Atomistic modelling

From the various experimental investigations, it is clear that carbonate motions, as well as phenyl ring motions, are involved in the mechanical p transition of BPA-PC. The intermolecular contribution has been evidenced by several authors and the cooperative character of the motions has been pointed out. However, neither of the considered techniques can provide detailed information about the nature of intra- or inter-cooperativity occurring in the glassy state. 

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Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

The current understanding of the protein folding process has benefited much from studies that focus on computer simulations of simplified lattice models. These studies try to construct as simple a model as possible that will capture some of the more important properties of the real polypeptide chain. Once such a model is defined it can be explored and studied at a level of detail that is hard to achieve with more realistic (and thus more complex) atomistic models. 

L. Monnerie, U. W. Suter, eds. Atomistic Modeling of Physical Properties. Advances in Polymer Science No. 116. Berlin Springer, 1994. 

A. A. Gusev, F. Muller-Plathe, U. W. Suter, W. F. van Gunsteren. In L. Monnerie, U. W. Suter, eds. Atomistic Modeling of Physical Properties, Advances in Polymer Science No. 116. Berlin Springer 1994, pp. 207-248. 

The simplest atomistic model for the formation of a crystal in continuous space requires the definition of some effective attractive potential between any two atoms, which is defined independently of the other atoms in the cluster or crystal. The most frequently studied potential is the Lennard-Jones potential... 

In table 5 we present results of our TB methodology for surface energies comparing them to experiment, and atomistic models. The surface energy is expressed as the energy required to create a unit area of new surface, and is given by the following formula ... 

For the deformation of NiAl in a soft orientation our calculations give by far the lowest Peierls barriers for the (100) 011 glide system. This glide system is also found in many experimental observations and generally accepted as the primary slip system in NiAl [18], Compared to previous atomistic modelling [6], we obtain Peierls stresses which are markedly lower. The calculated Peierls stresses (see table 1) are in the range of 40-150 MPa which is clearly at the lower end of the experimental low temperature deformation data [18]. This may either be attributed to an insufficiency of the interaction model used here or one may speculate that the low temperature deformation of NiAl is not limited by the Peierls stresses but by the interaction of the dislocations with other obstacles (possibly point defects and impurities). 

The question arises as to how useful atomistic models may be in predicting the phase behaviour of real liquid crystal molecules. There is some evidence that atomistic models may be quite promising in this respect. For instance, in constant pressure simulations of CCH5 [25, 26] stable nematic and isotropic phases are seen at the right temperatures, even though the simulations of up to 700 ps are too short to observe spontaneous formation of the nematic phase from the isotropic liquid. However, at the present time one must conclude that atomistic models can only be expected to provide qualitative data about individual systems rather than quantitative predictions of phase transition temperatures. Such predictions must await simulations on larger systems, where the system size dependency has been eliminated, and where constant... 

In simple single-site liquid crystal models, such as hard-ellipsoids or the Gay-Berne potential, a number of elegant techniques have been devised to calculate key bulk properties which are useful for display applications. These include elastic constants for nematic systems [87, 88]. However, these techniques are dependent on large systems and long runs, and (at the present time) limitations in computer time prevent the extension of these methods to fully atomistic models. 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

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