Cieśla Michał, Dybiec Bartłomiej, Krasowska Monika, Siwy Zuzanna, Strzelewicz Anna
Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, ul. St. Łojasiewicza 11, 30-348 Kraków, Poland.
Faculty of Chemistry, Silesian University of Technology, Strzody 9, 44-100 Gliwice, Poland.
Molecules. 2024 Aug 10;29(16):3795. doi: 10.3390/molecules29163795.
The transport of molecules and particles through single pores is the basis of biological processes, including DNA and protein sequencing. As individual objects pass through a pore, they cause a transient change in the current that can be correlated with the object size, surface charge, and even chemical properties. The majority of experiments and modeling have been performed with spherical objects, while much less is known about the transport characteristics of aspherical particles, which would act as a model system, for example, for proteins and bacteria. The transport kinetics of aspherical objects is an especially important, yet understudied, problem in nanopore analytics. Here, using the Wiener process, we present a simplified model of the diffusion of rod-shaped particles through a cylindrical pore, and apply it to understand the translation and rotation of the particles as they pass through the pore. Specifically, we analyze the influence of the particles' geometrical characteristics on the effective diffusion type, the first passage time distribution, and the particles' orientation in the pore. Our model shows that thicker particles pass through the channel slower than thinner ones, while their lengths do not affect the passage time. We also demonstrate that both spherical and rod-shaped particles undergo normal diffusion, and the first passage time distribution follows an exponential asymptotics. The model provides guidance on how the shape of the particle can be modified to achieve an optimal passage time.
分子和粒子通过单个孔道的传输是包括DNA和蛋白质测序在内的生物过程的基础。当单个物体通过一个孔时，它们会引起电流的瞬态变化，这种变化可以与物体的大小、表面电荷甚至化学性质相关联。大多数实验和建模都是针对球形物体进行的，而对于非球形粒子的传输特性了解较少，非球形粒子可以作为例如蛋白质和细菌的模型系统。在纳米孔分析中，非球形物体的传输动力学是一个特别重要但尚未充分研究的问题。在这里，我们使用维纳过程，提出了一个棒状粒子通过圆柱形孔道扩散的简化模型，并将其应用于理解粒子通过孔道时的平移和旋转。具体来说，我们分析了粒子的几何特征对有效扩散类型、首次通过时间分布以及粒子在孔道中的取向的影响。我们的模型表明，较粗的粒子通过通道的速度比较细的粒子慢，而它们的长度不影响通过时间。我们还证明了球形和棒状粒子都经历正常扩散，并且首次通过时间分布遵循指数渐近线。该模型为如何修改粒子形状以实现最佳通过时间提供了指导。
