arXiv subjects

Paul C Bressloff

Publications and source records attributed to Paul C Bressloff.

50 records · Page 3Linked to original sources

arXiv2022

Spectral theory of diffusion in partially absorbing media

A probabilistic framework for studying single-particle diffusion in partially absorbing media has recently been developed in terms of an encounter-based approach. The latter computes the joint probability density (generalized propagator) for particle position $\X_t$ and a Brownian functional ${\mathcal U}_t$ that specifies the amount of time the particle is in contact with a reactive component $\calM$. Absorption occurs as soon as $\calU_t$ crosses a randomly distributed threshold (stopping time). Laplace transforming the propagator with respect to $\calU_t$ leads to a classical boundary value problem (BVP) in which the reactive component has a constant rate of absorption $z$, where $z$ is the corresponding Laplace variable. Hence, a crucial step in the encounter-based approach is finding the inverse Laplace transform. In the case of a reactive boundary $\partial \calM$, this can be achieved by solving a classical Robin BVP in terms of the spectral decomposition of a Dirichlet-to-Neumann operator. In this paper we develop the analogous construction in the case of a reactive substrate $\calM$. In particular, we show that the Laplace transformed propagator can be computed in terms of the spectral decomposition of a pair of Dirichlet-to-Neumann operators. However, inverting the Laplace transform with respect to $z$ is more involved. We illustrate the theory by considering a 1D example where the Dirichlet-to-Neumann operators reduce to scalars.

cond-mat.stat-mech↗

arXiv2022

Accumulation time of diffusion in a 2D 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 in 2D domains. The standard measure of the relaxation rate is in terms of the principal nonzero 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.

math.AP↗

arXiv2022

Accumulation time of diffusion in a 3D singularly perturbed domain

Boundary value problems for diffusion in singularly perturbed domains (domains with small holes removed from the interior) is a topic of considerable current interest. Applications include intracellular diffusive transport and the spread of pollutants or heat from localized sources. In a previous paper, we introduced a new method for characterizing the approach to steady-state in the case of two-dimensional (2D) diffusion. This was based on a local measure of the relaxation rate known as the accumulation time $T(\x)$. The latter was calculated by solving the diffusion equation in Laplace space using a combination of matched asymptotics and Green's function methods. We thus obtained an asymptotic expansion of $T(\x)$ in powers of $ν=-1/\ln ε$, where $ε$ specifies the relative size of the holes. In this paper, we develop the corresponding theory for three-dimensional (3D) diffusion. The analysis is a non-trivial extension of the 2D case due to differences in the singular nature of the Laplace transformed Green's function. In particular, the asymptotic expansion of the solution of the 3D diffusion equation in Laplace space involves terms of order $O((ε/s)^n)$, where $s$ is the Laplace variable. These $s$-singularities have to be removed by partial series resummations in order to obtain an asymptotic expansion of $T(\x)$ in powers of $ε$.

math.AP↗

arXiv2021

Queuing model of axonal transport

The motor-driven intracellular transport of vesicles to synaptic targets in the axons and dendrites of neurons plays a crucial role in normal cell function. Moreover, stimulus-dependent regulation of active transport is an important component of long-term synaptic plasticity, whereas the disruption of vesicular transport can lead to the onset of various neurodegenerative diseases. In this paper we investigate how the discrete and stochastic nature of vesicular transport in axons contributes to fluctuations in the accumulation of resources within synaptic targets. We begin by solving the first passage time problem of a single motor-cargo complex (particle) searching for synaptic targets distributed along a one-dimensional axonal cable. We then use queuing theory to analyze the accumulation of synaptic resources under the combined effects of multiple search-and-capture events and degradation. In particular, we determine the steady-state mean and variance of the distribution of synaptic resources along the axon in response to the periodic insertion of particles. The mean distribution recovers the spatially decaying distribution of resources familiar from deterministic population models. However, the discrete nature of vesicular transport can lead to Fano factors that are greater than unity (non-Poissonian) across the array of synapses, resulting in significant fluctuation bursts. We also find that each synaptic Fano factor is independent of the rate of particle insertion but increases monotonically with the amount of protein cargo in each vesicle. This implies that fluctuations can be reduced by increasing the injection rate while decreasing the cargo load of each vesicle.

q-bio.NC↗

arXiv2021

Accumulation time of stochastic processes with resetting

One of the characteristic features of a stochastic process under resetting is that the probability density converges to a nonequilibrium stationary state (NESS). In addition, the approach to the stationary state exhibits a dynamical phase transition, which can be interpreted as a traveling front separating spatial regions for which the probability density has relaxed to the NESS from those where it has not. One can establish the existence of the phase transition by carrying out an asymptotic expansion of the exact solution. In this paper we develop an alternative, direct method for characterizing the approach to the NESS of a stochastic process with resetting that is based on the calculation of the so-called accumulation time. The latter is the analog of the mean first passage time of a search process, in which the survival probability density is replaced by an accumulation fraction density. In the case of one-dimensional Brownian motion with Poissonian resetting, we derive the asymptotic formula $|x-x_0|\approx \sqrt{4rD}T(x)$ for $|x-x_0|\gg\sqrt{D/r}$, where $T(x)$ is the accumulation time at $x$, $r$ is the constant resetting rate, $D$ is the diffusivity and $x_0$ is the reset point. This is identical in form to the traveling front condition for the dynamical phase transition. We also derive an analogous result for diffusion in higher spatial dimensions and for non-Poissonian resetting. We then consider the effects of delays such as refractory periods and finite return times. In both cases we establish that the asymptotic behavior of $T(x)$ is independent of the delays. Finally, we extend the analysis to a run-and-tumble particle with resetting. We thus establish the accumulation time of a stochastic process with resetting as a useful quantity for characterizing the approach to an NESS (if it exists) that is relatively straightforward to calculate.

cond-mat.stat-mech↗

arXiv2021

Drift-diffusion on a Cayley tree with stochastic resetting: the localization-delocalization transition

In this paper we develop the theory of drift-diffusion on a semi-infinite Cayley tree with stochastic resetting. In the case of a homogeneous tree with a closed terminal node and no resetting, it is known that the system undergoes a classical localization-delocalization (LD) transition at a critical mean velocity $v_c= -(D/L)\ln (z-1)$ where $D$ is the diffusivity, $L$ is the branch length and $z$ is the coordination number of the tree. If $v v_c $ (diffusion-dominated delocalized state). This is equivalent to the transition between recurrent and transient transport on the tree, with the mean first passage time (MFPT) to be absorbed by an open terminal node switching from a finite value to infinity. Here we show how the LD transition provides a basic framework for understanding analogous phase transitions in optimal resetting rates. First, we establish the existence of an optimal resetting rate $r^{**}(z)$ that maximizes the steady-state solution at a closed terminal node. In addition, we show that there is a phase transition at a critical velocity $v_c^{**}(z)$ such that $r^{**}>0$ for $v>v_c^{**}$ and $r^{**}=0$ for $v<v_c^{**}$. We then identify a critical velocity $v^*(z)$ for a phase transition in a second optimal resetting rate $r^*$ that minimizes the MFPT to be absorbed by an open terminal node. Previous results for the semi-infinite line are recovered on setting $z=2$. The critical velocity of the LD transition provides an upper bound for the other critical velocities such that $v_c^*(z)<v_c^{**}(z)<v_c(z)$ for all finite $z$. Only $v_c(z)$ has a simple universal dependence on the coordination number $z$. We end by considering the combined effects of quenched disorder and stochastic resetting.

cond-mat.stat-mech↗

arXiv2021

Trapping of a run-and-tumble particle in an inhomogeneous domain: the weak noise limit

A one-dimensional run-and-tumble particle (RTP) switches randomly between a left and right moving state of constant speed $v$. This type of motion arises in a wide range of applications in cell biology, including the unbiased growth and shrinkage of microtubules or cytonemes, the bidirectional motion of molecular motors, and the "run-and-tumble" motion of bacteria such as {\em E. coli}. RTPs are also of more general interest within the non-equilibrium statistical physics community, both at the single particle level and at the interacting population level, where it provides a simple example of active matter. In this paper we use asymptotic methods to calculate the mean first passage time (MFPT) for a one-dimensional RTP to escape an effective trapping potential generated by space-dependent switching rates. Such methods are part of a more general framework for studying metastability in so-called piecewise deterministic Markov processes (PDMPs), which include the RTP as a special case.

cond-mat.stat-mech↗

arXiv2020

Asymptotic analysis of target fluxes in the three-dimensional narrow capture problem

We develop an asymptotic analysis of target fluxes in the three-dimensional (3D) narrow capture problem. The latter concerns a diffusive search process in which the targets are much smaller than the size of the search domain. The small target assumption allows us to use matched asymptotic expansions and Green's functions to solve the diffusion equation in Laplace space. In particular, we derive an asymptotic expansion of the Laplace transformed flux into each target in powers of the non-dimensionalized target size $ε$. One major advantage of working directly with fluxes is that one can generate statistical quantities such as splitting probabilities and conditional first passage time moments without having to solve a separate boundary value problem in each case. However, in order to derive asymptotic expansions of these quantities, it is necessary to eliminate Green's function singularities that arise in the limit $s\rightarrow 0$, where $s$ is the Laplace variable. We achieve this by considering a triple expansion in $ε$, $s$ and $Λ\sim ε/s$. This allows us to perform partial summations over infinite power series in $Λ$, which leads to multiplicative factors of the form $Λ^n/(1+Λ)^n $. Since $Λ^n/(1+Λ)^n \rightarrow 1$ as $s\rightarrow 0$, the singularities in $s$ are eliminated. We then show how corresponding asymptotic expansions of the splitting probabilities and conditional MFPTs can be derived in the small-$s$ limit. Finally, we illustrate the theory by considering a pair of targets in a spherical search domain, for which the Green's functions can be calculated explicitly.

cond-mat.stat-mech↗

arXiv2020

First-passage processes and the target-based accumulation of resources

Random search for one or more targets in a bounded domain occurs widely in nature, with examples ranging from animal foraging to the transport of vesicles within cells. Most theoretical studies take a searcher-centric viewpoint, focusing on the first passage time (FTP) problem to find a target. This single search-and-capture event then triggers a downstream process or provides the searcher with some resource such as food. In this paper we take a target-centric viewpoint, by considering the accumulation of resources in one or more targets due to multiple rounds of search-and-capture events combined with resource degradation; whenever a searcher finds a target it delivers a resource packet to the target, after which it escapes and returns to its initial position. The searcher is then resupplied with cargo and a new search process is initiated after a random delay. It has previously been show how queuing theory can be used to derive general expressions for the steady-state mean and variance of the resulting resource distributions. Here we apply the theory to some classical FPT problems involving diffusion in simple geometries with absorbing boundaries, including concentric spheres, wedge domains, and branching networks. In each case, we determine how the resulting Fano factor depends on the degradation rate, the delay distribution, and various geometric parameters. We thus establish that the Fano factor can deviate significantly from Poisson statistics and exhibits a non-trivial dependence on model parameters, including non-monotonicity and crossover behavior. This indicates the non-trivial nature of the higher-order statistics of resource accumulation.

cond-mat.stat-mech↗

arXiv2020

Asymptotic analysis of extended two-dimensional narrow capture problems

In this paper we extend our recent work on two-dimensional (2D) 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 2D is that matched asymptotics generates a series expansion in $ν=-1/\ln ε$ rather than $ε$, $0<ε\ll 1$, 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 FPT 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.

cond-mat.stat-mech↗

arXiv2020

Multi-spike solutions of a hybrid reaction-transport model

Numerical simulations of classical pattern forming reaction-diffusion systems indicate that they often operate in the strongly nonlinear regime, with the final steady-state consisting of a spatially repeating pattern of localized spikes. In activator-inhibitor systems such as the two-component Gierer-Meinhardt (GM) model, one can consider the singular limit $D_a\ll D_h$, where $D_a$ and $D_h$ are the diffusivities of the activator and inhibitor, respectively. Asymptotic analysis can then be used to analyze the existence and linear stability of multi-spike solutions. In this paper, we analyze multi-spike solutions in a hybrid reaction-transport model, consisting of a slowly diffusing activator and an actively transported inhibitor that switches at a rate $α$ between right-moving and left-moving velocity states. This class of model was recently introduced to account for the formation and homeostatic regulation of synaptic puncta during larval development in {\em C. elegans}. We exploit the fact that that the hybrid model can be mapped onto the classical GM model in the fast switching limit $α\rightarrow \infty$, which allows us to establish the existence of multi-spike solutions. Linearization about the multi-spike solution leads to a non-local eigenvalue problem that is used to derive stability conditions for the multi-spike solution for finite $α$

nlin.PS↗

arXiv2020

Directional search-and-capture model of cytoneme-based morphogenesis

In this paper we develop a directional search-and-capture model of cytoneme-based morphogenesis. We consider a single cytoneme nucleating from a source cell and searching for a set of $N$ target cells $Ω_k\subset \R^d$, $k=1,\ldots,N$, with $d\geq 2$. We assume that each time the cytoneme nucleates, it grows in a random direction so that the probability of being oriented towards the $k$-th target is $p_k$ with $\sum_{k=1}^Np_k<1$. Hence, there is a non-zero probability of failure to find a target unless there is some mechanism for returning to the nucleation site and subsequently nucleating in a new direction. We model the latter as a one-dimensional search process with stochastic resetting, finite returns times and refractory periods. We use a renewal method to calculate the splitting probabilities and conditional mean first passage times (MFPTs) for the cytoneme to be captured by a given target cell. We then determine the steady-state accumulation of morphogen over the set of target cells following multiple rounds of search-and-capture events and morphogen degradation. This then yields the corresponding morphogen gradient across the set of target cells, whose steepness depends on the resetting rate. We illustrate the theory by considering a single layer of target cells, and discuss the extension to multiple cytonemes.

cond-mat.stat-mech↗

arXiv2020

Diffusive search for a stochastically-gated target with resetting

In this paper, we analyze the mean first passage time (MFPT) for a single Brownian particle to find a stochastically-gated target under the additional condition that the position of the particle is reset to a fixed position $\x_r$ at a rate $r$. The gate switches between an open and closed state according to a two-state Markov chain and can only be detected by the searcher in the open state. One possible example of such a target is a protein switching between different conformational states. As expected, the MFPT with or without resetting is an increasing function of the fraction of time $ρ_0$ that the gate is closed. However, the interplay between stochastic resetting and stochastic gating has non-trivial effects with regards the optimization of the search process under resetting. First, by considering the diffusive search for a gated target at one end of an interval, we show that the fractional change in the MFPT under resetting exhibits a non-monotonic dependence on $ρ_0$. In particular, the percentage reduction of the MFPT at the optimal resetting rate (when it exists) increases with $ρ_0$ up to some critical value, after which it decreases and eventually vanishes. Second, in the case of a spherical target in $\R^d$, the dependence of the MFPT on the spatial dimension $d$ is significantly amplified in the presence of stochastic gating.

cond-mat.stat-mech↗

arXiv2020

Occupation time of a run-and-tumble particle with resetting

We study the positive occupation time of a run-and-tumble particle (RTP) subject to stochastic resetting. Under the resetting protocol, the position of the particle is reset to the origin at a random sequence of times that is generated by a Poisson process with rate $r$. The velocity state is reset to $\pm v$ with fixed probabilities $ρ_1$ and $ρ_{-1}=1-ρ_1$, where $v$ is the speed. We exploit the fact that the moment generating functions with and without resetting are related by a renewal equation, and the latter generating function can be calculated by solving a corresponding Feynman-Kac equation. This allows us to numerically locate in Laplace space the largest real pole of the moment generating function with resetting, and thus derive a large deviation principle (LDP) for the occupation time probability density using the Gartner-Ellis theorem. We explore how the LDP depends on the switching rate $α$ of the velocity state, the resetting rate $r$ and the probability $ρ_1$. In particular, we show that the corresponding LDP for a Brownian particle with resetting is recovered in the fast switching limit $α\rightarrow \infty$. On the other hand, the behavior in the slow switching limit depends on $ρ_1$ in the resetting protocol.

cond-mat.stat-mech↗