空间网络上的扩散搜索和轨迹：传播算子方法
Diffusive search and trajectories on spatial networks: a propagator approach
摘要：
真核细胞中的几种细胞器，包括线粒体和内质网，形成贯穿整个细胞的相互连接的小管网络。这些管状网络承载许多生化途径，这些生化途径依赖于蛋白质在网络中扩散搜索以遇到结合伴侣或定位的靶区域。在这项工作中，我们开发了精确的分析方法来计算平均首次通过时间和有效的动力学蒙特卡罗算法来模拟粒子在管状网络中扩散的轨迹。我们的方法利用精确的传播函数的网络节点之间的过渡时间的分布，并允许由网络结构确定的大的模拟时间步长。该方法适用于合成平面网络和细胞器网络结构，展示关键的一般功能，如在不同的网络区域的搜索时间的异质性和广泛分布的目标网站在整个网络的功能优势。所提出的算法铺平了道路，为未来的探索管状网络结构和生物分子反应动力学之间的相互关系。
英文摘要：
Several organelles in eukaryotic cells, including mitochondria and the endoplasmic reticulum, form interconnected tubule networks extending throughout the cell. These tubular networks host many biochemical pathways that rely on proteins diffusively searching through the network to encounter binding partners or localized target regions. In this work we develop both exact analytical methods to compute mean first passage times and efficient kinetic Monte Carlo algorithms to simulate trajectories of particles diffusing in a tubular network. Our approach leverages exact propagator functions for the distribution of transition times between network nodes and allows large simulation time steps determined by the network structure. The methodology is applied to both synthetic planar networks and organelle network structures, demonstrating key general features such as the heterogeneity of search times in different network regions and the functional advantage of broadly distributing target sites throughout the network. The proposed algorithms pave the way for future exploration of the interrelationship between tubular network structure and biomolecular reaction kinetics.
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