We extend the theoretical framework used to study search processes with stochastic resetting to the case of partially absorbing targets. Instead of an absorption event occurring when the search particle reaches the boundary of a target, the particle can diffuse freely in and out of the target region and is absorbed at a rate $κ$ when inside the target. In the context of cell biology, the target could represent a chemically reactive substrate within a cell or a region where a particle can be offloaded onto a nearby compartment. We apply this framework to a partially absorbing interval and to spherically symmetric targets in $\R^d$. In each case, we determine how the mean first passage time (MFPT) for absorption depends on $κ$, the resetting rate $r$, and the target geometry. For the given examples, we find that the MFPT is a monotonically decreasing function of $κ$, whereas it is a unimodal function of $r$ with a unique minimum at an optimal resetting rate $r_{\rm opt}$. The variation of $r_{\rm opt}$ with $κ$ depends on the spatial dimension $d$, decreasing in sensitivity as $d$ increases. For finite $κ$, $ r_{\rm opt}$ is a non-trivial function of the target size and distance between the target and the reset point. We also show how our results converge to those obtained previously for problems with totally absorbing targets and similar geometries when the absorption rate becomes infinite. Finally, we generalize the theory to take into account an extended chemical reaction scheme within a target.
First passage of stochastic processes under resetting has recently been an active research topic in the field of statistical physics. However, most of previous studies mainly focused on the systems with continuous time and space. In this paper, we study the effect of stochastic resetting on first passage properties of discrete-time absorbing Markov chains, described by a transition matrix $\brm{Q}$ between transient states and a transition matrix $\brm{R}$ from transient states to absorbing states. Using a renewal approach, we exactly derive the unconditional mean first passage time (MFPT) to …
We consider a particle undergoing diffusion with stochastic resetting in a bounded domain $\calU\subset \R^d$ for $d=2,3$. The domain is perforated by a set of partially absorbing targets within which the particle may be absorbed at a rate $κ$. Each target is assumed to be much smaller than $|\calU|$, which allows us to use asymptotic and Green's function methods to solve the diffusion equation in Laplace space. In particular, we construct an inner solution within the interior and local exterior of each target, and match it with an outer solution in the bulk of $\calU$. This yields an asymptot…
In this paper we consider diffusion in a domain $Ω$ containing a partially absorbing target $\calM$ with position and occupation time resetting. The occupation time $A_t$ is a Brownian functional that determines the amount of time that the particle spends in $ \calM$ over the time interval $[0,t]$. We assume that there exists some internal state $\calU_t$ of the particle at time $t$ which is modified whenever the particle is diffusing within $\calM $. The state $\calU_t$ is taken to be a monotonically increasing function of $A_t$, and absorption occurs as soon as $\calU_t$ crosses some fixed t…
Mirror transitions in diffusion with stochastic resetting confined on a ring
Universidad Autónoma Metropolitana（墨西哥自治 metropolitan 大学）；Universidad Autónoma de Chiapas（恰帕斯自治大学）；Instituto de Física, Universidad Nacional Autónoma de México（墨西哥国立自治大学物理研究所）
Diffusion and first passage in the presence of stochastic resetting and potential bias have been of recent interest. We study a few models, systematically progressing in their complexity, to understand the usefulness of resetting. In the parameter space of the models, there are multiple continuous and discontinuous transitions where the advantage of resetting vanishes. We show these results analytically exactly for a tent-potential, and numerically accurately for a quartic-potential relevant to a magnetic system at low temperatures. We find that the spatial asymmetry of the potential across th…
Diffusion with stochastic resetting has recently emerged as a powerful modeling tool with a myriad of potential applications. Here, we study local time in this model, covering situations of free and biased diffusion with, and without, the presence of an absorbing boundary. Given a Brownian trajectory that evolved for $t$ units of time, the local time is simply defined as the total time the trajectory spent in a small vicinity of its initial position. However, as Brownian trajectories are stochastic --- the local time itself is a random variable which fluctuates round and about its mean value. …
We consider a particle undergoing run and tumble dynamics, in which its velocity stochastically reverses, in one dimension. We study the addition of a Poissonian resetting process occurring with rate $r$. At a reset event the particle's position is returned to the resetting site $X_r$ and the particle's velocity is reversed with probability $η$. The case $η= 1/2$ corresponds to position resetting and velocity randomization whereas $η=0$ corresponds to position-only resetting. We show that, beginning from symmetric initial conditions, the stationary state does not depend on $η$ i.e. it is indep…
The effects of Poissonian resetting at a constant rate $r$ on the reaction time between a Brownian particle and a stochastically gated target are studied. The target switches between a reactive state and a non-reactive one. We calculate the mean time at which the particle subject to resetting hits the target for the first time, while the latter is in the reactive state. The search time is minimum at a resetting rate that depends on the target transition rates. When the target relaxation rate is much larger than both the resetting rate and the inverse diffusion time, the system becomes equivale…
We consider the mean time to absorption by an absorbing target of a diffusive particle with the addition of a process whereby the particle is reset to its initial position with rate $r$. We consider several generalisations of the model of M. R. Evans and S. N. Majumdar (2011), Diffusion with stochastic resetting, Phys. Rev. Lett. 106, 160601: (i) a space dependent resetting rate $r(x)$ ii) resetting to a random position $z$ drawn from a resetting distribution ${\cal P}(z)$ iii) a spatial distribution for the absorbing target $P_T(x)$. As an example of (i) we show that the introduction of a non…
We consider the motion of a randomly accelerated particle in one dimension under stochastic resetting mechanism. Denoting the position and velocity by $x$ and $v$ respectively, we consider two different resetting protocols - (i) complete resetting: here both $x$ and $v$ reset to their initial values $x_0$ and $v_0$ at a constant rate $r$, (ii) partial resetting: here only $x$ resets to $x_0$ while $v$ evolves without interruption. For complete resetting, we find that the particle attains stationary state in both $x$ and $v$. We compute the non-equilibrium joint stationary state of $x$ and $v$ …
We consider diffusion in arbitrary spatial dimension d with the addition of a resetting process wherein the diffusive particle stochastically resets to a fixed position at a constant rate $r$. We compute the non-equilibrium stationary state which exhibits non-Gaussian behaviour. We then consider the presence of an absorbing target centred at the origin and compute the survival probability and mean time to absorption of the diffusive particle by the target. The mean absorption time is finite and has a minimum value at an optimal resetting rate $r^*$ which depends on dimension. Finally we consid…
We study the non-equilibrium steady states and first passage properties of a Brownian particle with position $X$ subject to an external confining potential of the form $V(X)=μ|X|$, and that is switched on and off stochastically. Applying the potential intermittently generates a physically realistic diffusion process with stochastic resetting toward the origin, a topic which has recently attracted a considerable interest in a variety of theoretical contexts but has remained challenging to implement in lab experiments. The present system exhibits rich features, not observed in previous resetting…
We consider a Brownian particle diffusing in a one dimensional interval with absorbing end points. We study the ramifications when such motion is interrupted and restarted from the same initial configuration. We provide a comprehensive study of the first passage properties of this trapping phenomena. We compute the mean first passage time and derive the criterion upon which restart always expedites the underlying completion. We show how this set-up is a manifestation of a success-failure problem. We obtain the success and failure rates and relate them with the splitting probabilities, namely, …
We investigate the first passage properties of a Brownian particle diffusing freely inside a $d$-dimensional sphere with absorbing spherical surface subject to stochastic resetting. We derive the mean time to absorption (MTA) as functions of resetting rate $γ$ and initial distance $r$ of the particle to the center of the sphere. We find that when $r>r_c$ there exists a nonzero optimal resetting rate $γ_{\rm opt}$ at which the MTA is a minimum, where $r_c=\sqrt {d/\left( {d + 4} \right)} R$ and $R$ is the radius of sphere. As $r$ increases, $γ_{\rm opt}$ exhibits a continuous transition from ze…
The calculation of the diffusion-controlled reaction rate for partially absorbing, non-spherical boundaries presents a formidable problem of broad relevance. In this paper we take the reference case of a spherical boundary and work out a perturbative approach to get a simple analytical formula for the first-order correction to the diffusive flux onto a non-spherical partially absorbing surface of revolution. To assess the range of validity of this formula, we derive exact and approximate expressions for the reaction rate in the case of partially absorbing prolate and oblate spheroids. We also …
We explore the effect of stochastic resetting on the first-passage properties of Feller process. The Feller process can be envisioned as space-dependent diffusion, with diffusion coefficient $D(x)=x$, in a potential $U(x)=x\left(\frac{x}{2}-θ\right)$ that owns a minimum at $θ$. This restricts the process to the positive side of the origin and therefore, Feller diffusion can successfully model a vast array of phenomena in biological and social sciences, where realization of negative values is forbidden. In our analytically tractable model system, a particle that undergoes Feller diffusion is su…
We explore the effect of stochastic resetting on the first-passage properties of space-dependent diffusion in presence of a constant bias. In our analytically tractable model system, a particle diffusing in a linear potential $U(x)\proptoμ|x|$ with a spatially varying diffusion coefficient $D(x)=D_0|x|$ undergoes stochastic resetting, i.e., returns to its initial position $x_0$ at random intervals of time, with a constant rate $r$. Considering an absorbing boundary placed at $x_a<x_0$, we first derive an exact expression of the survival probability of the diffusing particle in the Laplace spac…
The effect of partial absorption on a diffusive particle which stochastically resets its position with a finite rate $r$ is considered. The particle is absorbed by a target at the origin with absorption `velocity' $a$; as the velocity $a$ approaches $\infty$ the absorption property of the target approaches that of a perfectly-absorbing target. The effect of partial absorption on first-passage time problems is studied, in particular, it is shown that the mean time to absorption (MTA) is increased by an additive term proportional to $1/a$. The results are extended to multiparticle systems where …
In this paper, we investigate the effects of stochastic resetting on diffusion in $\R^d\backslash \calU$, where $\calU$ is a bounded obstacle with a partially absorbing surface $\partial \calU$. We begin by considering a Robin boundary condition with a constant reactivity $κ_0$, and show how previous results are recovered in the limits $κ_0\rightarrow 0,\infty$. We then generalize the Robin boundary condition to a more general probabilistic model of diffusion-mediated surface reactions using an encounter-based approach. The latter considers the joint probability density or propagator $P(\x,\el…
We study minimal mean-field models of viral drug resistance development in which the efficacy of a therapy is described by a one-dimensional stochastic resetting process with mixed reflecting-absorbing boundary conditions. We derive analytical expressions for the mean survival time for the virus to develop complete resistance to the drug. We show that the optimal therapy resetting rates that achieve a minimum and maximum mean survival times undergo a second and first-order phase transition-like behaviour as a function of the therapy efficacy drift. We illustrate our results with simulations of…
We consider the Larkin model of a directed polymer with Gaussian-distributed random forces, with the addition of a resetting process whereby the transverse position of the end-point of the polymer is reset to zero with constant rate $r$. We express the average over disorder of the mean time to absorption by an absorbing target at a fixed value of the transverse position. Thanks to the independence properties of the distribution of the random forces, this expression is analogous to the mean time to absorption for a diffusive particle under resetting, which possesses a single minimum at an optim…
During a random search, resetting the searcher's position from time to time to the starting point often reduces the mean completion time of the process. Although many different resetting models have been studied over the past ten years, only a few can be physically implemented. Here we study theoretically a protocol that can be realised experimentally and which exhibits unusual optimization properties. A Brownian particle is subject to an arbitrary confining potential $v(x)$ which is switched on and off intermittently at fixed rates. Motion is constrained between an absorbing wall located at t…
In this paper we consider the diffusive search for a bounded target $Ω\in \R^d$ with its boundary $\partial Ω$ totally absorbing. We assume that the target is surrounded by a semipermeable interface given by the closed surface $\partial \calM$ with $Ω\subset \calM\subset \R^d$. That is, the interface totally surrounds the target and thus partially screens the diffusive search process. We also assume that the position of the diffusing particle (searcher) randomly resets to its initial position $\x_0$ according to a Poisson process with a resetting rate $r$. The location $\x_0$ is taken to be ou…
Heterogeneous planar diffusion with axisymmetric power-law decaying diffusion coefficient under stochastic resetting
Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts（马其顿科学院与艺术院计算机科学与信息技术研究中心）；Institute of Physics, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University（圣西里尔和梅托迪乌斯大学自然科学与数学学院物理研究所）；Department of Physics, Korea University（高丽大学物理系）；Laboratoire de Physique et Chimie Théoriques (CNRS UMR 7019), Université de Lorraine Nancy（洛林大学南锡分校理论与物理化学实验室）；Centro de Física Teórica e Computacional, Universidade de Lisboa（里斯本大学理论与计算物理中心）；Departamento de Física, Universidade Estadual de Maringá（马里纳州立大学物理系）
Stochastic resetting, a diffusive process whose amplitude is "reset" to the origin at random times, is a vividly studied strategy to optimize encounter dynamics, e.g., in chemical reactions. We here generalize the resetting step by introducing a random resetting amplitude, such that the diffusing particle may be only partially reset towards the trajectory origin, or even overshoot the origin in a resetting step. We introduce different scenarios for the random-amplitude stochastic resetting process and discuss the resulting dynamics. Direct applications are geophysical layering (stratigraphy) a…
We consider subdiffusion of a particle in a one-dimensional system with a thin partially permeable wall. Passing through the wall, the particle can be absorbed with a certain probability. We call such a wall partially permeable partially absorbing wall (PPAW). Using the diffusion model in a system with discrete time and spatial variable, probability densities (Green's functions) describing subdiffusion in the system have been derived. Knowing the Green's functions we derive boundary conditions at the wall. The boundary conditions take a specific form in which time derivatives of the fractional…
Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random walk along the DNA template. Recovery of polymerases from the transcriptionally-inactive backtracked state is determined by a kinetic competition between 1D diffusion and RNA cleavage. Here we describe backtrack recovery as a continuous-time random walk, where the time for a polymerase to recover from a backtrack of a given depth is described as a first-pass…
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…
We present an analytical study of the time dependent diffusion coefficient in a dilute suspension of spheres with partially absorbing boundary condition. Following Kirkpatrick (J. Chem. Phys. 76, 4255) we obtain a perturbative expansion for the time dependent particle density using volume fraction $f$ of spheres as an expansion parameter. The exact single particle $t$-operator for partially absorbing boundary condition is used to obtain a closed form time-dependent diffusion coefficient $D(t)$ accurate to first order in the volume fraction $f$. Short and long time limits of $D(t)$ are checked …
In this paper we develop an encounter-based model of reaction-subdiffusion in a domain $Ω$ with a partially absorbing interior trap $\calU\subset Ω$. We assume that the particle can freely enter and exit $\calU$, but is only absorbed within $\calU$. We take the probability of absorption to depend on the amount of time a particle spends within the trap, which is specified by a Brownian functional known as the occupation time $A(t)$. The first passage time (FPT) for absorption is identified with the point at which the occupation time crosses a random threshold $\widehat{A}$ with probability dens…
Analytic and Monte Carlo Approximations to the Distribution of the First Passage Time of the Drifted Diffusion with Stochastic Resetting and Mixed Boundary Conditions
Consider a particle which is randomly accelerated by Gaussian white noise on the line segment $0<x<1$ and is absorbed as soon as it reaches $x=0$ or $x=1$. The mean absorption time $T(x,v)$, where $x$ and $v$ denote the initial position and velocity, was calculated exactly by Masoliver and Porrà in 1995. We consider a more general boundary condition. On arriving at either boundary, the particle is absorbed with probability $1-p$ and reflected with probability $p$. The reflections are inelastic, with coefficient of restitution $r$. With exact analytical and numerical methods and simulations, we…
On the Kemeny time for continuous-time reversible and irreversible Markov processes with applications to stochastic resetting and to conditioning towards forever-survival
We study the mean first passage time (MFPT) to an absorbing target of a one-dimensional Brownian particle subject to an external potential $v(x)$ in a finite domain. We focus on the cases in which the external potential is confining, of the form $v(x)=k|x-x_0|^n/n$, and where the particle's initial position coincides with $x_0$. We first consider a particle between an absorbing target at $x=0$ and a reflective wall at $x=c$. At fixed $x_0$, we show that when the target distance $c$ exceeds a critical value, there exists a nonzero optimal stiffness $k_{\rm opt}$ that minimizes the MFPT to the t…
Morphogen gradients play an essential role in the spatial regulation of cell patterning during early development. The classical mechanism of morphogen gradient formation involves the diffusion of morphogens away from a localized source combined with some form of bulk absorption. Morphogen gradient formation plays a crucial role during early development, whereby a spatially varying concentration of morphogen protein drives a corresponding spatial variation in gene expression during embryogenesis. In most models, the absorption rate is taken to be a constant multiple of the local concentration. …
Partial Localization and Multifractality in Heterogeneous Population Growth with Resetting
Université Paris-Saclay（巴黎萨克雷大学）；ENS and PSL University, Sorbonne Université, Université Paris Cité（巴黎高等师范学院与巴黎文理研究大学，索邦大学，巴黎西岱大学）；Capital Fund Management（资本基金管理公司）
