Related papers: Interacting Ions in Biophysics: Real is not Ideal
Water adopts many different crystal structures in its solid form. These provide insight into potential structures of water even in its liquid phase, and they can be used to calibrate pair potentials used for simulation of water. In crowded…
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
Studying chemical reactions at very low temperatures is of importance for the understanding of fundamental physical and chemical processes. At very low energies, collisions are dominated by only a few partial waves. Thus, studies in this…
It is economical to devise ways and means to simplify a multi-species particle system. The single fluid MHD description of a plasma is sufficiently adequate to study plasma phenomena . A plasma containing multi-species of particles can also…
A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…
Accurate modeling of aqueous monovalent ions is essential for understanding the function of biomolecules, such as nucleic acid stability and binding of charged drugs to protein targets. The 1D and 3D reference interaction site models (1D-…
Electrostatic interactions involving proteins depend not just on the ionic charges involved but also on their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of…
We propose a platform for observing and controlling the interactions between atomic ions and a quantum gas of polar molecules in the ultracold regime. This approach is based on the combination of several recently developed methods in two…
Identifying universal properties of non-equilibrium quantum states is a major challenge in modern physics. A fascinating prediction is that classical hydrodynamics emerges universally in the evolution of any interacting quantum system.…
The formation of dynamical patterns is one of the most striking features of nonequilibrium physical systems. Recent work has shown that such patterns arise generically from forces that violate Newton's third law, known as nonreciprocal…
Ionic transport in nanopores or nanochannels is key to many cellular processes and is now being explored as a method for DNA/polymer sequencing and detection. Although apparently simple in its scope, the study of ionic dynamics in confined…
Accurate calculations of electrostatic potentials and treatment of substrate polarizability are critical for predicting the permeation of ions inside water-filled nanopores. The {\it ab initio} molecular dynamics method (AIMD), based on…
We calculate the ion and composition distributions around colloid particles in an aqueous mixture, accounting for preferential adsorption, electrostatic interaction, selective solvation among ions and polar molecules, and…
The computational treatment of many-electron systems capable of exchanging {electrons and nuclei} with the environment represents one of the outermost frontiers in simulation methodology. The exchanging process occurs in a large variety of…
Soft matter materials, such as polymers, membranes, proteins, are often electrically charged. This makes them water soluble, which is of great importance in technological application and a prerequisite for biological function. We discuss a…
The energy and baryon densities in heavy ion collisions are estimated by analytically solving a 1+1 dimensional hydrodynamical model with source terms. Particularly, a competition between the energy and baryon sources and the expansion of…
Experience shows that disciplinary science cannot describe life without contradictions. We show that one of the fundamental reasons is the disciplinarity itself: the disciplines deal with a limited set of quantities. This way some 'outlaw'…
Using molecular dynamics simulations and methods of importance sampling, we study the thermodynamics and dynamics of sodium chloride in the aqueous premelting layer formed spontaneously at the interface between ice and its vapor. We uncover…
The theory of real relativistic fluids is in the rather unique situation that there is a natural relativistic extension of the nonrelativistic theory, but it is physically untenable. On the other hand, mounting evidence that matter created…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…