Related papers: Computing the Field in Proteins and Channels
A model for ionic and electronic grain boundary transport through thin films, scales or membranes with columnar grain structure is introduced. The grain structure is idealized as a lattice of identical hexagonal cells - a honeycomb pattern.…
This study investigates the flux ratios of ionic flows using Poisson-Nernst-Planck (PNP) models. The flux ratio measures the effect of permanent charge on the ion fluxes and can exhibit bifurcation, where a small parameter change causes a…
The extracellular space has an ambiguous role in neuroscience. It is present in every physiologically relevant system and often used as a measurement site in experimental recordings, but it has received subordinate attention compared to the…
The frequency-dependent spectrum of current fluctuations through nano-scale channels is studied using analytical and computational techniques. Using a stochastic Nernst-Planck description and neglecting the interactions between the ions…
Experiments measuring currents through single protein channels show unstable currents, a phenomena called the gating of a single channel. Channels switch between an 'open' state with a well defined single amplitude of current and 'closed'…
Starting with a microscopic (individual-based) Brownian dynamics model of charged particles (ions), its macroscopic description is derived as a system of partial differential equations that govern the evolution of ion concentrations in…
Electrochemical devices often consist of multicomponent electrolyte solutions. Two processes influence the overall dynamics of these devices: the formation of electrical double layers and chemical conversion due to redox reactions. However,…
The microscopic theory of chemical reactions is based on transition state theory, where atoms or ions transfer classically over an energy barrier, as electrons maintain their ground state. Electron transfer is fundamentally different and…
I believe an atomic biology is needed to supplement present day molecular biology, if we are to design and understand proteins, as well as define, make, and use them. Topics in the paper are molecular biology and atomic biology.…
The transport and distribution of charged particles are crucial in the study of many physical and biological problems. In this paper, we employ an Energy Variational Approach to derive the coupled Poisson-Nernst-Planck-Navier-Stokes system.…
A rigorous theory of diffraction scattering from extended objects is proposed. The present theory is based on a multiple asymptotic expansion of an integral equation for the exact wave function in terms of the large parameters of the…
In this letter we analyze the effects of an externally applied electric field on thermal fluctuations for a fluid containing charged species. We show in particular that the fluctuating Poisson-Nernst-Planck equations for charged…
The interpretation electrical phenomena in biomembranes is usually based on the assumption that the experimentally found discrete ion conduction events are due to a particular class of proteins called ion channels while the lipid membrane…
We investigate the effects of the relative dielectric coefficient on ionic flows in open ion channels, using mathematical analysis of reasonably general Poisson-Nernst-Planck type models that can include the finite sizes of ions. The value…
Mobile charge in an electrolytic solution can in principle be represented as the divergence of ionic polarization. After adding explicit solvent polarization a finite volume of electrolyte can then be treated as a composite non-uniform…
Voltage gated channel proteins cooperate in the transmission of membrane potentials between nerve cells. With the recent progress in atomic-scaled biological chemistry it has now become established that these channel proteins provide highly…
Membrane protein transporters alternate their substrate-binding sites between the extracellular and cytosolic side of the membrane according to the alternating access mechanism. Inspired by this intriguing mechanism devised by nature, we…
We describe an open source software which we have realized and made publicly available at the website http://jljp.sourceforge.net. It provides the potential difference and the ion fluxes across a liquid junction between the solutions of two…
The description of a conducting medium in thermal equilibrium, such as an electrolyte solution or a plasma, involves nonlinear electrostatics, a subject rarely discussed in the standard electricity and magnetism textbooks. We consider in…
A new computational method is presented for study suspensions of charged soft particles undergoing fluctuating hydrodynamic and electrostatic interactions. The proposed model is appropriate for polymers, proteins and porous particles…