Atomistic level modeling

Coarse-grained (CG) models have proven to be useful in many fields of chemical research [1-10], allowing molecular simulations to be performed on larger system sizes and access longer timescales than is possible with atomistic-level models. 

Surprisingly, no atomistic-level modelling has been published on the topic of carbon corrosion. 

In addition to the MD method, a wealth of Monte Carlo methods is used also at the atomistic level [6]. They use essentially the same models, force fields, for polymers. Their main advantage, however, is that by introduction of clever moves one can beat the slow physical dynamics of the systems and can run through phase space much faster than by MD. These methods are still in their infancy, but will certainly become more important. 

From this short discussion, it is clear that atomistically detailed molecular dynamics or Monte Carlo simulations can provide a wealth of information on systems on a local molecular atomistic level. They can, in particular, address problems where small changes in chemical composition have a drastic effect. Since chemical detail is avoided in mesoscopic models, these can often capture such effects only indirectly. 

In order to ensure accurate CG potentials, one needs to conduct MD simulations with a reliable atomistic potential model. The most desirable theoretical approach for the atomistic-scale simulations would be to use a level of quantum mechanics (QM) that can treat both intermolecular and intramolecular interactions with acceptable accuracy. Realistically, the minimal QM levels of theory that can adequately treat all different types of chemical forces are second order perturbation theory [32] (MP2)... 

The so-called micromodels are models of a particular component, or of a part of a cell component, conducted at molecular or atomistic level. Due to the high level of detail related to the material properties and characteristics, the information provided by such models is usually limited to the specific phenomenon analyzed, and provides only limited indications on the resulting fuel cell performance and operating conditions. However, the results of such models play a fundamental role in understanding, analyzing and designing improved solutions for SOFC. Moreover, the results of such analyses may be used as an input for macro-models, i.e. models conducted at fuel cell level. 

Classical molecular simulation methods such as MC and MD represent atomistic/molecular-level modeling, which discards the electronic degrees of freedom while utilizing parameters transferred from quantum level simulation as force field information. A molecule in the simulation is composed of beads representing atoms, where the interactions are described by classical potential functions. Each bead has a dispersive pair-wise interaction as described by the Lennard-Jones (LJ) potential, ULj(Ly) ... 

Atomistic MD models can be extended to the coarse-grained level introduced in the previous section, which is determined by the dimension of the backbone chain and branch. For the precise description of water molecular behavior, simple point charge (SPC) model was adopted (Krishnan et al., 2001), which can be used to simulate complex composition systems and quantitatively express vibrational spectra of water molecules in vapor, liquid, and solid states. The six-parameter (Doh, o , fi, Lye, Lyy, and Lee) SPC potential used for the water molecules is shown in Equation (24) ... 

The development of multiscale simulation techniques that involve the atomistic modeling of various structures and processes still remains at its early stage. There are many problems to be solved associated with more accurate and detailed description of these structures and processes. These problems include the development of efficient and fast methods for quantum calculations at the atomistic level, the development of transferable interatomic potentials (especially, reactive potentials) for molecular dynamic simulations, and the development of strategies for the application of multiscale simulation methods to other important processes and materials (optical, magnetic, sensing, etc.). 

The first attempts in the direction of simulating theoretically at an atomistic level the diffusion of simple gas molecules in a polymer matrix were made more than two decades ago (100). But, the systematic development of ab initio computer simulations of penetrant diffusion in polymeric systems dates only from the late 80 s (101-104). At the beginning of the 90 s it was achieved to simulate some qualitative aspects such as the diffusion mechanism, temperature, and pressure dependence of diffusion coefficients (105-109). The polymers chosen for investigation mainly fell into two categories either they were easily described (model elastomers or polyethylene) or they were known to have, for simple permanent gases like H2, 02, N2, H20 or CH4,... 

As announced above these findings are in astonishing agreement with the heuristic pictures of the diffusion mechanism discussed in the framework of some microscopic diffusion models. But, besides being free of the conceptual drawbacks (the ad hoc assumptions) of the classical diffusion models, the MD method of computer simulation of diffusion in polymers makes it possible to get an even closer look at the diffusion mechanism and explain from a true atomistic level well known experimental findings. For example the results reported in (119,120) on the hopping mechanism reveal the following additional features. 

Computer simulation studies aim to provide reliable models at the atomistic level, which fulfill three main roles first they can provide general insight and understanding of the systems simulated secondly they can provide models, which can directly assist the interpretation of experimental data and thirdly they can provide accurate numerical data on important parameters, which may be either difficult to measure or entirely inaccessible to experiment. As an example of the... 

The area of polymer modeling has been summarized in several notable accounts. A review on modeling of polymer glasses at the atomistic level by... 

The first applications of CG lipid models looked for qualitative, rather than quantitative predictions, and therefore did not use any information from atomistic-level calculations in their parameterisation. One of the first models produced during this time was by Smit et al This model was used to investigate the phases of an oil/... 

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