Ion transport between two baths of fixed ionic concentrations and applied electrostatic (ES) potential is analysed using a one-dimensional drift-diffusion (Poisson–Nernst–Planck, PNP) system designed to model biological ion channels. The ions are described as charged, hard spheres with excess chemical potentials computed from equilibrium density functional theory (DFT). method Rosenfeld (Rosenfeld Y 1993 J. Chem. Phys. 98 8126) generalized calculate the ES in A numerical algorithm for...

Nanotubes can selectively conduct ions across membranes to make ionic devices with transport characteristics similar biological ion channels and semiconductor electron devices. Depending on the surface charge profile of nanopore, ohmic resistors, rectifiers, diodes be made. Here we show that a uniformly charged conical nanopore have all these properties by changing species their concentrations each side membrane. Moreover, cation versus anion selectivity pores changed. We find polyvalent...

An approximate electrostatic (ES) excess free energy functional for charged, hard sphere fluids is presented. This designed systems with large density variations, but may also be applied to without such variations. Based on the Rosenfeld method of perturbation about a bulk (homogeneous) reference fluid [Y. Rosenfeld, J. Chem. Phys. 98, 8126 (1993)], new ES replaces densities particle densities, called RFD functional. The first-order direct correlation function (DCF) in computed using as...

It is proposed that the layering of large ions at wall/liquid interface nanofluidic channels can be used to achieve high efficiency (possibly >50%) in conversion hydrostatic energy into electrical power. Large tend produce peaks and troughs their concentration profiles charged walls, producing concentrations far from walls where ions' pressure-driven velocity high. This increases streaming conductance efficiency.

The efficient calculation of induced charges in an inhomogeneous dielectric is important simulations and coarse-grained models molecular biology, chemical physics, electrochemistry. We present the charge computation (ICC) method for polarization based on variational formulation Allen et al. [Phys. Chem. Phys. 3, 4177 (2001)]. give a different solution their extremum condition that produces matrix formulation. are directly calculated by solving linear equation Ah=c, where h contains...

Biological ion channels are proteins that passively conduct ions across membranes otherwise impermeable to ions. Here, we present a model of permeation and selectivity through single, open ryanodine receptor (RyR) channel. Combining recent mutation data with electrodiffusion finite-sized ions, the reproduces current/voltage curves cardiac RyR (RyR2) in KCl, LiCl, NaCl, RbCl, CsCl, CaCl2, MgCl2, their mixtures over large concentrations applied voltage ranges. It also reduced K+ conductances...

Ion channels are proteins with a narrow hole down their middle that control wide range of biological function by controlling the flow spherical ions from one macroscopic region to another. do not change conformation on time scale once they open, so can be described combination Poisson and drift-diffusion (Nernst-Planck) equations called PNP in biophysics. We use singular perturbation techniques analyse steady-state system for channel general geometry piecewise constant permanent charge...

A physical model of selective “ion binding” in the L-type calcium channel is constructed, and consequences are compared with experimental data. This reduced treats only ions carboxylate oxygens EEEE locus explicitly restricts interactions to hard-core repulsion ion–ion ion–dielectric electrostatic forces. The structural atoms provide a flexible environment for passing cations, thus resulting self-organized induced-fit selectivity filter. Experimental conditions involving binary mixtures...

Density functional theory (DFT) of electrolytes is applied to the electrical double layer under a wide range conditions. The ions are charged, hard spheres different size and valence, wall creating uncharged, weakly strongly charged. Under all conditions, density electrostatic potential profiles calculated using recently proposed RFD (Gillespie et al 2002 J. Phys.: Condens. Matter 14 12129; 2003 Phys. Rev. E 68 031503) compare well Monte Carlo simulations. When results agree with simpler...

Calcium-selective ion channels are known to have carboxylate-rich selectivity filters, a common motif that is primarily responsible for their high Ca2+ affinity. Different affinities ranging from micromolar (the L-type Ca channel) millimolar ryanodine receptor closely related the different physiological functions of these channels. To understand physical mechanism this range given similar amino acids in we use grand canonical Monte Carlo simulations assess binding monovalent and divalent...

Monte Carlo simulation and density functional theoretical (DFT) results are reported for the selective adsorption of two competing cationic species at a highly charged planar interface. The cations differ in both their diameter (2 4.25 Å) valence (mono- divalent). Our show that general smaller or divalent cation is preferentially adsorbed electrode. In case when ion larger monovalent smaller, we find competitive situation: lower surface charges electrostatic advantage ions dominates, whereas...

Calcium-selective ion channels often contain a selectivity filter made of similar amino acids, rich in carboxlylates, although the ${\mathrm{Ca}}^{2+}$ affinities these range from micromolar to millimolar. To understand physical mechanism for this affinities, we use grand canonical Monte Carlo simulations study competition ${\mathrm{Na}}^{+}$ and reduced model Ca channel. We show that affinity is increased dramatically when both volume dielectric coefficient protein are reduced.

Classical density functional theory (DFT) of fluids is a valuable tool to analyze inhomogeneous fluids. However, few numerical solution algorithms for three-dimensional systems exist. Here we present an efficient scheme charged, hard spheres that uses O(N log N) operations and O(N) memory, where N the number grid points. This system-size scaling significant because very large required systems. The algorithm fast Fourier transforms (FFTs) evaluate convolutions DFT Euler–Lagrange equations...

In cardiac muscle, Ca(2+)-induced Ca(2+) release (CICR) from the sarcoplasmic reticulum (SR) is mediated by ryanodine receptor (RyR) channels. The inherent positive feedback of CICR normally well-controlled. Understanding this control mechanism a priority because its malfunction has life-threatening consequences.We show that local governed SR load, largely load determines single RyR current amplitude drives inter-RyR CICR.We differentially manipulated flux and in permeabilized ventricular...

We propose a procedure to compute the steady-state transport of charged particles based on Nernst-Planck (NP) equation electrodiffusion. To close NP and establish relation between concentration electrochemical potential profiles, we introduce Local Equilibrium Monte Carlo (LEMC) method. In this method, Grand Canonical simulations are performed using specified for distinct volume elements. An iteration that self-consistently solves flux continuity equations with LEMC is shown converge...

A functional for the electrostatic excess free-energy charged, hard sphere fluids is proposed. The derived from two complementary, but equivalent, interpretations of mean spherical approximation (MSA). first combines fundamental measure theory (FMT) hard-core interactions with idea that MSA can be interpreted in terms interaction shells charge. This formulation gives density as a function weighted densities. When all ions have same size, adopts an FMT-like form. second effect...

Significance We show that calsequestrin, the main Ca 2+ storing protein of muscle, is polymerized inside sarcoplasmic reticulum (SR) and its mobility increases greatly upon SR depletion, indicating depolymerization. Deep depletion causes massive calsequestrin migration radical remodeling, often accompanied by a surge in intra-SR free . The changes polymerization observed aqueous solutions therefore also occur vivo. These help explain some uniquely advantageous properties as source calcium...

Biological L-type calcium channels selectively accumulate Ca2+, even when there is 105 more Na+ in the surrounding electrolyte solution. Like other Ca2+-chelating molecules, channel has four carboxylate groups that contain eight oxygen ions. In this modeling study, these oxygens are confined to a small subvolume of protein (the “filter”) embedded bulk solution “bath”). With system equilibrium, concentrations ions and water filter computed, given their bath. The excess thermodynamic...