1,721,078 research outputs found
From the potential of the mean force to a quasiparticle's effective potential in narrow ion channels
Full text linkWe consider the selective permeation of ions through narrow water-filled channels in the presence of strong interaction between the ions. These interactions lead to highly correlated ionic motion, which can conveniently be described via the concept of a quasiparticle. Here, we connect the quasiparticle's effective potential and the multi-ion potential of the mean force, found through molecular dynamics simulations, and we validate the method on an analytical toy model of the KcsA channel. Possible future applications of the method to the connection between molecular dynamical calculations and the experimentally measured current-voltage and current-concentration characteristics of the channel are discussed
Physics of selective conduction and point mutation in biological ion channels
Full text linkWe introduce a statistical and linear response theory of selective conduction in biological ion channels with multiple binding sites and possible point mutation. We derive an effective grand-canonical ensemble and generalized Einstein relations for the selectivity filter, assuming strongly coordinated ionic motion, and allowing for ionic Coulomb blockade. The theory agrees well with data from the KcsA K+ channel and a mutant. We show that the Eisenman relations for thermodynamic selectivity follow from the condition for fast conduction and find that maximum conduction requires the binding sites to be nearly identical
Field-dependent dehydration and optimal ionic escape paths for C2N membranes
Full text linkMost analytic theories describing electrostatically driven ion transport through water-filled nanopores assume that the corresponding permeation barriers are bias-independent. While this assumption may hold for sufficiently wide pores under infinitely small bias, transport through subnanometer pores under finite bias is difficult to interpret analytically. Given recent advances in subnanometer pore fabrication and the rapid progress in detailed computer simulations, it is important to identify and understand the specific field-induced phenomena arising during ion transport. Here we consider an atomistic model of electrostatically driven ion permeation through subnanoporous C2N membranes. We analyze probability distributions of ionic escape trajectories and show that the optimal escape path switches between two different configurations depending on the bias magnitude. We identify two distinct mechanisms contributing to field-induced changes in transport-opposing barriers: a weak one arising from field-induced ion dehydration and a strong one due to the field-induced asymmetry of the hydration shells. The simulated current-voltage characteristics are compared with the solution of the 1D Nernst-Planck model. Finally, we show that the deviation of simulated currents from analytic estimates for large fields is consistent with the field-induced barriers and the observed changes in the optimal ion escape path
Origin and control of ionic hydration patterns in nanopores
Full text linkIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns
Optimal fluctuations and the control of chaos.
Full text linkThe energy-optimal migration of a chaotic oscillator from one attractor to another coexisting attractor is investigated via an analogy between the Hamiltonian theory of fluctuations and Hamiltonian formulation of the control problem. We demonstrate both on physical grounds and rigorously that the Wentzel-Freidlin Hamiltonian arising in the analysis of fluctuations is equivalent to Pontryagin's Hamiltonian in the control problem with an additive linear unrestricted control. The deterministic optimal control function is identied with the optimal fluctuational force. Numerical and analogue experiments undertaken to verify these ideas demonstrate that, in the limit of small noise intensity, fluctuational escape from the chaotic attractor occurs via a unique (optimal) path corresponding to a unique (optimal) fluctuational force. Initial conditions on the chaotic attractor are identified. The solution of the boundary value control problem for the Pontryagin Hamiltonian is found numerically. It is shown that this solution is approximated very accurately by the optimal fluctuational force found using statistical analysis of the escape trajectories. A second series of numerical experiments on the deterministic system (i.e. in the absence of noise) show that a control function of precisely the same shape and magnitude is indeed able to instigate escape. It is demonstrated that this control function minimizes the cost functional and the corresponding energy is found to be smaller than that obtained with some earlier adaptive control algorithms
Polarization switches in vertical-cavity surface-emitting lasers
Full text linkThe polarization dynamics of a vertical cavity surface emitting laser is investigated as a nonlinear stochastic dynamical system. The polarization switches in the device are considered as activation processes in a two dimensional system with a saddle cycle; the optimal way of switching is determined as the solution of a boundary value problem. The theoretical results are in good agreement with the numerical simulations
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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