In this study we investigated, using a simple polymer model of bacterial chromosome, the subdiffusive behaviors of both cytoplasmic particles and various loci in different cell wall confinements. Non-Gaussian subdiffusion of cytoplasmic particles as well as loci were obtained in our Langevin dynamic simulations, which agrees with fluorescence microscope observations. The effects of cytoplasmic particle size, locus position, confinement geometry, and density on motions of particles and loci were examined systematically. It is demonstrated that the cytoplasmic subdiffusion can largely be attributed to the mechanical properties of bacterial chromosomes rather than the viscoelasticity of cytoplasm. Due to the randomly positioned bacterial chromosome segments, the surrounding environment for both particle and loci is heterogeneous. Therefore, the exponent characterizing the subdiffusion of cytoplasmic particle/loci as well as Laplace displacement distributions of particle/loci can be reproduced by this simple model. Nevertheless, this bacterial chromosome model cannot explain the different responses of cytoplasmic particles and loci to external compression exerted on the bacterial cell wall, which suggests that the nonequilibrium activity, e.g., metabolic reactions, play an important role in cytoplasmic subdiffusion.

中文翻译：

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细菌染色体和细胞质纳米颗粒的中尺度模拟

在这项研究中，我们使用细菌染色体的简单聚合物模型研究了细胞质颗粒和不同基因座在不同细胞壁限制下的亚扩散行为。在我们的Langevin动态模拟中获得了细胞质颗粒以及基因座的非高斯亚扩散，这与荧光显微镜观察相符。系统地检查了细胞质颗粒大小，基因座位置，限制几何形状和密度对颗粒和基因座运动的影响。结果表明，细胞质的扩散主要归因于细菌染色体的机械特性，而不是细胞质的粘弹性。由于细菌染色体段的位置随机，因此粒子和基因座的周围环境是异质的。所以，这个简单的模型可以再现表征细胞质颗粒/位置的再扩散以及颗粒/位置的拉普拉斯位移分布的指数。然而，这种细菌染色体模型不能解释细胞质颗粒和基因座对施加在细菌细胞壁上的外部压缩的不同反应，这表明非平衡活性，例如代谢反应，在细胞质亚扩散中起重要作用。