Instituut-Lorentz, Leiden University, P.O. Box 9506, 2300 RA Leiden, The Netherlands.
J Chem Phys. 2013 Jun 14;138(22):224901. doi: 10.1063/1.4807723.
The fractal globule, a self-similar compact polymer conformation where the chain is spatially segregated on all length scales, has been proposed to result from a sudden polymer collapse. This state has gained renewed interest as one of the prime candidates for the non-entangled states of DNA molecules inside cell nuclei. Here, we present Monte Carlo simulations of collapsing polymers. We find through studying polymers of lengths between 500 and 8000 that a chain collapses into a globule, which is neither fractal, nor as entangled as an equilibrium globule. To demonstrate that the non-fractalness of the conformation is not just the result of the collapse dynamics, we study in addition the dynamics of polymers that start from fractal globule configurations. Also in this case the chain moves quickly to the weakly entangled globule where the polymer is well mixed. After a much longer time the chain entangles reach its equilibrium conformation, the molten globule. We find that the fractal globule is a highly unstable conformation that only exists in the presence of extra constraints such as cross-links.
分形球是一种自相似的聚合物紧密构象，其中链在所有长度尺度上都被空间分隔开，据推测是由于聚合物突然坍塌而产生的。由于分形球是细胞核内 DNA 分子非缠结状态的主要候选者之一，因此它重新引起了人们的兴趣。在这里，我们进行了聚合物坍塌的蒙特卡罗模拟。通过研究长度在 500 到 8000 之间的聚合物，我们发现链会坍塌成一个既不是分形也不像平衡球那样缠结的球。为了证明构象的非分形性不仅仅是坍塌动力学的结果，我们还研究了从分形球构型开始的聚合物的动力学。在这种情况下，链也会迅速移动到弱缠结的球中，在那里聚合物得到很好的混合。经过更长的时间后，链的缠结达到其平衡构象，即熔融球。我们发现，分形球是一种极不稳定的构象，只有在存在交联等额外约束的情况下才会存在。
