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具有开放边界条件的受动力蛋白启发的多车道排除过程。

Dynein-Inspired Multilane Exclusion Process with Open Boundary Conditions.

作者信息

Nandi Riya, Täuber Uwe C

机构信息

Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland.

Department of Physics (MC 0435) & Center for Soft Matter and Biological Physics, Faculty of Health Sciences, Virginia Tech, Blacksburg, VA 24061, USA.

出版信息

Entropy (Basel). 2021 Oct 14;23(10):1343. doi: 10.3390/e23101343.

Abstract

Motivated by the sidewise motions of dynein motors shown in experiments, we use a variant of the exclusion process to model the multistep dynamics of dyneins on a cylinder with open ends. Due to the varied step sizes of the particles in a quasi-two-dimensional topology, we observe the emergence of a novel phase diagram depending on the various load conditions. Under high-load conditions, our numerical findings yield results similar to the TASEP model with the presence of all three standard TASEP phases, namely the low-density (LD), high-density (HD), and maximal-current (MC) phases. However, for medium- to low-load conditions, for all chosen influx and outflux rates, we only observe the LD and HD phases, and the maximal-current phase disappears. Further, we also measure the dynamics for a single dynein particle which is logarithmically slower than a TASEP particle with a shorter waiting time. Our results also confirm experimental observations of the dwell time distribution: The dwell time distribution for dyneins is exponential in less crowded conditions, whereas a double exponential emerges under overcrowded conditions.

摘要

受实验中所展示的动力蛋白马达侧向运动的启发,我们使用一种排除过程的变体来模拟动力蛋白在两端开放的圆柱体上的多步动力学。由于在准二维拓扑结构中粒子的步长各不相同,我们观察到根据各种负载条件出现了一种新颖的相图。在高负载条件下,我们的数值研究结果产生了与具有所有三个标准TASEP相(即低密度(LD)、高密度(HD)和最大电流(MC)相)的TASEP模型相似的结果。然而,对于中低负载条件,对于所有选定的流入和流出速率,我们只观察到LD相和HD相,最大电流相消失。此外,我们还测量了单个动力蛋白粒子的动力学,其速度比具有较短等待时间的TASEP粒子慢对数倍。我们的结果也证实了对停留时间分布的实验观察:在不太拥挤的条件下,动力蛋白的停留时间分布是指数型的,而在过度拥挤的条件下则出现双指数分布。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3b67/8534927/de88c8bab5aa/entropy-23-01343-g001.jpg

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