Explanipedia

Ionic Coulomb blockade controls the current in a short narrow carbon nanotube Open

W. A. T. Gibby, Miraslau L. Barabash, I. A. Khovanov, D. G. Luchinsky, P. V. E. McClintock · 2024

We use all-atom molecular dynamics simulations to investigate ionic conduction in a short, charged, single-wall carbon nanotube. They reveal ionic Coulomb blockade (ICB) oscillations in the current as a function of the fixed charge on the …

Origin and control of ionic hydration patterns in nanopores Open

Miraslau L. Barabash, W. A. T. Gibby, Carlo Guardiani, Alex Smolyanitsky, D. G. Luchinsky , et al. · 2021

Field-Dependent Dehydration and Optimal Ionic Escape Paths for C2N Membranes Open

Miraslau L. Barabash, W. A. T. Gibby, Carlo Guardiani, D. G. Luchinsky, Binquan Luan , et al. · 2021

Most 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 unde…

Physics of Selective Conduction and Point Mutation in Biological Ion Channels Open

W. A. T. Gibby, Miraslau L. Barabash, Carlo Guardiani, D. G. Luchinsky, P. V. E. McClintock · 2021

We 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 rela…

Application of a Statistical and Linear Response Theory to Multi-Ion Na+ Conduction in NaChBac Open

W. A. T. Gibby, O. A. Fedorenko, Carlo Guardiani, Miraslau L. Barabash, Thomas Mumby , et al. · 2021

Biological ion channels are fundamental to maintaining life. In this manuscript we apply our recently developed statistical and linear response theory to investigate Na+ conduction through the prokaryotic Na+ channel NaChBac. This work is …

Towards Predicting And Controlling Ionic Hydration Patterns In Nanopores Open

Miraslau L. Barabash, Aaron Dines, W. A. T. Gibby, Carlo Guardiani, Alex Smolyanitsky , et al. · 2021

We propose a method to describe analytically the ionic hydration patterns near sub-nanopores. It agrees well with molecular dynamics simulations, predicts the locations of the trapped water molecules, and captures the intrinsic and extrins…

Origin and control of ionic hydration patterns in nanopores Open

Miraslau L. Barabash, W. A. T. Gibby, Carlo Guardiani, Alex Smolyanitsky, D. G. Luchinsky , et al. · 2020

In 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 …

Ionic Coulomb blockade and the determinants of selectivity in the NaChBac bacterial sodium channel Open

O. A. Fedorenko, I. Kh. Kaufman, W. A. T. Gibby, Miraslau L. Barabash, D. G. Luchinsky , et al. · 2020

Mutation-induced transformations of conductivity and selectivity in NaChBac bacterial channels are studied experimentally and interpreted within the framework of ionic Coulomb blockade (ICB), while also taking account of resonant quantised…

Statistical theory of mixed-valence selectivity in biological ion channels Open

W. A. T. Gibby, Miraslau L. Barabash, Carlo Guardiani, Dmitry Luchninsky, P. V. E. McClintock · 2019

In this article we apply our multi-component statistical and linear response theory to the process of mixed-valence ionic transport in a biological sodium ion channel. We analyse the free energy spectra, and statistical fluctuations (which…

Prehistory probability distribution of ionic transitions through a graphene nanopore Open

Carlo Guardiani, Miraslau L. Barabash, W. A. T. Gibby, D. G. Luchinsky, I. A. Khovanov , et al. · 2019

We analyze selective ionic conduction through an artificial nanopore in a single graphene sheet, using molecular dynamics simulations and the prehistory probability distribution. We assess position-dependent changes in the number and orien…

The dynamics of quasiparticles in a toy model of the KcsA biological ion channel Open

Miraslau L. Barabash, W. A. T. Gibby, Carlo Guardiani, D. G. Luchinsky, I. A. Khovanov , et al. · 2019

We study the highly-concerted motion of ions in a narrow biological ion channel (KcsA) by considering the notion of a quasiparticle, with specific focus on the transition process. Namely, we show that the ion entering or exi…

Prehistory probability distribution of ion transition through graphene nanopore Open

Carlo Guardiani, Miraslau L. Barabash, W. A. T. Gibby, D. G. Luchinsky, I. A. Khovanov , et al. · 2019

We analyze selective ionic conduction through an artificial nanopore in a single graphene sheet, using molecular dynamics simulations and the prehistory probability distribution. We assess position-dependent changes in the number and orien…

Theory and Experiments on Multi-Ion Permeation and Selectivity in the NaChBac Ion Channel Open

W. A. T. Gibby, Miraslau L. Barabash, Carlo Guardiani, D. G. Luchinsky, O. A. Fedorenko , et al. · 2019

The highly selective permeation of ions through biological ion channels is an unsolved problem of noise and fluctuations. In this paper, we motivate and introduce a non-equilibrium and self-consistent multi-species kinetic model, with the …

From the Potential of the Mean Force to a Quasiparticle’s Effective Potential in Narrow Ion Channels Open

Miraslau L. Barabash, W. A. T. Gibby, Carlo Guardiani, D. G. Luchinsky, P. V. E. McClintock · 2019

We 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 th…

Exploring the pore charge dependence of K+ and Cl− permeation across a graphene monolayer: a molecular dynamics study Open

Carlo Guardiani, W. A. T. Gibby, Miraslau L. Barabash, D. G. Luchinsky, P. V. E. McClintock · 2019

Increase of graphene pore charge determines decrease of PMF barrier that turns into well: current increases, reaches plateau and declines.

Quantized Dehydration and the Determinants of Selectivity in the NaChBac Bacterial Sodium Channel Open

O. A. Fedorenko, Igor Khaimovich Kaufman, W. A. T. Gibby, D. G. Luchinsky, Stephen K. Roberts , et al. · 2018

A discrete electrostatic/diffusion model has been developed to describe the selective permeation of ion channels, based on ionic Coulomb blockade (ICB) and quantised dehydration (QD). It has been applied to describe selectivity phenomena m…

Statistical theory of selectivity and conductivity in narrow biological ion channels Open

W. A. T. Gibby · 2018

Biological ion channels are essential for maintaining life, and appear as a seemingly paradoxical combination of both large conductivity and strong selection between ionic species. This process involves many complicated interactions, and t…

Kinetic model of selectivity and conductivity of the KcsA filter Open

W. A. T. Gibby, D. G. Luchinsky, I.Kh. Kaufman A. Ward, P. V. E. McClintock · 2017

We introduce a self-consistent multi-species kinetic theory based on the structure of the narrow voltage-gated potassium channel. Transition rates depend on a complete energy spectrum with contributions including the dehydration amongst sp…

Ionic Coulomb blockade and anomalous mole fraction effect in the NaChBac bacterial ion channel and its charge-varied mutants Open

I. Kh. Kaufman, O. A. Fedorenko, D. G. Luchinsky, W. A. T. Gibby, Stephen K. Roberts , et al. · 2017

Background. The selectivity of biological cation channels is defined by a short, narrow selectivity filter, having a negative net fixed charge Qf. Voltage gated bacterial channels (NaChBac and some others) are frequently used in biophysics…

Ionic Coulomb blockade and anomalous mole fraction effect in NaChBac bacterial ion channels Open

I. Kh. Kaufman, O. A. Fedorenko, D. G. Luchinsky, W. A. T. Gibby, Stephen K. Roberts , et al. · 2016

We report an experimental study of the influences of the fixed charge and bulk ionic concentrations on the conduction of biological ion channels, and we consider the results within the framework of the ionic Coulomb blockade model of perme…

Putative resolution of the EEEE selectivity paradox in L-type Ca2+and bacterial Na+biological ion channels Open

I. Kh. Kaufman, D. G. Luchinsky, W. A. T. Gibby, P. V. E. McClintock, Bob Eisenberg · 2016

The highly selective permeation of ions through biological ion channels can be described and explained in terms of fluctuational dynamics under the influence of powerful electrostatic forces. Hence valence selectivity, e.g. between Ca2+ an…

Statistical Theory of Selectivity and Conductivity in Biological Channels Open

D. G. Luchinsky, W. A. T. Gibby, I. Kh. Kaufman, Doǧan A. Timuçin, P. V. E. McClintock · 2016

We present an equilibrium statistical-mechanical theory of selectivity in biological ion channels. In doing so, we introduce a grand canonical ensemble for ions in a channel's selectivity filter coupled to internal and external bath soluti…

Insights into Ion Channel Selectivity with Ionic Coulomb Blockade Open

W. A. T. Gibby, D. G. Luchinsky, I. Kh. Kaufman, P. V. E. McClintock, Aneta Stefanovska , et al. · 2016

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