2021/03/08 by Zubenelgenubi C. Scott, Scott, Zubenelgenubi C., Aidan I. Brown +7
Biochemistry, Genetics and Molecular Biology · Neuroscience · Physics and Astronomy · #Advanced Fluorescence Microscopy Techniques #Biological Physics (physics.bio-ph) #Diffusion and Search Dynamics #FOS: Biological sciences #FOS: Physical sciences #Gene Regulatory Network Analysis #Photoreceptor and optogenetics research #Spectroscopy and Quantum Chemical Studies #Subcellular Processes (q-bio.SC)
paper · pdf · doi:10.48550/arxiv.2103.05065
openalex publication_date 2021/03/08 · openalex created_date 2022/07/25 · openalex updated_date 2026/07/28
Several organelles in eukaryotic cells, including mitochondria and the\nendoplasmic reticulum, form interconnected tubule networks extending throughout\nthe cell. These tubular networks host many biochemical pathways that rely on\nproteins diffusively searching through the network to encounter binding\npartners or localized target regions. In this work we develop both exact\nanalytical methods to compute mean first passage times and efficient kinetic\nMonte Carlo algorithms to simulate trajectories of particles diffusing in a\ntubular network. Our approach leverages exact propagator functions for the\ndistribution of transition times between network nodes and allows large\nsimulation time steps determined by the network structure. The methodology is\napplied to both synthetic planar networks and organelle network structures,\ndemonstrating key general features such as the heterogeneity of search times in\ndifferent network regions and the functional advantage of broadly distributing\ntarget sites throughout the network. The proposed algorithms pave the way for\nfuture exploration of the interrelationship between tubular network structure\nand biomolecular reaction kinetics.\n