6,444 research outputs found
From Structure to Function in Open Ionic Channels
We consider a simple working hypothesis that all permeation properties of
open ionic channels can be predicted by understanding electrodiffusion in fixed
structures, without invoking conformation changes, or changes in chemical
bonds. We know, of course, that ions can bind to specific protein structures,
and that this binding is not easily described by the traditional electrostatic
equations of physics textbooks, that describe average electric fields, the
so-called `mean field'. The question is which specific properties can be
explained just by mean field electrostatics and which cannot. I believe the
best way to uncover the specific chemical properties of channels is to invoke
them as little as possible, seeking to explain with mean field electrostatics
first. Then, when phenomena appear that cannot be described that way, by the
mean field alone, we turn to chemically specific explanations, seeking the
appropriate tools (of electrochemistry, Langevin, or molecular dynamics, for
example) to understand them. In this spirit, we turn now to the structure of
open ionic channels, apply the laws of electrodiffusion to them, and see how
many of their properties we can predict just that way.Comment: Nearly final version of publicatio
Modeling and Simulation of Thermo-Fluid-Electrochemical Ion Flow in Biological Channels
In this article we address the study of ion charge transport in the
biological channels separating the intra and extracellular regions of a cell.
The focus of the investigation is devoted to including thermal driving forces
in the well-known velocity-extended Poisson-Nernst-Planck (vPNP)
electrodiffusion model. Two extensions of the vPNP system are proposed: the
velocity-extended Thermo-Hydrodynamic model (vTHD) and the velocity-extended
Electro-Thermal model (vET). Both formulations are based on the principles of
conservation of mass, momentum and energy, and collapse into the vPNP model
under thermodynamical equilibrium conditions. Upon introducing a suitable
one-dimensional geometrical representation of the channel, we discuss
appropriate boundary conditions that depend only on effectively accessible
measurable quantities. Then, we describe the novel models, the solution map
used to iteratively solve them, and the mixed-hybrid flux-conservative
stabilized finite element scheme used to discretize the linearized equations.
Finally, we successfully apply our computational algorithms to the simulation
of two different realistic biological channels: 1) the Gramicidin-A channel
considered in~\cite{JeromeBPJ}; and 2) the bipolar nanofluidic diode considered
in~\cite{Siwy7}
Recommended from our members
How Water's Properties Are Encoded in Its Molecular Structure and Energies.
How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties
Roadmap on semiconductor-cell biointerfaces.
This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world
A Conservative Finite Difference Scheme for Poisson-Nernst-Planck Equations
A macroscopic model to describe the dynamics of ion transport in ion channels
is the Poisson-Nernst-Planck(PNP) equations. In this paper, we develop a
finite-difference method for solving PNP equations, which is second-order
accurate in both space and time. We use the physical parameters specifically
suited toward the modelling of ion channels. We present a simple iterative
scheme to solve the system of nonlinear equations resulting from discretizing
the equations implicitly in time, which is demonstrated to converge in a few
iterations. We place emphasis on ensuring numerical methods to have the same
physical properties that the PNP equations themselves also possess, namely
conservation of total ions and correct rates of energy dissipation. We describe
in detail an approach to derive a finite-difference method that preserves the
total concentration of ions exactly in time. Further, we illustrate that, using
realistic values of the physical parameters, the conservation property is
critical in obtaining correct numerical solutions over long time scales
- …