Packing arrangement, simulated

Fig. 7. Simulated packing arrangement of formylurea white, hydrogen atoms light gray, carbon atoms dark gray, nitrogen atoms and black, oxygen atoms.

Secondary structure prediction methods have been complemented by packing analyses of amino acid residues in globular proteins. Packing arrangements have been examined extensively [13, 14] in attempts to identify preferred interaction patterns between non-contiguous amino acid residues. While there is no straightforward way to cast this information into a scheme for prediction of protein structure from sequence, it can certainly be used for plausibility checks on hypothetical protein models or to score protein models obtained by protein folding simulations on lattices [15]. 

The Rietveld refinement is applied, in which the packing arrangement and molecular structure are optimized so that the simulated pattern of the proposed structure fits the experimental pattern. 

Gavalda et al. (2001, 2002) used Monte Carlo type moves to simulate the packing arrangements of the carbon aerogel spheres (Figure 3.18(b)), size about 6 nm diameter. The inter-particulate mesoporosity had dimensions of 3-15 nm and dimensions assigned to the microporosity of 0.7-1.5 nm. 

All the macroscopic properties of polymers depend on a number of different factors prominent among them are the chemical structures as well as the arrangement of the macromolecules in a dense packing [1-6]. The relationships between the microscopic details and the macroscopic properties are the topics of interest here. In principle, computer simulation is a universal tool for deriving the macroscopic properties of materials from the microscopic input [7-14]. Starting from the chemical structure, quantum mechanical methods and spectroscopic information yield effective potentials that are used in Monte Carlo (MC) and molecular dynamics (MD) simulations in order to study the structure and dynamics of these materials on the relevant length scales and time scales, and to characterize the resulting thermal and mechanical proper-... 

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