We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an individual monomer to eject grows exponentially with the number of ejected monomers. By measurements of the force at the pore we show this dependence to be a consequence of the excess free energy of the polymer due to confinement growing exponentially with the number of monomers initially inside the capsid. This growth relates closely to the divergence of mixing energy in the Flory-Huggins theory at large concentration. We show that the pressure inside the capsid driving the ejection dominates the process that is characterized by the ejection time growing linearly with the lengths of different polymers. Waiting time profiles would indicate that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids.
Bacterial chromosome organization II: few special cross-links, cell confinement, and molecular crowders play the pivotal roles
使用{ \em C. crescentus}和{ \em E. coli}的研究表明，只有$33$和$38$沿着DNA链轮廓在特定位置的有效交联可以导致DNA聚合物的大规模组织，其中细胞壁的限制效应在组织中起关键作用。从{ \em C.}的接触图数据中选择$33$交联沿链轮廓的位置。crescentus}。我们代表$1000$碱基对作为一个粗粒度的单体在我们的珠弹簧柔性环聚合物模型的DNA。因此，柔性环聚合物上的$4017$珠代表{ \em C}。具有$4017$千碱基对的crescentus} DNA。从我们前面的研究中选择合适的参数，我们还将分子拥挤的作用和链的能力，以释放拓扑约束。我们验证了我们对{ \em C. crescentus}与可用的实验接触图数据，并且还给出了在3D中细胞内的不同段的近似位置的预测。对于{ \em E. coli}染色体具有$4.6$百万碱基对，我们需要大约$38$有效的交联与圆柱形限制来组织染色体。我们还预测了{ \em E.大肠杆菌}染色体片段的圆柱体内，代表细胞壁。
