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Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations…
Using a stochastic generalization of the Hodgkin–Huxley model, we consider the influence of intrinsic channel noise on the synchronization between the spiking activity of the excitable membrane and an externally applied periodic…
Potassium and sodium ions are crucial for many physiological processes in living systems and play different roles when interacting with proteins and enzymes. Intracellular concentration of potassium is always maintained higher than that of…
The influence of the salts KCl, NaCl, and NaI at molar concentrations on the {\alpha}-helical folding kinetics of the alanine-based oligopeptide Ace-AEAAAKEAAAKA-Nme is investigated by means of (explicit-water) molecular dynamics…
Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately…
We investigate out of equilibrium stationary distributions induced by a stochastic dichotomous noise on double and multi-well models for ion channels. Ion-channel dynamics is analyzed both through over-damped Langevin equations and master…
In these companion papers, we study how the interrelated dynamics of sodium and potassium affect the excitability of neurons, the occurrence of seizures, and the stability of persistent states of activity. In this first paper, we construct…
Potassium (K-) channels catalyze K+ ion permeation across cellular membranes while simultaneously discriminating their permeation over Na+ ions by more than a factor of a thousand. Structural studies show bare K+ ions occupying the…
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…
The activation of a $K^+$ channel sensor in two sequential stages during a voltage clamp may be described as the translocation of a Brownian particle in an energy landscape with two large barriers between states. A solution of the…
In the present study, the ionic transport and selectivity of electrokinetically-driven flow of power-law fluids in a long pH-regulated rectangular nanochannel are analyzed. The electrical potential and momentum equations are numerically…
Action potential generation underlies some of the most consequential dynamical systems on Earth, from brains to hearts. It is therefore interesting to develop synthetic cell-free systems, based on the same molecular mechanisms, which may…
The effect of intrinsic channel noise is investigated for the dynamic response of a neuronal cell with a delayed feedback loop. The loop is based on the so-called autapse phenomenon in which dendrites establish not only connections to…
We identify a unifying measure for stochastic resonance (SR) in voltage dependent ion channels which comprises periodic (conventional), aperiodic and nonstationary SR. Within a simplest setting, the gating dynamics is governed by two-state…
We suggest that the propagation of the action potential is driven by a pressure pulse propagating in the axoplasm along the axon length. The pressure pulse mechanically activates Na ion channels embedded in the axon membrane. This…
The non-selective voltage activated cation channel from the human red cells, which is activated at depolarizing potentials, has been shown to exhibit counter-clockwise gating hysteresis. We have analyzed the phenomenon with the simplest…
Fundamentally, action potentials in the squid axon are consequence of the entrance of sodium ions during the depolarization of the rising phase of the spike mediated by the outflow of potassium ions during the hyperpolarization of the…
A hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of…
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…
Excitability is an attribute of life, and is a driving force in the descent of complexity. Cellular electrical activity as realized by membrane proteins that act as either channels or transporters is the basis of excitability. Electrical…