Related papers: Crowded Charges in Ion Channels
Ionic transport in nanopores is a fundamentally and technologically important problem in view of its occurrence in biological processes and its impact on novel DNA sequencing applications. Using microscopic calculations, here we show that…
Over the past few decades the experimental literature has consistently reported observations of attraction between like-charged colloidal particles and macromolecules in solution. Examples include nucleic acids and colloidal particles in…
Bioelectrochemical systems are electrochemical cells that rely on conductive biofilms covering an electrode. We consider the example of a microbial fuel cell, and we derive a dynamic model of ion transport, biochemical reactions and…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
The Poisson-Boltzmann mean-field description of ionic solutions has been successfully used in predicting charge distributions and interactions between charged macromolecules. While the electrostatic model of charged fluids, on which the…
The presence of chirality in the main molecules of life may well be not just a structural artifact, but of pure biological advantage. The possibility of the existence of a phenomenon of a special mode of interaction, labeled as "chiral…
Electrolytes play an important role in a plethora of applications ranging from energy storage to biomaterials. Notwithstanding this, the structure of concentrated electrolytes remains enigmatic. Many theoretical approaches attempt to model…
We have studied the dynamics of chloride and potassium ions in the interior of the OmpF porin under the influence of an external electric field. From the results of extensive all-atom molecular dynamics simulations of the system we computed…
Inhomogeneity of ion correlation widely exists in many physicochemical, soft matter, and biological systems. Here, we apply the modified Gaussian renormalized fluctuation theory to study the classic example of the vapor-liquid interface of…
Classical molecular dynamics and electro-diffusion theories have achieved profound success in elucidating ion selectivity and gating mechanisms. However, reconciling strict selectivity with high flux permeation in Angstrom-scaled biological…
Life has a special status, it even has its own science: biology. In many ways, the logic of life seems to differ from that of atoms, molecules, planets, or any other `inanimate object'. However, life is increasingly measured using…
The solvation structures and ion dynamics of CaCl$_2$ aqueous electrolytes have been investigated using ab initio molecular dynamics simulations and molecular dynamics simulations with deep learning potentials. We found multiple solvation…
We have used molecular simulation and methods of importance sampling to study the thermodynamics and kinetics of ionic charge separation at a liquid water-metal interface. We have considered this process using canonical examples of two…
The physiology of voltage gated ion channels is complex and insights into their gating mechanism is incomplete. Their function is best represented by Markov models with relatively large number of distinct states that are connected by…
Charge regulation is a fundamental mechanism in most chemical, geochemical, and biochemical systems. Various minerals surfaces and proteins are well-known to change their charge state as a function of the activity of the hydronium ions,…
We give an explicit formula for the membrane potential of cells in terms of the intracellular and extracellular ionic concentrations, and derive equations for the ionic currents that flow through channels, exchangers and electrogenic pumps.…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
Ionic liquids are widely used as electrolytes in electrochemical devices. In this context, many experimental and theoretical approaches have been recently developed for characterizing their interface with electrodes. In this perspective…
Electrostatic interaction between ions in an ionic channel and the charge fluctuations in the channel mouth are considered. It is shown that the charge fluctuations can be enhanced in the channels with low dielectric constant and result in…
Machine learning has emerged as a powerful tool in atomistic simulations, enabling the identification of complex patterns in molecular systems limiting human intervention and bias. However, the practical implementation of these methods…