Comparative study of polymer looping kinetics in passive and active environments
Comparative study of polymer looping kinetics in passive and active environments
复制标题
被动和主动环境中聚合物成环动力学的比较研究
DOI：
10.1039/d1cp00591j
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发表时间：
2021
影响因子：
3.3
通讯作者：
Zhao Nanrong
中科院分区：
文献类型：
--
作者：
Zhang Bingjie;Lei Ting;Zhao Nanrong
复杂环境中的链内环对于促进我们对生命生物过程的理解具有重要意义。我们采用朗格万动力学模拟对被动和主动环境下聚合物环动力学进行了比较研究。通过对循环数量（包括循环解循环时间和循环概率）的分析，我们揭示了活跃人群规模、活跃度和拥挤度的有趣影响。首先，我们在主动群体大小和主动力参数空间中绘制了一种新的促进-抑制转变的相图，明确了活度的双重作用。特别是，我们发现与聚合物单体相当大小的活性颗粒最有利于促进环化，而与聚合物旋转半径相似大小的活性颗粒最严重阻碍环化。其次，通过扩散、聚合物构象变化和自由能势垒之间的相互作用，合理地解释了不同活性聚体尺寸下的潜在环机制。对于小的活跃人群，活动显著促进端到端距离扩散，这主要促进了循环和解环过程。在活性适中的情况下，聚合物链肿胀突出，不可避免地会发生抑制环。对于大型活性分子，活性通过产生更高的有效温度和更大的非环能势垒，对环动力学产生反直觉的非笼效应。这与在被动介质中观察到的笼化现象形成鲜明对比。最后，主动浴池中循环量的体积分数依赖性显示出与被动浴池中循环量的巨大差异，这突出了活动和拥挤的对比效果。
Intra-chain looping in complex environments is significant in advancing our understanding of biological processes in life. We adopt Langevin dynamics simulations to perform a comparative study of polymer looping kinetics in passive and active environments. From the analysis of looping quantities, including looping-unlooping times and looping probabilities, we unraveled the intriguing effects of active crowder size, activity and crowding. Firstly, we figured out the phase diagram involving a novel facilitation-inhibition transition in the parameter space of active crowder size and active force, and the two-fold roles of activity are clarified. In particular, we find that active particles of a size comparable to the polymer monomer are most favorable for facilitated looping, while those with a similar size to the polymer gyration radius impede the looping most seriously. Secondly, the underlying looping mechanisms in different active crowder size regimes are rationalized by the interplay among diffusion, polymer conformational change and the free-energy barrier. For small active crowders, activity significantly promotes end-to-end distance diffusion, which dominantly facilitates both looping and unlooping processes. In the case of moderate active crowders, the polymer chain suffers from prominent swelling, and thus inevitable inhibited looping will occur. For large active crowders, activity induces a counterintuitive non-cage effect on the looping kinetics, through yielding a higher effective temperature and larger unlooping free-energy barrier. This is in sharp contrast to the caging phenomena observed in passive media. Lastly, the volume-fraction dependence of the looping quantities in an active bath demonstrates dramatic discrepancies from that in a passive bath, which highlights the contrasting effects of activity and crowding.