遍存在的，并受熵的控制。通常，在相互作用的桥连分子的情况下链更紧密，因为在这种情况下相互作用不受价数限制。但是，此结果取决于我们的仿真方法能否将系统向其基态松弛。特别是，我们阐明了，除非使用反应动力学来一步改变回路的长度，否则系统将易于陷于亚稳态，紧凑的长回路结构中。此结果取决于我们的仿真方法能够使系统朝基态松弛的能力。特别是，我们阐明了，除非使用反应动力学来一步改变回路的长度，否则系统将易于陷于亚稳态，紧凑的长回路结构中。此结果取决于我们的仿真方法能够使系统朝基态松弛的能力。特别是，我们阐明了，除非使用反应动力学来一步改变回路的长度，否则系统将易于陷于亚稳态，紧凑的长回路结构中。