Numerical approximation of diffusive capture rates by planar and spherical surfaces with absorbing pores
From MaRDI portal
(Redirected from Publication:4602779)
Theoretical approximation in context of PDEs (35A35) Singular perturbations in context of PDEs (35B25) Asymptotic expansions of solutions to PDEs (35C20) Laplace operator, Helmholtz equation (reduced wave equation), Poisson equation (35J05) Green's functions for elliptic equations (35J08) Brownian motion (60J65)
Abstract: In 1977 Berg & Purcell published a landmark paper entitled "Physics of Chemoreception" which examined how a bacterium can sense a chemical attractant in the fluid surrounding it. At small scales the attractant molecules move by Brownian motion and diffusive processes dominate. This example is the archetype of diffusive signaling problems where an agent moves via a random walk until it either strikes or eludes a target. Berg & Purcell modeled the target as a sphere with a set of small circular targets (pores) that can capture a diffusing agent. They argued that, in the limit of small radii and wide spacing, each pore could be modeled independently as a circular pore on an infinite plane. Using a known exact solution, they showed the capture rate to be proportional to the combined perimeter of the pores. In this paper we study how to improve this approximation by including inter-pore competition effects and verify this result numerically for a finite collection of pores on a plane or sphere. Asymptotically we have found the corrections to the Berg-Purcell formula that account for enhancement of capture due to the curvature of the spherical target and inhibition of capture due to spatial interactions of the pores. Numerically we develop a spectral boundary element method for the exterior mixed Neumann-Dirichlet boundary value problem. Our formulation reduces the problem to a linear integral equation, specifically a Neumann to Dirichlet map, which is supported only on the individual pores. The difficulty is that both the kernel and the flux are singular, a notorious obstacle in such problems. A judicious choice of singular boundary elements allows us to resolve the flux singularity at the edge of the pore. In biological systems there can be thousands of receptors whose radii are 0.1% the cell radius. Our numerics resolve this realistic limit with an accuracy of roughly one part in 10^8.
Recommendations
- First Passage Statistics for the Capture of a Brownian Particle by a Structured Spherical Target with Multiple Surface Traps
- Diffusion on a sphere with localized traps: mean first passage time, eigenvalue asymptotics, and Fekete points
- Boundary homogenization and capture time distributions of semipermeable membranes with periodic patterns of reactive sites
- How receptor surface diffusion and cell rotation increase association rates
- The narrow escape problem -- a short review of recent results
Cites work
- A guide to first-passage processes
- An asymptotic analysis of the mean first passage time for narrow escape problems. II: The sphere
- Asymptotics for minimal discrete energy on the sphere
- Boundary Homogenization for Periodic Arrays of Absorbers
- Diffusion on a sphere with localized traps: mean first passage time, eigenvalue asymptotics, and Fekete points
- Distributing many points on a sphere
- Effective Membrane Permeability: Estimates and Low Concentration Asymptotics
- Effective Motion of a Virus Trafficking Inside a Biological Cell
- Equilibrium configurations of particles on a sphere: the case of logarithmic interactions
- Experimental study of energy-minimizing point configurations on spheres
- First Passage Statistics for the Capture of a Brownian Particle by a Structured Spherical Target with Multiple Surface Traps
- scientific article; zbMATH DE number 43978 (Why is no real title available?)
- scientific article; zbMATH DE number 486467 (Why is no real title available?)
- scientific article; zbMATH DE number 3226385 (Why is no real title available?)
- Laplace's equation and the Dirichlet-Neumann map in multiply connected domains
- Logarithmic expansions and the stability of periodic patterns of localized spots for reaction-diffusion systems in R^2
- Measurement of areas on a sphere using Fibonacci and latitude-longitude lattices
- Minimal discrete energy on the sphere
- Mixed boundary value problems
- Narrow escape. I
- Optimizing the principal eigenvalue of the Laplacian in a sphere with interior traps
- Renormalized energy and asymptotic expansion of optimal logarithmic energy on the sphere
- Second-kind integral formulations of the capacitance problem
- Vectorized adaptive quadrature in MATLAB
Cited in
(12)- Mathematical modeling accurately predicts the dynamics and scaling of nuclear growth in discrete cytoplasmic volumes
- A probabilistic approach to extreme statistics of Brownian escape times in dimensions 1, 2, and 3
- Boundary homogenization and capture time distributions of semipermeable membranes with periodic patterns of reactive sites
- Asymptotic and numerical analysis of a stochastic PDE model of volume transmission
- How receptor surface diffusion and cell rotation increase association rates
- First Passage Statistics for the Capture of a Brownian Particle by a Structured Spherical Target with Multiple Surface Traps
- Survival in a nanoforest of absorbing pillars
- A fast solver for the narrow capture and narrow escape problems in the sphere
- Mean first passage times for transport equations
- The lightning method for the heat equation
- Boundary integral methods for particle diffusion in complex geometries: shielding, confinement, and escape
- The effective reactivity for capturing Brownian motion by partially reactive patches on a spherical surface
This page was built for publication: Numerical approximation of diffusive capture rates by planar and spherical surfaces with absorbing pores
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q4602779)
