Artificial Biochemistry

2009-03-30 06:01:44 1 Artificial Biochemistry Luca Cardelli Microsoft Research Abstract We model chemical and biochemical systems as collectives of interacting stochastic automata, with each automaton representing a molecule that undergoes state transitions. In this artificial biochemis- try, automata interact by the equivalent of the law of mass action. We investigate several simple but intriguing automata collectives by stochastic simulation and by ODE analysis. 1 Introduction Macromolecules Molecular biology investigates the structure and function of biochemical systems starting from their basic

building blocks: macromolecules. A macromole- cule is a large, complex molecule (a protein or a nucleic acid) that usually has inner mutable state and external activity. Informal explanations of bio- chemical events trace individual macromolecules through their state changes and their interaction his- tories: a macromolecule is endowed with an identity that is retained through its transformations, even through changes in molecular energy and mass. A macromolecule, therefore, is qualitatively different from the small molecules of inorganic chemistry. Such molecules are stateless: in the standard notation for chemical reactions they are seemingly created and destroyed, and their atomic structure is used mainly for the bookkeeping required by the conservation of mass. Attributing identity and state transitions to mo- lecules provides more than just a different way of looking at a chemical event: it solves a fundamental difficulty with chemical-style descriptions. Each ma- cromolecule can have a huge number of internal states, exponentially with respect to its size, and can join with other macromolecules to from even larger state configurations, corresponding to the product of their states. If each molecular state is to be represented as a stateless chemical species, trans- formed by chemical reactions, then we have a huge explosion...

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