Related papers: Tuning ion coordination preferences to enable sele…
The formation of complexes between like-charged polyelectrolytes challenges conventional electrostatic intuition and highlights the central role of ions in mediating macromolecular organization. Here, we investigate the salt-dependent…
We are interested in the subtle variations of function among the members of a protein family. A protein family is usually subdivided into subfamilies based on functional differences. Existence of this functional diversity is essential for…
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…
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.…
For a wide range of modern soft functional materials the selective transport of sub-nanometer-sized molecules (`penetrants') through a stimuli-responsive polymeric membrane is key to the desired function. In this study, we investigate the…
The interplay between intra-molecular H-O covalent bond contraction, due to molecular under-coordination, and inter-molecular O:H expansion, due to inter-electron pair Coulomb repulsion, has been shown to be the source of the anomalous…
A quantized physical framework, called the five-anchor model, is developed for a general understanding of the working mechanism of ion channels. According to the hypotheses of this model, the following two basic physical principles are…
Electrostatic interaction between ions in an ionic channel and the charge fluctuations in the channel mouth are considered. It is shown that the charge fluctuations can be enhanced in the channels with low dielectric constant and result in…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
We review modeling of astrocyte ion dynamics with a specific focus on the implications of so-called spatial potassium buffering, where excess potassium in the extracellular space (ECS) is transported away to prevent pathological neural…
Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water has been a challenging task from ab initio molecular dynamics (AIMD). The difficulty mainly comes from a lack of accurate and efficient…
The influence of intrinsic channel noise on the spontaneous spiking activity of poisoned excitable membrane patches is studied by use of a stochastic generalization of the Hodgkin-Huxley model. Internal noise stemming from the stochastic…
The distribution of ions at the air/water interface plays a decisive role in many natural processes. It is generally understood that polarizable ions with low charge density are surface-active, implying they sit on top of the water surface.…
Ionic Coulomb blockade in nanopores is a phenomenon that shares some similarities but also differences with its electronic counterpart. Here, we investigate extensively this phenomenon using all-atom molecular dynamics of ionic transport…
Electrical neural signalling typically takes place at the time-scale of milliseconds, and is typically modeled using the cable equation. This is a good approximation for processes when ionic concentrations vary little during the time course…
We study the permeability and selectivity (`permselectivity') of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations. The permeability…
Clays control carbon, water and nutrient transport in the lithosphere, promote cloud formation5 and lubricate fault slip through interactions among hydrated mineral interfaces. Clay mineral properties are difficult to model because their…
The concentration of intracellular calcium ion (Ca$^{2+}$) exhibits complex oscillations, including bursting and chaos, as observed experimentally. These dynamics are influenced by inherent fluctuations within cells, which serve as crucial…
The intricate role of shear viscosity and ion-pair relaxations on ionic conductivity mechanisms and the underlying changes induced by salt concentration ($c$) in organic liquid electrolytes remain poorly understood despite their widespread…
Understanding the molecular and electronic structure of electrolytes at interfaces requires an analysis of the interactions between the electrode surface, the ions, and the solvent environment on equal footing. Here, we tackle this…