A Language for Molecular Computation

Chemical Wave Computing from Labware to Electrical Systems

Unconventional and, specifically, wave computing has been repeatedly studied in laboratory based experiments by utilizing chemical systems like a thin film of Belousov–Zhabotinsky (BZ) reactions. Nonetheless, the principles demonstrated by this chemical computer were mimicked by mathematical models to enhance the understanding of these systems and enable a more detailed investigation of their capacity. As expected, the computerized counterparts of the laboratory based experiments are faster and less expensive. A further step of acceleration in wave-based computing is the development of electrical circuits that imitate the dynamics of chemical computers. A key component of the electrical circuits is the memristor which facilitates the non-linear behavior of the chemical systems. As part of this concept, the road-map of the inspiration from wave-based computing on chemical media towards the implementation of equivalent systems on oscillating memristive circuits was studied here. For illustration reasons, the most straightforward example was demonstrated, namely the approximation of Boolean gates.

In-vitro reconfigurability of native chemical automata, the inclusiveness of their hierarchy and their thermodynamics

Living systems process information using chemistry. Computations can be viewed as language recognition problems where both languages and automata recognizing them form an inclusive hierarchy. Chemical realizations, without using biochemistry, of the main classes of computing automata, Finite Automata (FA), 1-stack Push Down Automata (1-PDA) and Turing Machine (TM) have recently been presented. These use chemistry for the representation of input information, its processing and output information. The Turing machine uses the Belousov-Zhabotinsky (BZ) oscillatory reaction to recognize a representative Context-Sensitive Language (CSL), the 1-PDA uses a pH network to recognize a Context Free Language (CFL) and a FA for a Regular Language (RL) uses a precipitation reaction. By chemically reconfiguring them to recognize representative languages in the lower classes of the Chomsky hierarchy we illustrate the inclusiveness of the hierarchy of native chemical automata. These examples open the door for chemical programming without biochemistry. Furthermore, the thermodynamic metric originally introduced to identify the accept/reject state of the chemical output for the CSL, can equally be used for recognizing CFL and RL by the automata. Finally, we point out how the chemical and thermodynamic duality of accept/reject criteria can be used in the optimization of the energetics and efficiency of computations.