Hybrid asymptotic-numerical approach for estimating first-passage-time densities of the two-dimensional narrow capture problem

Cellular diffusion processes in singularly perturbed domains

There are many processes in cell biology that can be modeled in terms of particles diffusing in a two-dimensional (2D) or three-dimensional (3D) bounded domain Ω ⊂ R d containing a set of small subdomains or interior compartments U j , j = 1 , … , N (singularly-perturbed diffusion problems). The domain Ω could represent the cell membrane, the cell cytoplasm, the cell nucleus or the extracellular volume, while an individual compartment could represent a synapse, a membrane protein cluster, a biological condensate, or a quorum sensing bacterial cell. In this review we use a combination of matched asymptotic analysis and Green's function methods to solve a general type of singular boundary value problems (BVP) in 2D and 3D, in which an inhomogeneous Robin condition is imposed on each interior boundary ∂ U j . This allows us to incorporate a variety of previous studies of singularly perturbed diffusion problems into a single mathematical modeling framework. We mainly focus on steady-state solutions and the approach to steady-state, but also highlight some of the current challenges in dealing with time-dependent solutions and randomly switching processes.

Asymptotic analysis of particle cluster formation in the presence of anchoring sites

The aggregation or clustering of proteins and other macromolecules plays an important role in the formation of large-scale molecular assemblies within cell membranes. Examples of such assemblies include lipid rafts, and postsynaptic domains (PSDs) at excitatory and inhibitory synapses in neurons. PSDs are rich in scaffolding proteins that can transiently trap transmembrane neurotransmitter receptors, thus localizing them at specific spatial positions. Hence, PSDs play a key role in determining the strength of synaptic connections and their regulation during learning and memory. Recently, a two-dimensional (2D) diffusion-mediated aggregation model of PSD formation has been developed in which the spatial locations of the clusters are determined by a set of fixed anchoring sites. The system is kept out of equilibrium by the recycling of particles between the cell membrane and interior. This results in a stationary distribution consisting of multiple clusters, whose average size can be determined using an effective mean-field description of the particle concentration around each anchored cluster. In this paper, we derive corrections to the mean-field approximation by applying the theory of diffusion in singularly perturbed domains. The latter is a powerful analytical method for solving two-dimensional (2D) and three-dimensional (3D) diffusion problems in domains where small holes or perforations have been removed from the interior. Applications range from modeling intracellular diffusion, where interior holes could represent subcellular structures such as organelles or biological condensates, to tracking the spread of chemical pollutants or heat from localized sources. In this paper, we take the bounded domain to be the cell membrane and the holes to represent anchored clusters. The analysis proceeds by partitioning the membrane into a set of inner regions around each cluster, and an outer region where mean-field interactions occur. Asymptotically matching the inner and outer stationary solutions generates an asymptotic expansion of the particle concentration, which includes higher-order corrections to mean-field theory that depend on the positions of the clusters and the boundary of the domain. Motivated by a recent study of light-activated protein oligomerization in cells, we also develop the analogous theory for cluster formation in a three-dimensional (3D) domain. The details of the asymptotic analysis differ from the 2D case due to the contrasting singularity structure of 2D and 3D Green's functions.

Watching Molecular Nanotubes Self-Assemble in Real Time

Molecular self-assembly is a fundamental process in nature that can be used to develop novel functional materials for medical and engineering applications. However, their complex mechanisms make the short-lived stages of self-assembly processes extremely hard to reveal. In this article, we track the self-assembly process of a benchmark system, double-walled molecular nanotubes, whose structure is similar to that found in biological and synthetic systems. We selectively dissolved the outer wall of the double-walled system and used the inner wall as a template for the self-reassembly of the outer wall. The reassembly kinetics were followed in real time using a combination of microfluidics, spectroscopy, cryogenic transmission electron microscopy, molecular dynamics simulations, and exciton modeling. We found that the outer wall self-assembles through a transient disordered patchwork structure: first, several patches of different orientations are formed, and only on a longer time scale will the patches interact with each other and assume their final preferred global orientation. The understanding of patch formation and patch reorientation marks a crucial step toward steering self-assembly processes and subsequent material engineering.

Short-time diffusive fluxes over membrane receptors yields the direction of a signalling source

An essential ability of many cell types is to detect stimuli in the form of shallow chemical gradients. Such cues may indicate the direction that new growth should occur, or the location of a mate. Amplification of these faint signals is due to intra-cellular mechanisms, while the cue itself is generated by the noisy arrival of signalling molecules to surface bound membrane receptors. We employ a new hybrid numerical-asymptotic technique coupling matched asymptotic analysis and numerical inverse Laplace transform to rapidly and accurately solve the parabolic exterior problem describing the dynamic diffusive fluxes to receptors. We observe that equilibration occurs on long timescales, potentially limiting the usefulness of steady-state quantities for localization at practical biological timescales. We demonstrate that directional information is encoded primarily in early arrivals to the receptors, while equilibrium quantities inform on source distance. We develop a new homogenization result showing that complex receptor configurations can be replaced by a uniform effective condition. In the extreme scenario where the cell adopts the angular direction of the first impact, we show this estimate to be surprisingly accurate.

Accumulation time of diffusion in a two-dimensional singularly perturbed domain

A general problem of current interest is the analysis of diffusion problems in singularly perturbed domains, within which small subdomains are removed from the domain interior and boundary conditions imposed on the resulting holes. One major application is to intracellular diffusion, where the holes could represent organelles or biochemical substrates. In this paper, we use a combination of matched asymptotic analysis and Green’s function methods to calculate the so-called accumulation time for relaxation to steady state. The standard measure of the relaxation rate is in terms of the principal non-zero eigenvalue of the negative Laplacian. However, this global measure does not account for possible differences in the relaxation rate at different spatial locations, is independent of the initial conditions, and relies on the assumption that the eigenvalues have sufficiently large spectral gaps. As previously established for diffusion-based morphogen gradient formation, the accumulation time provides a better measure of the relaxation process.

Narrow capture problem: An encounter-based approach to partially reactive targets

A general topic of current interest is the analysis of diffusion problems in singularly perturbed domains with small interior targets or traps (the narrow capture problem). One major application is to intracellular diffusion, where the targets typically represent some form of reactive biochemical substrate. Most studies of the narrow capture problem treat the target boundaries as totally absorbing (Dirichlet), that is, the chemical reaction occurs immediately on first encounter between particle and target surface. In this paper, we analyze the three-dimensional narrow capture problem in the more realistic case of partially reactive target boundaries. We begin by considering classical Robin boundary conditions. Matching inner and outer solutions of the single-particle probability density, we derive an asymptotic expansion of the Laplace transformed flux into each reactive surface in powers of ε, where ερ is a given target size. In turn, the fluxes determine the splitting probabilities for target absorption. We then extend our analysis to more general types of reactive targets by combining matched asymptotic analysis with an encounter-based formulation of diffusion-mediated surface reactions. That is, we derive an asymptotic expansion of the joint probability density for particle position and the so-called boundary local time, which characterizes the amount of time that a Brownian particle spends in the neighborhood of a point on a totally reflecting boundary. The effects of surface reactions are then incorporated via an appropriate stopping condition for the boundary local time. Robin boundary conditions are recovered in the special case of an exponential law for the stopping local times. Finally, we illustrate the theory by exploring how the leading-order contributions to the splitting probabilities depend on the choice of surface reactions. In particular, we show that there is an effective renormalization of the target radius of the form ρ→ρ-Ψ[over ̃](1/ρ), where Ψ[over ̃] is the Laplace transform of the stopping local time distribution.

Asymptotic analysis of extended two-dimensional narrow capture problems

In this paper, we extend our recent work on two-dimensional diffusive search-and-capture processes with multiple small targets (narrow capture problems) by considering an asymptotic expansion of the Laplace transformed probability flux into each target. The latter determines the distribution of arrival or capture times into an individual target, conditioned on the set of events that result in capture by that target. A characteristic feature of strongly localized perturbations in two dimensions is that matched asymptotics generates a series expansion in ν  = −1/ln ϵ rather than ϵ , 0 <  ϵ  ≪ 1, where ϵ specifies the size of each target relative to the size of the search domain. Moreover, it is possible to sum over all logarithmic terms non-perturbatively. We exploit this fact to show how a Taylor expansion in the Laplace variable s for fixed ν provides an efficient method for obtaining corresponding asymptotic expansions of the splitting probabilities and moments of the conditional first-passage-time densities. We then use our asymptotic analysis to derive new results for two major extensions of the classical narrow capture problem: optimal search strategies under stochastic resetting and the accumulation of target resources under multiple rounds of search-and-capture.

Globally optimal volume-trap arrangements for the narrow-capture problem inside a unit sphere

The determination of statistical characteristics for particles undergoing Brownian motion in constrained domains has multiple applications in various areas of research. This work presents an attempt to systematically compute globally optimal configurations of traps inside a three-dimensional domain that minimize the average of the mean first passage time (MFPT) for the narrow capture problem, the average time it takes a particle to be captured by any trap. For a given domain, the mean first passage time satisfies a linear Poisson problem with Dirichlet-Neumann boundary conditions. While no closed-form general solution of such problems is known, approximate asymptotic MFPT expressions for small traps in a unit sphere have been found. These solutions explicitly depend on trap parameters, including locations, through a pairwise potential function. After probing the applicability limits of asymptotic formulas through comparisons with numerical and available exact solutions of the narrow capture problem, full three-dimensional global optimization was performed to find optimal trap positions in the unit sphere for 2≤N≤100 identical traps. The interaction energy values and geometrical features of the putative optimal trap arrangements are presented.