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The escape dynamics of sticky particles from textured surfaces is poorly understood despite importance to various scientific and technological domains. In this work, we address this challenge by investigating the escape time of adsorbates from prevalent surface topographies, including holes/pits, pillars, and grooves. Analytical expressions for the probability density function and the mean of the escape time are derived. A particularly interesting scenario is that of very deep and narrow confining spaces within the surface. In this case, the joint effect of the entrapment and stickiness prolongs the escape time, resulting in an effective desorption rate that is dramatically lower than that of the untextured surface. This rate is shown to abide a universal scaling law, which couples the equilibrium constants of adsorption with the relevant confining length scales. While our results are analytical and exact, we also present an approximation for deep and narrow cavities based on an effective description of one-dimensional diffusion that is punctuated by motionless adsorption events. This simple and physically motivated approximation provides high-accuracy predictions within its range of validity and works relatively well even for cavities of intermediate depth. All theoretical results are corroborated with extensive Monte Carlo simulations.
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We develop a theory of reversible diffusion-controlled reactions with generalized binding/unbinding kinetics. In this framework, a diffusing particle can bind to the reactive substrate after a random number of arrivals onto it, with a given threshold distribution. The particle remains bound to the substrate for a random waiting time drawn from another given distribution and then resumes its bulk diffusion until the next binding and so on. When both distributions are exponential, one retrieves the conventional first-order forward and backward reactions whose reversible kinetics is described by generalized Collins-Kimball's (or back-reaction) boundary condition. In turn, if either of distributions is not exponential, one deals with generalized (non-Markovian) binding or unbinding kinetics (or both). Combining renewal technique with the encounter-based approach, we derive spectral expansions for the propagator, the concentration of particles, and the diffusive flux on the substrate. We study their long-time behavior and reveal how anomalous rarity of binding or unbinding events due to heavy tails of the threshold and waiting time distributions may affect such reversible diffusion-controlled reactions. Distinctions between time-dependent reactivity, encounter-dependent reactivity, and a convolution-type Robin boundary condition with a memory kernel are elucidated.
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We review the milestones in the century-long development of the theory of diffusion-controlled reactions. Starting from the seminal work by von Smoluchowski, who recognized the importance of diffusion in chemical reactions, we discuss perfect and imperfect surface reactions, their microscopic origins, and the underlying mathematical framework. Single-molecule reaction schemes, anomalous bulk diffusions, reversible binding/unbinding kinetics, and many other extensions are presented. An alternative encounter-based approach to diffusion-controlled reactions is introduced, with emphasis on its advantages and potential applications. Some open problems and future perspectives are outlined.
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Certain biochemical reactions can only be triggered after binding a sufficient number of particles to a specific target region such as an enzyme or a protein sensor. We investigate the distribution of the reaction time, i.e., the first instance when all independently diffusing particles are bound to the target. When each particle binds irreversibly, this is equivalent to the first-passage time of the slowest (last) particle. In turn, reversible binding to the target renders the problem much more challenging and drastically changes the distribution of the reaction time. We derive the exact solution of this problem and investigate the short-time and long-time asymptotic behaviors of the reaction time probability density. We also analyze how the mean reaction time depends on the unbinding rate and the number of particles. Our exact and asymptotic solutions are compared to Monte Carlo simulations.
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Cinética , Difusão , Método de Monte CarloRESUMO
Spiky coatings (also known as nanoforests or Fakir-like surfaces) have found many applications in chemical physics, material sciences, and biotechnology, such as superhydrophobic materials, filtration and sensing systems, and selective protein separation, to name but a few. In this paper, we provide a systematic study of steady-state diffusion toward a periodic array of absorbing cylindrical pillars protruding from a flat base. We approximate a periodic cell of this system by a circular tube containing a single pillar, derive an exact solution of the underlying Laplace equation, and deduce a simple yet exact representation for the total flux of particles onto the pillar. The dependence of this flux on the geometric parameters of the model is thoroughly analyzed. In particular, we investigate several asymptotic regimes, such as a thin pillar limit, a disk-like pillar, and an infinitely long pillar. Our study sheds light onto the trapping efficiency of spiky coatings and reveals the roles of pillar anisotropy and diffusional screening.
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DifusãoRESUMO
Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation, and filtration processes. Their current description via diffusion equations with mixed boundary conditions is limited to simple surface reactions with infinite or constant reactivity. In this Letter, we propose a probabilistic approach based on the concept of boundary local time to investigate the intricate dynamics of diffusing particles near a reactive surface. Reformulating surface-particle interactions in terms of stopping conditions, we obtain in a unified way major diffusion-reaction characteristics such as the propagator, the survival probability, the first-passage time distribution, and the reaction rate. This general formalism allows us to describe new surface reaction mechanisms such as for instance surface reactivity depending on the number of encounters with the diffusing particle that can model the effects of catalyst fooling or membrane degradation. The disentanglement of the geometric structure of the medium from surface reactivity opens far-reaching perspectives for modeling, optimization, and control of diffusion-mediated surface phenomena.
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Modelos Biológicos , Modelos Químicos , Membrana Celular/química , DNA/química , Difusão , Proteínas/química , Propriedades de Superfície , TermodinâmicaRESUMO
Several classic problems for particles diffusing outside an arbitrary configuration of non-overlapping partially reactive spherical traps in three dimensions are revisited. For this purpose, we describe the generalized method of separation of variables for solving boundary value problems of the associated modified Helmholtz equation. In particular, we derive a semi-analytical solution for the Green function that is the key ingredient to determine various diffusion-reaction characteristics such as the survival probability, the first-passage time distribution, and the reaction rate. We also present modifications of the method to determine numerically or asymptotically the eigenvalues and eigenfunctions of the Laplace operator and the Dirichlet-to-Neumann operator in such perforated domains. Some potential applications in chemical physics and biophysics are discussed, including diffusion-controlled reactions for mortal particles.
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A living cell's interior is one of the most complex and intrinsically dynamic systems, providing an elaborate interplay between cytosolic crowding and ATP-driven motion that controls cellular functionality. Here, we investigated two distinct fundamental features of the merely passive, non-biomotor-shuttled material transport within the cytoplasm of Dictyostelium discoideum cells: the anomalous non-linear scaling of the mean-squared displacement of a 150-nm-diameter particle and non-Gaussian distribution of increments. Relying on single-particle tracking data of 320,000 data points, we performed a systematic analysis of four possible origins for non-Gaussian transport: 1) sample-based variability, 2) rarely occurring strong motion events, 3) ergodicity breaking/aging, and 4) spatiotemporal heterogeneities of the intracellular medium. After excluding the first three reasons, we investigated the remaining hypothesis of a heterogeneous cytoplasm as cause for non-Gaussian transport. A, to our knowledge, novel fit model with randomly distributed diffusivities implementing medium heterogeneities suits the experimental data. Strikingly, the non-Gaussian feature is independent of the cytoskeleton condition and lag time. This reveals that efficiency and consistency of passive intracellular transport and the related anomalous scaling of the mean-squared displacement are regulated by cytoskeleton components, whereas cytoplasmic heterogeneities are responsible for the generic, non-Gaussian distribution of increments.
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Dictyostelium/metabolismo , Espaço Intracelular/metabolismo , Actinas/metabolismo , Transporte Biológico , Dictyostelium/citologia , Microtúbulos/metabolismo , Modelos Biológicos , Movimento (Física) , Nanopartículas/química , ProbabilidadeRESUMO
We study diffusion of particles on the surface of a sphere toward a partially reactive circular target with partly reversible binding kinetics. We solve the coupled diffusion-reaction equations and obtain the exact expressions for the time-dependent concentration of particles and the total diffusive flux. Explicit asymptotic formulas are derived in the small target limit. This study reveals the strong effects of reversible binding kinetics onto diffusion-mediated reactions that may be relevant for many biochemical reactions on cell membranes.
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Difusão , Modelos Químicos , Membrana Celular/química , Cinética , Propriedades de SuperfícieRESUMO
We propose a general theoretical description of chemical reactions occurring on a catalytic surface with heterogeneous reactivity. The propagator of a diffusion-reaction process with eventual absorption on the heterogeneous partially reactive surface is expressed in terms of a much simpler propagator toward a homogeneous perfectly reactive surface. In other words, the original problem with the general Robin boundary condition that includes, in particular, the mixed Robin-Neumann condition, is reduced to that with the Dirichlet boundary condition. Chemical kinetics on the surface is incorporated as a matrix representation of the surface reactivity in the eigenbasis of the Dirichlet-to-Neumann operator. New spectral representations of important characteristics of diffusion-controlled reactions, such as the survival probability, the distribution of reaction times, and the reaction rate, are deduced. Theoretical and numerical advantages of this spectral approach are illustrated by solving interior and exterior problems for a spherical surface that may describe either an escape from a ball or hitting its surface from outside. The effect of continuously varying or piecewise constant surface reactivity (describing, e.g., many reactive patches) is analyzed.
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The first-passage time (FPT), i.e., the moment when a stochastic process reaches a given threshold value for the first time, is a fundamental mathematical concept with immediate applications. In particular, it quantifies the statistics of instances when biomolecules in a biological cell reach their specific binding sites and trigger cellular regulation. Typically, the first-passage properties are given in terms of mean first-passage times. However, modern experiments now monitor single-molecular binding-processes in living cells and thus provide access to the full statistics of the underlying first-passage events, in particular, inherent cell-to-cell fluctuations. We here present a robust explicit approach for obtaining the distribution of FPTs to a small partially reactive target in cylindrical-annulus domains, which represent typical bacterial and neuronal cell shapes. We investigate various asymptotic behaviours of this FPT distribution and show that it is typically very broad in many biological situations, thus, the mean FPT can differ from the most probable FPT by orders of magnitude. The most probable FPT is shown to strongly depend only on the starting position within the geometry and to be almost independent of the target size and reactivity. These findings demonstrate the dramatic relevance of knowing the full distribution of FPTs and thus open new perspectives for a more reliable description of many intracellular processes initiated by the arrival of one or few biomolecules to a small, spatially localised region inside the cell.
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Células/química , Modelos Químicos , Cinética , Processos Estocásticos , Fatores de TempoRESUMO
In many biological situations, a species arriving from a remote source diffuses in a domain confined between two parallel surfaces until it finds a binding partner. Since such a geometric shape falls in between two- and three-dimensional settings, the behavior of the macroscopic reaction rate and its dependence on geometric parameters are not yet understood. Modeling the geometric setup by a capped cylinder with a concentric disk-like reactive region on one of the lateral surfaces, we provide an exact semi-analytical solution of the steady-state diffusion equation and compute the diffusive flux onto the reactive region. We explore the dependence of the macroscopic reaction rate on the geometric parameters and derive asymptotic results in several limits. Using the self-consistent approximation, we also obtain a simple fully explicit formula for the reaction rate that exhibits a transition from two-dimensional to three-dimensional behavior as the separation distance between lateral surfaces increases. Biological implications of these results are discussed.
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Retículo Endoplasmático/metabolismo , Ácido Glutâmico/metabolismo , Modelos Biológicos , Neurônios/metabolismo , Receptores de Glutamato/metabolismo , Animais , Simulação por Computador , Difusão , Espaço Extracelular , Cinética , Neurônios/citologia , Organelas/metabolismoRESUMO
The purpose of this paper is twofold. First, we provide a concise introduction to the generalized method of separation of variables for solving diffusion problems in canonical domains beyond conventional arrays of spheres. Second, as an important example of its application in the theory of diffusion-influenced reactions, we present an exact solution of the axially symmetric problem on diffusive competition in an array of two active particles (including Janus dumbbells) constructed of a prolate spheroid and a sphere. In particular, we investigate how the reaction rate depends on sizes of active particles, spheroid aspect ratio, particles' surface reactivity, and distance between their centers.
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We study the mean first exit time (Tε) of a particle diffusing in a circular or a spherical micro-domain with an impenetrable confining boundary containing a small escape window (EW) of an angular size ε. Focusing on the effects of an energy/entropy barrier at the EW, and of the long-range interactions (LRIs) with the boundary on the diffusive search for the EW, we develop a self-consistent approximation to derive for Tε a general expression, akin to the celebrated Collins-Kimball relation in chemical kinetics and accounting for both rate-controlling factors in an explicit way. Our analysis reveals that the barrier-induced contribution to Tε is the dominant one in the limit ε â 0, implying that the narrow escape problem is not "diffusion-limited" but rather "barrier-limited". We present the small-ε expansion for Tε, in which the coefficients in front of the leading terms are expressed via some integrals and derivatives of the LRI potential. Considering a triangular-well potential as an example, we show that Tε is non-monotonic with respect to the extent of the attractive LRI, being minimal for the ones having an intermediate extent, neither too concentrated on the boundary nor penetrating too deeply into the bulk. Our analytical predictions are in good agreement with the numerical simulations.
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We investigate the first passage problem for multiple particles that diffuse towards a target, partially adsorb there, and then desorb after a finite exponentially distributed residence time. We search for the first time when m particles undergoing such reversible target-binding kinetics are found simultaneously on the target that may trigger an irreversible chemical reaction or a biophysical event. Even if the particles are independent, the finite residence time on the target yields an intricate temporal coupling between particles. We compute analytically the mean first passage time (MFPT) for two independent particles by mapping the original problem to higher-dimensional surface-mediated diffusion and solving the coupled partial differential equations. The respective effects of the adsorption and desorption rates on the MFPT are revealed and discussed.
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We derive a general exact formula for the mean first passage time (MFPT) from a fixed point inside a planar domain to an escape region on its boundary. The underlying mixed Dirichlet-Neumann boundary value problem is conformally mapped onto the unit disk, solved exactly, and mapped back. The resulting formula for the MFPT is valid for an arbitrary space-dependent diffusion coefficient, while the leading logarithmic term is explicit, simple, and remarkably universal. In contrast to earlier works, we show that the natural small parameter of the problem is the harmonic measure of the escape region, not its perimeter. The conventional scaling of the MFPT with the area of the domain is altered when diffusing particles are released near the escape region. These findings change the current view of escape problems and related chemical or biochemical kinetics in complex, multiscale, porous or fractal domains, while the fundamental relation to the harmonic measure opens new ways of computing and interpreting MFPTs.
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We study the spectral properties of the Dirichlet-to-Neumann operator and the related Steklov problem in spheroidal domains ranging from a needle to a disk. An explicit matrix representation of this operator for both interior and exterior problems is derived. We show how the anisotropy of spheroids affects the eigenvalues and eigenfunctions of the operator. As examples of physical applications, we discuss diffusion-controlled reactions on spheroidal partially reactive targets and the statistics of encounters between the diffusing particle and the spheroidal boundary.
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We revise the encounter-based approach to imperfect diffusion-controlled reactions, which employs the statistics of encounters between a diffusing particle and the reactive region to implement surface reactions. We extend this approach to deal with a more general setting, in which the reactive region is surrounded by a reflecting boundary with an escape region. We derive a spectral expansion for the full propagator and investigate the behavior and probabilistic interpretations of the associated probability flux density. In particular, we obtain the joint probability density of the escape time and the number of encounters with the reactive region before escape, and the probability density of the first-crossing time of a prescribed number of encounters. We briefly discuss generalizations of the conventional Poissonian-type surface reaction mechanism described by Robin boundary condition and potential applications of this formalism in chemistry and biophysics.