title: One-dimensional description of diffusion in a tube of abruptly changing diameter: Boundary homogenization based approach.
abstract: Reduction of three-dimensional (3D) description of diffusion in a tube of variable cross section to an approximate one-dimensional (1D) description has been studied in detail previously only in tubes of slowly varying diameter. Here we discuss an effective 1D description in the opposite limiting case when the tube diameter changes abruptly, i.e., in a tube composed of any number of cylindrical sections of different diameters. The key step of our approach is an approximate description of the particle transitions between the wide and narrow parts of the tube as trapping by partially absorbing boundaries with appropriately chosen trapping rates. Boundary homogenization is used to determine the trapping rate for transitions from the wide part of the tube to the narrow one. This trapping rate is then used in combination with the condition of detailed balance to find the trapping rate for transitions in the opposite direction, from the narrow part of the tube to the wide one. Comparison with numerical solution of the 3D diffusion equation allows us to test the approximate 1D description and to establish the conditions of its applicability. We find that suggested 1D description works quite well when the wide part of the tube is not too short, whereas the length of the narrow part can be arbitrary. Taking advantage of this description in the problem of escape of diffusing particle from a cylindrical cavity through a cylindrical tunnel we can lift restricting assumptions accepted in earlier theories: We can consider the particle motion in the tunnel and in the cavity on an equal footing, i.e., we can relax the assumption of fast intracavity relaxation used in all earlier theories. As a consequence, the dependence of the escape kinetics on the particle initial position in the system can be analyzed. Moreover, using the 1D description we can analyze the escape kinetics at an arbitrary tunnel radius, whereas all earlier theories are based on the assumption that the tunnel is narrow.
authors.affiliation: Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA. berezh@helix.nih.gov
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Berezhkovskii
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Barzykin
authors.forename: Vladimir Yu
authors.initials: VY
authors.lastname: Zitserman
mesh_terms: D004058:Diffusion; D007700:Kinetics; D010316:Particle Size; D012212:Rheology