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Register a new userThe narrow escape problem revisited
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The time needed for a particle to exit a confining domain through a small window, called the narrow escape time (NET), is a limiting factor of various processes, such as some biochemical reactions in cells. Obtaining an estimate of the mean NET for a given geometric environment is therefore a requisite step to quantify the reaction rate constant of such processes, which has raised a growing interest in the last few years. In this Letter, we determine explicitly the scaling dependence of the mean NET on both the volume of the confining domain and the starting point to aperture distance. We show that this analytical approach is applicable to a very wide range of stochastic processes, including anomalous diffusion or diffusion in the presence of an external force field, which cover situations of biological relevance.
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In the scenario of the narrow escape problem (NEP) a particle diffuses in a finite container and eventually leaves it through a small escape window in the otherwise impermeable boundary, once it arrives to this window and over-passes an entropic barrier at the entrance to it. This generic problem is mathematically identical to that of a diffusion-mediated reaction with a partially-reactive site on the containers boundary. Considerable knowledge is available on the dependence of the mean first-reaction time (FRT) on the pertinent parameters. We here go a distinct step further and derive the full FRT distribution for the NEP. We demonstrate that typical FRTs may be orders of magnitude shorter than the mean one, thus resulting in a strong defocusing of characteristic temporal scales. We unveil the geometry-control of the typical times, emphasising the role of the initial distance to the target as a decisive parameter. A crucial finding is the further FRT defocusing due to the barrier, necessitating repeated escape or reaction attempts interspersed with bulk excursions. These results add new perspectives and offer a broad comprehension of various features of the by-now classical NEP that are relevant for numerous biological and technological systems.
The narrow escape problem deals with the calculation of the mean escape time (MET) of a Brownian particle from a bounded domain through a small hole on the domains boundary. Here we develop a formalism that allows us to evaluate the emph{non-escape probability} of a gas of diffusing particles that may interact with each other. In some cases the non-escape probability allows us to evaluate the MET of the first particle. The formalism is based on the fluctuating hydrodynamics and the recently developed macroscopic fluctuation theory. We also uncover an unexpected connection between the narrow escape of interacting particles and thermal runaway in chemical reactors.
We consider the problem of inferring the interactions between a set of N binary variables from the knowledge of their frequencies and pairwise correlations. The inference framework is based on the Hopfield model, a special case of the Ising model where the interaction matrix is defined through a set of patterns in the variable space, and is of rank much smaller than N. We show that Maximum Lik elihood inference is deeply related to Principal Component Analysis when the amp litude of the pattern components, xi, is negligible compared to N^1/2. Using techniques from statistical mechanics, we calculate the corrections to the patterns to the first order in xi/N^1/2. We stress that it is important to generalize the Hopfield model and include both attractive and repulsive patterns, to correctly infer networks with sparse and strong interactions. We present a simple geometrical criterion to decide how many attractive and repulsive patterns should be considered as a function of the sampling noise. We moreover discuss how many sampled configurations are required for a good inference, as a function of the system size, N and of the amplitude, xi. The inference approach is illustrated on synthetic and biological data.
We present a stochastic approach for ion transport at the mesoscopic level. The description takes into account the self-consistent electric field generated by the fixed and mobile charges as well as the discrete nature of these latter. As an application we study the noise in the ion transport process, including the effect of the displacement current generated by the fluctuating electric field. The fluctuation theorem is shown to hold for the electric current with and without the displacement current.
We study spectral behavior of sparsely connected random networks under the random matrix framework. Sub-networks without any connection among them form a network having perfect community structure. As connections among the sub-networks are introduced, the spacing distribution shows a transition from the Poisson statistics to the Gaussian orthogonal ensemble statistics of random matrix theory. The eigenvalue density distribution shows a transition to the Wigners semicircular behavior for a completely deformed network. The range for which spectral rigidity, measured by the Dyson-Mehta $Delta_3$ statistics, follows the Gaussian orthogonal ensemble statistics depends upon the deformation of the network from the perfect community structure. The spacing distribution is particularly useful to track very slight deformations of the network from a perfect community structure, whereas the density distribution and the $Delta_3$ statistics remain identical to the undeformed network. On the other hand the $Delta_3$ statistics is useful for the larger deformation strengths. Finally, we analyze the spectrum of a protein-protein interaction network for Helicobacter, and compare the spectral behavior with those of the model networks.
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