Hierarchical order

One of the most widely used - and successful representations of the constitution, the topology, of a molecule is the HOSE code (Hierarchical Ordered description of the Substructure Environment) [9]. It is an atom-centered code taking into account... 

Figure 10.2-1. The structural environment is described in hierarchical Order by starting from a selected carbon atom and walking through the molecule in spheres, Only the non-hydrogen atoms are considered explicitly.

The first requirement for threading is to have a database of all the known different protein folds. Eisenberg has used his own library of about 800 folds, which represents a minimally redundant set of the more than 6000 structures deposited at the Protein Data Bank. Other groups use databases available on the World Wide Web, where the folds are hierarchically ordered according to structural and functional similarities, such as SCOP, designed by Alexey Murzin and Cyrus Chothia in Cambridge, UK. 

One may now ask whether natural systems have the necessary structural evolution needed to incorporate high-performance properties. An attempt is made here to compare the structure of some of the advanced polymers with a few natural polymers. Figure 1 gives the cross-sectional microstructure of a liquid crystalline (LC) copolyester, an advanced polymer with high-performance applications [33]. A hierarchically ordered arrangement of fibrils can be seen. This is compared with the microstructure of a tendon [5] (Fig. 2). The complexity and higher order of molecular arrangement of natural materi-... 

The objectives of the inflammatory response can be viewed as a hierarchical ordered panel of events. The most successful consequence of an inflammatory response is the complete restoration of function and structure of the affected tissue, also denoted as resolution. If this is not possible, inflammation aims for healing by repair and replacement of lost tissue by scar tissue. 

The hierarchical order of El, E2 and E3 activity correlates with an increase in enzymatic specificity which ensures selective ubiquitin modification of distinct... 

Addition of third components to nanohybrids of proteins and mesoporous materials sometimes brings advantages in their functions. Kim, Hyeon, and coworkers immobilized enzyme molecules together with magnetite (Fe304) nanoparticles in hierarchically ordered, mesocellular, mesoporous silica (HMMS) (Figure 4.25)... 

Fig. 4.25 I mmobilization of enzyme molecules and magnetite nanoparticles in hierarchically ordered mesocellular mesoporous silica with the aid of cross-linking via glutaraldehyde treatment.

Bone is an extremely dense connective tissue that, in various shapes, constitutes the skeleton. Although it is one of the hardest structures in the body, bone maintains a degree of elasticity owing to its structure and composition. It possesses a hierarchical structure and, as most of the tissues, is nanostructured in fact, it is a nanoscaled composite of collagen (organic extracellular matrix) and hydroxycarbonate apatite, (HCA, bone mineral). This nanostructure is in intimate contact with the bone cells (several microns in size), which result (at the macroscopic level) in the bone tissue. Figure 12.2 shows the bone hierarchical ordering from the bone to the crystalline structure of HCA. 

Vast tabulations of 13C chemical shift data have been assembled in computer searchable form. These databases form the basis for 13C chemical shift prediction algorithms. For the most part, carbon chemical shifts can be calculated using what is referred to as a Hierarchically Ordered Spherical Environment (HOSE) code approach [28]. To calculate a given carbon s chemical shift, the influence of each successive spherical shell is applied to the starting chemical shift for that carbon to calculate its overall chemical shift. Typically, programs will calculate shifts for 3 or 4 layers, beyond which the effects of most substituents are negligible. The spherical layers surrounding the 23-position of strychnine are shown in Fig. 10.8. 

If it was not a foregone conclusion that the hierarchically ordered white races ever would become a single, consanguine race of Caucasians in popular estimation, then what circumstances account for the transformation What are some of the social, political, and cultural forces that moved the white races so decisively in the direction of Caucasian whiteness ... 

Figure 3. A subset of the chemical substructures database, showing the hierarchical ordering.

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