Atomistic Computer Simulations Examples

Single crystals of /S-A1203 are essentially two dimensional conductors. The conducting plane has hexagonal symmetry (honeycomb lattice). This characteristic feature made -alumina a useful model substance for testing atomistic transport theory, for example with the aid of computer simulations. Low dimensionality and high symmetry reduce the computing time of the simulations considerably (e.g., for the calculation of correlation factors of solid solutions). 

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... 

For a general review of the molecular d)mamics method see, for example Klein ML (1985) Computer Simulation Studies of Solids. Ann Rev Phys Chem 36 525-548. Suter U, Monnerie L eds (1994) Atomistic Modelling of Physical Properties of Polymers. Springer, Berlin (Adv Polymer Sci, vol 116). 

If computational power permits, first-principles molecular modeling such as ab initio MD can provide the most accurate information without adjustable parameters. However, even the most powerful computer system available today is limited to first-principles solution of molecular information with a certain size. As a result, the hybrid methods such as QM/MM or ONIOM (where different levels of theory for one calculation are involved) are often used (Fig. 1). As an example of future prospects, molecular design and characterization of nanocomposites using computer simulation are also briefly mentioned. Atomistic modeling of clay nanocomposites is a very promising field in clay mineral materials science. 

Computer simulation offers an alternative way of providing guidelines for materials searching. For example, atomistic simulation of defects and transport in materials is well established however, it is hardly a rapid process and much of the effort is expended in the rationalization of existing experimental data. A change in scope is needed to exploit the potential of such techniques to predictive materials screening. 

Finally, one can even go beyond simulation. For example, loannis Kevrekidis has developed an approach to computing stability and bifurcation analysis using time steppers, in which the necessary functions are obtained directly from atomistic-scale simulations as the overall calculation proceeds. This... 

For standard problems in the physics and chemistry of condensed matter, such as simple fluids containing rare gas atoms or diatomic molecules, etc., computer simulation considers a small region of matter in full atomistic detail. " For example, for a simple fluid it often is sufficient to simulate a small box containing of the order of 10 atoms, which interact with each other with chemically realistic forces. These methods work because simple fluids are homogeneous on a scale of 10 A already the oscillations in the pair distribution function then are damped out under most circumstances. Also reliable models for the effective forces are usually available from quantum chemistry methods. 

Because of system sizes, these investigations are clearly not feasible with atomistic MD simulations for example a lipid vesicle of a radius of approximately 25 nm would contain around 18 000 lipids, corresponding to approximately 2 500 000 atoms using a fully atomistic force field, even before taking into account the unavoidable presence of water molecules. However, thanks to progresses both in hardware and in software technologies, such systems are nowadays computationally tractable using CG models such as the MARTINI or the SDK. 

The computational efficiency of this approach allows at the same time models with a resolution close to atomistic and simulations on very large length and timescales.""" For example, these models have been applied to study the interaction and the dynamical exchange of block copolymer chains between a spherical micelle (functioning as drug nanocarrier) and a lipid bilayer (as model of cell surface) also in the presence of drug molecules (iboprufen) in the micelle core. Simulations of 12 nm large micelles with membrane bilayers over several microseconds of simulations could be achieved on home-cluster facilities."" ... 

Consequently, we focus here on computer simulations exclusively. The outline of the remainder of this chapter is as follows Section 1.2 presents on overview of polymer models (from lattice models to atomistic descriptions) and will also describe the most important aspects of Monte Carlo simulations of these models. As an example, recent work on simple short alkanes and solutions of alkanes in supercritical carbon dioxide [47,48] will be presented, to clarify to what extent a comparison of Monte Carlo results on phase behavior and experimental data is sensible, and which experimental input into the models is indispensable to make them predictive. 

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