Cluster packing

Miracle, D. B. (2004b) A structural model for metallic glasses, Nature Mater., 3, 697-702. Miracle, D. B. (2006) The efficient cluster packing model - an atomic structural model for metallic glasses, Acta Mater., 54, 4317—4336. 

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

The structures of boron-rich borides (e.g. MB4, MBfi, MBio, MB12, MBe6) are even more effectively dominated by inter-B bonding, and the structures comprise three-dimensional networks of B atoms and clusters in which the metal atoms occupy specific voids or otherwise vacant sites. The structures are often exceedingly complicated (for the reasons given in Section 6.2.2) for example, the cubic unit cell of YB e has ao 2344 pm and contains 1584 B and 24 Y atoms the basic structural unit is the 13-icosahedron unit of 156 B atoms found in -rhombohedral B (p. 142) there are 8 such units (1248 B) in the unit cell and the remaining 336 B atoms are statistically distributed in channels formed by the packing of the 13-icosahedron units. 

The structures of the black crystalline benzene solvate C6o-4C6H6, the black charge-transfer complex with bis(ethylenedithio)tetrathiafulvene, [C6o(BEDT-TTF)2], and the black ferrocene adduct [C6o Fe(Cp)2)2] (Fig. 8.7b) ) have also been solved and all feature the packing of Cso clusters. 

I have found that the assumption that in atomic nuclei the nucleons are in large part aggregated into clusters arranged in closest packing leads to simple explanations of many properties of nuclei. Some aspects of the closest-packing theory of nuclear structure are presented in the following paragraphs.1... 

The Au(I)-Au(I) distance of 330.1 pm is longer than in metallic Au (288 pm), and in view of the d configuration in Au(I) compounds, such structures as V arise by packing factors in the solid rather than by metal-metal bonding (see 8.2.2.3). Similarly long Au—Au bonds are found in other Au(I) compounds and in mixed Au(I)-Au(III) compounds. Many other cluster compounds are known . 

When the fully conserved residue Thr 140, which is packed against the Pro loop, was substituted by Gly, His, or Arg in Rhodobacter capsulatus, the midpoint potential of the Rieske cluster was decreased by 50-100 mV, the cluster interacted with the quinone pool and the bci complex had 10-24% residual activity but the Rieske cluster was rapidly destroyed upon exposure to oxygen (49). In contrast, the residual activity was <5%, the cluster showed no interaction with the quinone pool, and the interaction with the inhibitor stigmatellin... 

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