Boundary homogenization for trapping patchy particles

Boundary homogenization for patchy surfaces trapping patchy particles

Trapping diffusive particles at surfaces is a key step in many systems in chemical and biological physics. Trapping often occurs via reactive patches on the surface and/or the particle. The theory of boundary homogenization has been used in many prior works to estimate the effective trapping rate for such a system in the case that either (i) the surface is patchy and the particle is uniformly reactive or (ii) the particle is patchy and the surface is uniformly reactive. In this paper, we estimate the trapping rate for the case that the surface and the particle are both patchy. In particular, the particle diffuses translationally and rotationally and reacts with the surface when a patch on the particle contacts a patch on the surface. We first formulate a stochastic model and derive a five-dimensional partial differential equation describing the reaction time. We then use matched asymptotic analysis to derive the effective trapping rate, assuming that the patches are roughly evenly distributed and occupy a small fraction of the surface and the particle. This trapping rate involves the electrostatic capacitance of a four-dimensional duocylinder, which we compute using a kinetic Monte Carlo algorithm. We further use Brownian local time theory to derive a simple heuristic estimate of the trapping rate and show that it is remarkably close to the asymptotic estimate. Finally, we develop a kinetic Monte Carlo algorithm to simulate the full stochastic system and then use these simulations to confirm the accuracy of our trapping rate estimates and homogenization theory.

Revising Berg-Purcell for finite receptor kinetics

From nutrient uptake to chemoreception to synaptic transmission, many systems in cell biology depend on molecules diffusing and binding to membrane receptors. Mathematical analysis of such systems often neglects the fact that receptors process molecules at finite kinetic rates. A key example is the celebrated formula of Berg and Purcell for the rate that cell surface receptors capture extracellular molecules. Indeed, this influential result is only valid if receptors transport molecules through the cell wall at a rate much faster than molecules arrive at receptors. From a mathematical perspective, ignoring receptor kinetics is convenient because it makes the diffusing molecules independent. In contrast, including receptor kinetics introduces correlations between the diffusing molecules because, for example, bound receptors may be temporarily blocked from binding additional molecules. In this work, we present a modeling framework for coupling bulk diffusion to surface receptors with finite kinetic rates. The framework uses boundary homogenization to couple the diffusion equation to nonlinear ordinary differential equations on the boundary. We use this framework to derive an explicit formula for the cellular uptake rate and show that the analysis of Berg and Purcell significantly overestimates uptake in some typical biophysical scenarios. We confirm our analysis by numerical simulations of a many-particle stochastic system.

Subdiffusion in a system with a partially permeable partially absorbing wall

We consider subdiffusion of a particle in a one-dimensional system with a thin partially permeable and partially absorbing wall. The system with the wall can be used to filter diffusing particles. Passing through the wall, the particle can be absorbed with a certain probability. Knowing the Green's functions we derive boundary conditions at the wall. The boundary conditions take a specific form in which fractional time derivatives are involved. The temporal evolution of the probability that a diffusing particle has not been absorbed is also considered.

Diffusion-Limited Reaction Kinetics of a Reactant with Square Reactive Patches on a Plane

We present a simple reaction model to study the influence of the size, number, and spatial arrangement of reactive patches on a reactant placed on a plane. Specifically, we consider a reactant whose surface has an N × N square grid structure, with each square cell (or patch) being chemically reactive or inert for partner reactant molecules approaching the cell via diffusion. We calculate the rate constant for various cases with different reactive N × N square patterns using the finite element method. For N = 2, 3, we determine the reaction kinetics of all possible reactive patterns in the absence and presence of periodic boundary conditions, and from the analysis, we find that the dependences of the kinetics on the size, number, and spatial arrangement are similar to those observed in reactive patches on a sphere. Furthermore, using square reactant models, we present a method to significantly increase the rate constant by sequentially breaking the patches into smaller patches and arranging them symmetrically. Interestingly, we find that a reactant with a symmetric patch distribution has a power–law relation between the rate constant and the number of reactive patches and show that this works well when the total reactive area is much less than the total surface area of the reactant. Since our N × N discrete models enable us to examine all possible reactive cases completely, they provide a solid understanding of the surface reaction kinetics, which would be helpful for understanding the fundamental aspects of the competitions between reactive patches arising in real applications.