Nuclear molecules control the functional properties of the chromatin fiber by shaping its morphological properties. The biophysical mechanisms controlling how bridging molecules compactify 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 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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非相互作用桥接因子过度表达驱动的染色质纤维展开

核分子通过塑造其形态特性来控制染色质纤维的功能特性。控制桥接分子如何压缩染色质的生物物理机制是一个有争议的问题。一方面，桥接分子可以交联遥远的位点，并通过形成环折叠纤维。相互作用的桥接分子还可以通过首先标记纤维的不同位置然后进行微相分离来介导远程吸引力。使用粗粒度模型和蒙特卡罗模拟，我们研究了导致相互作用和非相互作用桥接分子紧凑配置的条件。在第二种情况下，我们报告了高密度桥接分子的展开转变。我们阐明了这种转变如何，它因相互作用的桥接分子而消失，是普遍的并受熵项的控制。通常，在相互作用的桥接分子的情况下，链更紧凑，因为相互作用不受价数限制。然而，这个结果取决于我们的模拟方法将系统放松到其基态的能力。特别是，我们澄清了，除非使用反应动力学在一个步骤中改变循环的长度，否则系统很容易陷入亚稳态，具有长循环的紧凑配置。这个结果取决于我们的模拟方法能否将系统放松到其基态。特别是，我们澄清了，除非使用反应动力学在一个步骤中改变循环的长度，否则系统很容易陷入亚稳态，具有长循环的紧凑配置。这个结果取决于我们的模拟方法能否将系统放松到其基态。特别是，我们澄清了，除非使用反应动力学在一个步骤中改变循环的长度，否则系统很容易陷入亚稳态，具有长循环的紧凑配置。