Ionic atomistic simulation

Bhargava, B.L., and Balasubramanian, S., Refined potential model for atomistic simulations of ionic liquid, /. Chem. Phys., 127, 114510, 2007. 

S Atomistic simulation assisted synthesis and investigations The classical atomistic simulation techniques based on the pair potentials are suitable for the simulations of ceria nanoparticles even with a real sized model. Molecular d)mamics studies with several thousands of ions and up to hundreds of nanoseconds in a time scale have been carried out to interpret the diffusion, and crystal growth behaviors for pure and doped-ceria nanoparticles. Traditionally, the technique has been used to explore the oxygen ionic conductivity in ionic conductors such as ceria and zirconia (Maicaneanu et al., 2001 Sayle et al., 2006). 

The nature and energetics of electronic defects are major factors which control the properties of high-temperature superconductors. Atomistic simulation techniques allow an estimation of the formation energies of these defects. Within the framework of an ionic model, valence band holes are described in localized terms as Cu3 + (hCu) or 0 (h0) and defect electrons as Cu + (eCu)- The formation energy of these defects involves a contribution from the ionization potential/electron affinity of the appropriate ion in addition to a lattice energy term (including the effects of relaxation) and a band contribution, in the case of delocalized carriers (large polarons). 

Atomistic Potential Models for Ionic Liquid Simulations... 

Atomistic Simulations of Neat Ionic Liquids - Structure and Dynamics... 

In summary, the MRG-CG procedure is a systematic and reliable general approach to optimizing the interactions potentials for DNA and ions, reproducing important physical observables that characterize the Hamiltonian itself. This, in turn, leads to the similarity of the structural fluctuations of the macromolecule obtained from the CG and fully atomistic simulations. Application of this technique to coarse-graining DNA molecules resulted in a model that can be used reliably describe the DNA s structural dynamics, including complex anharmonic local deformations of the DNA chains. Likewise, this model also accurately describes the distribution of mobile ions around the DNA molecules and reproduces the experimentally measured dependence of DNA chain s persistence length on the solution ionic strength. 

Early atomistic simulations employed pair potentials, usually of the Morse or Lennard-jones type (Figure 11.6). Although such potentials have been and still are a useful model for fundamental studies of generic properties of materials, the agreement between simulation results and experiment can only be quantitative at best. While such potentials can be physically justified for inert elements and perhaps some ionic solids, they do not capture the nature of interatomic bonding even in simple metals, not to mention transition metals or covalent solids. 

For ionic oxides like these, empirical ion pair potentials can be used to perform atomistic simulations. Defect structures due to oxygen vacancies created by substitution of La + by divalent cations such as Ca, Sr, or Ba + can be simulated with these potentials. Evain et al. used empirical atom-atom... 

An atomistic simulation MD simulation of a common carbonate-based organic electrolyte, ethylene carbonate dimethyl carbonate (EC DMC = 3 7) with approximately 1 mol/kg LiPFs, referred to as the organic liquid electrolyte or OLE, and an ionic liquid-based electrolyte (ILE), 1-ethyl 3-methyl-imidazolium bis (fluorosulfonyl)imide (EMIM iFSE) with 1 mol/kg LiFSI, in contact with LiFeP04 has been carried out [107]. Simulations were carried out using quantum chemistry-based polarizable force at 363 K on a 3-D periodic orthorhombic... 

Kelkar MS, Shi W, Maginn EJ (2008) Determining the accuracy of classical force fields for ionic liquids atomistic simulation of the thermodynamic and transport properties of 1-ethyl-3-methylimidazolium ethylsulfate ([emim][EtS04]) and its mixtures with water. Ind Eng Chem Res 47 9115-9126... 

Atomistic Simulation. The simplest models of surfaces are based on an ionic model in which the structure of the surface is largely controlled by electrostatic considerations. In these cases, the electrostatic interaction between ions can be modeled using periodic adaptations of the Coulombic sum, usually the Ewald sum for the 3D periodic slab calculations and its 2D adaptations for dedicated surface simulation codes such as METADISE (397) and MARVIN (398). The inclusion of anion polarizability via the shell model is easily incorporated into these calculations since the shell can be treated as an additional interaction center and its interaction with its own core subtracted after the periodic sum has been carried out. 

The recent development of high-resolution experimental techniques allows for the structural analysis of protein channels with unprecedented detail. However, the fundamental problem of relating the structure of ion channels to their function is a formidable task. This chapter describes some of the most popular simulation approaches used to model channel systems. Particle-based approaches such as Brownian and molecular dynamics will continue to play a major role in the study of protein channels and in validating the results obtained with the extremely fast continuum models. Research in the area of atomistic simulations will focus mainly on the force-field schemes used in the ionic dynamics simulation engines. In particular, polar interactions between the various components of the system need to be computed with algorithms that are more accurate than those currently used. The effects of the local polarization fields need to be accounted for explicitly and, at the same time, efficiently. Continuum models will remain attractive for their efficiency in depicting the electrostatic landscape of protein channels. Both Poisson-Boltzmann and Poisson-Nemst-Plank solvers will continue to be used to... 

Maginn EJ (2007) Atomistic simulation of the thermodynamic and transport properties of Ionic Liquids. Acc Chem Res 40 1200-1207... 

Shi, W. and Maginn, E. J., Atomistic simulation of the absorption of carbon dioxide and water in the ionic liquid l-n-hexyl-3-methylimidazoliumbis(trifluoroinethylsulfonyl)iinide ([hmim][Tf2N], J. Phys. Chem. B 112, 2045-2055 (2008). 

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