Ionic screening in bulk and under confinement.

Recent experiments have shown that the repulsive force between atomically flat, like-charged surfaces confining room-temperature ionic liquids or concentrated electrolytes exhibits an anomalously large decay length. In our previous publication [J. Zeman, S.

Bulk ionic screening lengths from extremely large-scale molecular dynamics simulations.

Recent experiments have reported anomalously large screening lengths of interactions between charged surfaces confining concentrated electrolytes and ionic liquids. Termed underscreening, this effect was ascribed to bulk properties of dense ionic systems. Herein, we study bulk ionic screening with extremely large-scale molecular dynamics simulations, allowing us to assess the range of distances relevant to the experiments.

It's a match! Simulating compatibility-based learning in a network of networks.

In this article, we develop a new way to capture knowledge diffusion and assimilation in innovation networks by means of an agent-based simulation model. The model incorporates three essential characteristics of knowledge that have not been covered entirely by previous diffusion models: the network character of knowledge, compatibility of new knowledge with already existing knowledge, and the fact that transmission of knowledge requires some form of attention. We employ a network-of- networks approach, where agents are located within an innovation network and each agent itself contains another network composed of knowledge units (KUs).

A polarizable MARTINI model for monovalent ions in aqueous solution.

We present a new polarizable coarse-grained martini force field for monovalent ions, called refIon, which is developed mainly for the accurate reproduction of electrostatic properties in aqueous electrolyte solutions. The ion model relies on full long-range Coulomb interactions and introduces satellite charges around the central interaction site in order to model molecular polarization effects. All force field parameters are matched to reproduce the mass density and the static dielectric permittivity of aqueous NaCl solutions, such that experimental values are well-reproduced up to moderate salt concentrations of .

First-Principles Parametrization of Polarizable Coarse-Grained Force Fields for Ionic Liquids.

We present an ab initio parametrization scheme for explicitly dipole-polarizable force fields for the simulation of molecular liquids. The scheme allows for, in principle, arbitrarily coarse-grained representations. All parameters in the force field are derived from first-principles, based on simple physical arguments.

A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate.

We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range.

Validation of Trimethylamine-N-oxide (TMAO) Force Fields Based on Thermophysical Properties of Aqueous TMAO Solutions.

Five molecular models for trimethylamine N-oxide (TMAO) to be used in conjunction with compatible models for liquid water are evaluated by comparison of molecular dynamics (MD) simulation results to experimental data as functions of TMAO molality. The experimental data comprise thermodynamic properties (density, apparent molar volume, and partial molar volume at infinite dilution), transport properties (self-diffusion and shear viscosity), structural properties (radial distribution functions and degree of hydrogen bonding), and dielectric properties (dielectric spectra and static permittivity). The thermodynamic and transport properties turned out to be useful in TMAO model discrimination while the influence of the water model and the TMAO-water interaction are effectively probed through the calculation of dielectric spectra.

Preferential solvation and ion association properties in aqueous dimethyl sulfoxide solutions.

We study the solvation and the association properties of ion pairs in aqueous dimethyl sulfoxide (DMSO) solution by atomistic molecular dynamics (MD) simulations. The ion pair is composed of two lithium and a single sulfonated diphenyl sulfone ion whose properties are studied under the influence of different DMSO concentrations. For increasing mole fractions of DMSO, we observe a non-ideal behavior of the solution as indicated by the derivatives of the chemical activity.

Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA.

Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-5-protein (G5P) to a single-stranded DNA (dT25).

Nudged-elastic band used to find reaction coordinates based on the free energy.

Transition paths characterize chemical reaction mechanisms. In this paper, we present a new method to find mean reaction paths based on the free energy. A nudged elastic band (NEB) is optimized using gradients and Hessians of the free energy, which are obtained from umbrella integration.