相关论文: A potassium ion channel simulated with a universal…
The molecular mechanism of ion channel gating and substrate modulation is elusive for many voltage gated ion channels, such as eukaryotic sodium ones. The understanding of channel functions is a pressing issue in molecular biophysics and…
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…
The S$_2$ site of the KcsA K$^+$ channel has eight carbonyl ligands in the ion-binding site. A recent study suggests that the K$^+$-over-Na$^+$ selectivity of the S$_2$ site can be understood by noting the larger free energy change involved…
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…
The Hurst effect in the signals describing ion channels' activity has been known for many years. This effect is present in the experimental recordings of single-channel currents, but not only. The sequences of dwell times of functionally…
Ion channels are proteins with holes down their middle that control the flow of ions and electric current across otherwise impermeable biological membranes. The flow of sodium, potassium, calcium (divalent), and chloride ions have been…
Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for studying ion transport through biological ion channels. PNPF contains many more correlations than most models and simulations of channels, because…
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…
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, we here applied dissipation-corrected targeted Molecular…
We investigate calcium signaling feedback through calcium-activated potassium channels of a dendritic spine by applying the immersed boundary method with electrodiffusion. We simulate the stochastic gating of such ion channels and the…
We report Molecular Dynamics (MD) simulations of a generic hydrophobic nanopore connecting two reservoirs which are initially at different Na+ concentrations, as in a biological cell. The nanopore is impermeable to water under equilibrium…
A Poisson-Nernst-Planck-Fermi (PNPF) theory is developed for studying ionic transport through biological ion channels. Our goal is to deal with the finite size of particle using a Fermi like distribution without calculating the forces…
Traditionally, calcium dynamics in neurons are modeled using partial differential equations (PDEs) and ordinary differential equations (ODEs). The PDE component focuses on reaction-diffusion processes, while the ODE component addresses…
Within the framework of Kohn-Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated…
Molecular dynamics simulations are used to study the occupancy and flow of water through nanotubes comprised of hydrophobic and hydrophilic atoms, which are arranged on a honeycomb lattice to mimic functionalized carbon nanotubes (CNTs). We…
Ion channels are of major interest and form an area of intensive research in the fields of biophysics and medicine since they control many vital physiological functions. The aim of this work is on one hand to propose a fully stochastic and…
Interface-specific hydrogen- (H-)bonding network of water next to a substrate (including air) directly controls the energy transfer and chemical reaction pathway at many charged aqueous interfaces. Yet, experimental characterization of such…
The accumulation of potassium in the extracellular space surrounding nerve cells is a fundamental aspect of biophysics that has garnered significant attention in recent research. This phenomenon holds implications for various neurological…
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…
Nanofluidic transport is ubiquitous in natural systems from extra-cellular communication in biology to geological phenomena, and promotes the emergence of new technologies such as energy harvesting and water desalination. While experimental…