Related papers: Interacting Ions in Biophysics: Real is not Ideal
We have developed a molecular mean-field theory -- fourth-order Poisson-Nernst-Planck-Bikerman theory -- for modeling ionic and water flows in biological ion channels by treating ions and water molecules of any volume and shape with…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…
Transition metal ions play crucial roles in the structure and function of numerous proteins, contributing to essential biological processes such as catalysis, electron transfer, and oxygen binding. However, accurately modeling the…
The increasingly congested near earth environment requires accurate orbital modelling to prevent collision events that threaten access to space infrastructure. Ionospheric aerodynamics are the largest non-conservative source of orbital…
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…
Nanofluidics, the field interested in flows at the smallest scales, has grown at a fast pace, reaching an ever finer control offluidic and ionic transport at the molecular level. Still, artificial pores are far from reaching the wealth of…
Particle-in-cell (PIC) simulations are widely used as a tool to investigate instabilities that develop between a collisionless plasma and beams of charged particles. However, even on contemporary supercomputers, it is not always possible to…
Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimisation criteria in this information processing can be…
Ionic electrodiffusion and osmotic water flow are central processes in many physiological systems. We formulate a system of partial differential equations that governs ion movement and water flow in biological tissue. A salient feature of…
A new classical interaction potential for water simulations is presented. Water is modeled as a fully dissociable set of atoms with a point dipole, determined self-consistently, on every oxygen atom. The oxygen polarizability is not fixed…
In this tutorial we discuss the chemical potential of ions in water (i.e., in a salt solution, in an electrolyte phase) and inside (charged) nanoporous materials such as porous membranes. In water treatment, such membranes are often used to…
We compute ionic free energy adsorption profiles at aqueous graphene interface by developing a self-consistent approach. To do so, we design a microscopic model for water and put the liquid on an equal footing with the graphene described by…
Anions generally associate more favorably with the air-water interface than cations. In addition to solute size and polarizability, the intrinsic structure of the unperturbed interface has been discussed as an important contributor to this…
Water, a subject of human fascination for millennia, is likely the most studied substance on Earth, with an entire scientific field -- hydrodynamics -- dedicated to understanding water in motion. However, when water flows through…
We extend our previous analysis of holographic heavy ion collisions in non-conformal theories. We provide a detailed description of our numerical code. We study collisions at different energies in gauge theories with different degrees of…
The interaction of streamers in nitrogen-oxygen mixtures such as air is studied. First, an efficient method for fully three-dimensional streamer simulations in multiprocessor machines is introduced. With its help, we find two competing…
Brownian motion of particle interacting with atoms of ideal gas is discussed as a key problem of kinetics lying at the border between ``dead'' systems like the Lorentz gas or formal constructs of conceptual Boltzmannian kinetics and actual…
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…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…
The properties of a partially ionized plasma in a long cylindrical tube subject to a uniform axial electric field are investigated. The plasma is maintained by an external ionizing source balanced by bulk and surface recombinations.…