Dynamical hierarchies of structure and control in chemical reaction networks

• Published in: Nanotechnology 1999-12, Vol.10 (4), p.464-471
• Main Authors: Siehs, Christian, Mayer, Bernd
• Format: Article
• Language: English
• Subjects: Agglomeration; Automata theory; Biomaterials; Computer simulation; Data structures
• ISSN: 0957-4484; 1361-6528
• DOI: 10.1088/0957-4484/10/4/318

This paper presents the concept of dynamical hierarchies as a constructional and organizational principle in biomolecular materials design. Simple objects, characterized via a minimal set of explicit properties, self-organize into aggregates (higher-order objects) which show emergent properties (function) that are not explicitly encoded on the level of the individual chemical elements but are implicitly generated via the system dynamics. Object aggregation may span various levels of complexity, which are linked by both, up- and downward causalities, forming a unique organizational element; a dynamical hierarchy. This organization of individual objects is characterized by multiple levels of constructional complexity accompanied by respective emergent properties and overall, stabilized by implicit control. This concept is well suited to design multicomponent chemical aggregates or chemical reaction networks with complex functionality. We present the lattice molecular automaton (LMA) to simulate the generation of dynamical hierarchies in chemical systems. This simulation tool encodes chemical objects (substrates, enzymes, products) as data structures storing their explicit properties as well as object-object communication data. These two attributes are accessed by an update functional driving the system dynamics. We present LMA simulation results on dynamical hierarchies of structure and control in chemical reaction networks and discuss their implications for chemical information processing devices.