Self-organizing complex systems

If the qfstem under consideration is relatively simple, even if the matching of corresponding i nthons is completed, we would still have a relatively primitive spatial structure. However, we may imagine far more interesting situation, when  

T are four letters used by nature to compose the words, sentences, chaptets. essays and poems of the Book of Life (the DNA code). The complementarity of the related synthons is of prime importance. 

The multilevel molecular structure may depend very strongly on its environment. When this changes, the structure may decompose, and eventually another structure may emerge. 

A hierarchical multilevel structure may be formed, where the levels exhibit different stability with regard to external perturbations. The stability differs due to the different binding energies of the tynthons involved and/or on the steric constraints. 

The coiled-coil structure of oligopeptides described on p. 748 may serve as an example of such a multilevel structure, or the spontaneous folding of entymes to their native structure, e.g., rhodopsin is composed of seven a-helices linked by some oligopeptide links (Fig. 15.1). 

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Assembly and transformation of polysaccharides by molecular-scale tools is triggered by principles of self-organizing complex systems and include enzymatically catalyzed nonlinear formation/transformation and degradation based on molecular-level library command sequences (genetic code). 

Rates of M"" -promoted ET from electron donors to acceptors normally increase linearly or approach limited values with increasing concentration of M" (see below) (6-10). In contrast, self-organized MCET systems involving multiple molecular environment can lead to decreases of entropy equivalent to an increase of molecular electronic order for the activated complex, resulting in a substantial increase in the rate of ET (98,99). In such a case, the rate of ET is no longer linearly related to concentrations of reactants and promoting molecules for ET. New frontiers of ET may be exploited in such nonlinear dynamic and self-organized... 

Later Codd reduced the complexity of the Von Neuman machine inspired by insights in the physiology of the nervous system in animals. Important to our later discussion in Chapter 9 of the design of self organizing catalytic systems, he proposed a universal configuration of only eight-states per cell. 

The importance of numerical treatments, however, caimot be overemphasized in this context. Over the decades enonnous progress has been made in the numerical treatment of differential equations of complex gas-phase reactions [8, 70, 71], Complex reaction systems can also be seen in the context of nonlinear and self-organizing reactions, which are separate subjects in this encyclopedia (see chapter A3,14. chapter C3.6). 

Upon closer examination, we see that self-organization in complex system does not really violate the Second Law. The reason is that the Second Law requires a system to be isolated that is, it must not exchange energy or matter with its environment. 

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