一种研究纳米孔捕获分析物的高效动力学蒙特卡罗方法：瞬态、边界条件和时间依赖场
An efficient Kinetic Monte Carlo to study analyte capture by a nanopore: Transients, boundary conditions and time-dependent fields
摘要：
为了更好地理解纳米孔的捕获过程，我们引入了一种有效的动力学蒙特卡罗（KMC）算法，该算法可以通过将3D球对称系统中的点状粒子的动态映射到1D有偏随机游走来模拟长时间和大系统尺寸。我们的算法恢复的稳态解析解，并允许我们研究时间相关的过程，如瞬变。模拟结果表明，稳态耗尽区附近的孔是勉强大于孔半径和变窄，在较高的电场强度，因此，达到稳态的时间是远远小于所需的时间清空的捕获半径$λ_e$的大小的区域。当样品储存器具有有限尺寸时，第二耗尽区从外壁向内传播，并且当其达到捕获半径$λ_e$时捕获速率开始降低。我们还注意到，通常被忽略的孔隙附近的电场的平坦度引起交通堵塞，其可以将瞬态时间增加几个数量级。最后，我们提出了一个新的概念验证计划，使用时变场分离两种分析物的相同的流动性，但不同的扩散系数。
英文摘要：
To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically symmetric system onto the 1D biased random walk. Our algorithm recovers the steady-state analytical solution and allows us to study time-dependent processes such as transients. Simulation results show that the steady-state depletion zone near pore is barely larger than the pore radius and narrows at higher field intensities; as a result, the time to reach steady-state is much smaller than the time required to empty a zone of the size of the capture radius $λ_e$. When the sample reservoir has a finite size, a second depletion region propagates inward from the outer wall, and the capture rate starts decreasing when it reaches the capture radius $λ_e$. We also note that the flatness of the electric field near the pore, which is often neglected, induces a traffic jam that can increase the transient time by several orders of magnitude. Finally, we propose a new proof-of-concept scheme to separate two analytes of the same mobility but different diffusion coefficients using time-varying fields.
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