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Anomalous and normal diffusion of tracers in crowded environments: Effect of the size disparity between the tracer and crowders
yiding
Author NameAffiliationE-mail
yiding none yiding@mail.ustc.edu.cn 
Abstract:
The dynamics of tracers in crowded matrix is of interest in various areas of physics, such as the diffusion of proteins in living cells. By using two-dimensional (2D) Langevin dynamics simulations, we investigate the diffusive properties of a tracer of a diameter σt in crowded environments caused by randomly distributed crowders of a diameter σc. We show that the emergence of subdiffusion of a tracer at intermediate time scales depends on the size ratio of the tracer to crowders δ. If δ falls between a lower critical size ratio δc,1 and a upper one δc,2, the anomalous diffusion occurs purely due to the molecular crowding. Further analysis indicates that the physical origin of subdiffusion is the “cage effect”. Moreover, the subdiffusion exponent α decreases with the increasing medium viscosity and the degree of crowding, and gets a minimum αmin = 0.75 at δ = 1. At long time scales, normal diffusion of a tracer is recovered. For δ ≤ 1, the relative mobility of tracers is independent of the degree of crowding. Meanwhile, it is sensitive to the degree of crowding for δ > 1. Our results are helpful in deepening the understanding of the diffusive properties of biomacromolecules that lie within crowded intracellular environments, such as proteins, DNA and ribosomes.
Key words:  Subdiffusion, Langevin dynamics simulations, size disparity
FundProject:
粒子在拥挤环境下的亚扩散:示踪粒子与拥挤粒子的尺寸影响
yiding
摘要:
示踪粒子在拥挤环境下的扩散是很多物理过程中的重要问题,例如蛋白质在细胞中的扩散。本文中利用二维体系下的朗之万动力学模拟研究了直径为σt在拥挤剂直径为σc的环境下的扩散行为。我们发现在中等时间尺度下示踪粒子的扩散行为与示踪粒子与拥挤粒子的直径之比δ相关,δ在一定范围下,单纯的拥挤效应可以使示踪粒子表现出亚扩散行为。进一步我们发现粒子的亚扩散行为是由于拥挤剂对其的“笼闭效应”。亚扩散指数α随着体系粘度以及拥挤程度而下降,在δ=1时取得最小值αmin=0.75。长时间尺度下,示踪粒子表现出正常扩散行为。δ<1时,粒子的扩散系数与粒子大小无关,当δ>1时,扩散系数对随拥挤剂粒子增加而增加。本研究有助于进一步了解蛋白质、DNA、核糖体等生物大分子的扩散行为的物理本质
关键词:  亚扩散,郎之万动力学模拟,尺寸差别
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