Robust biomolecular finite automata

Robust Biomolecular Finite Automata

In this paper we present a uniform method for translating an arbitrary nondeterministic finite automaton (NFA) into a deterministic mass action biochemical reaction network (BRN) that simulates it. The BRN receives its input as a continuous time signal consisting of concentrations of chemical species that vary to represent the NFA’s input string in a natural way. The BRN exploits the inherent p...

Parallel biomolecular computation on surfaces with advanced finite automata.

A biomolecular, programmable 3-symbol-3-state finite automaton is reported. This automaton computes autonomously with all of its components, including hardware, software, input, and output being biomolecules mixed together in solution. The hardware consisted of two enzymes: an endonuclease, BbvI, and T4 DNA ligase. The software (transition rules represented by transition molecules) and the inpu...

Stochastic computing with biomolecular automata.

Stochastic computing has a broad range of applications, yet electronic computers realize its basic step, stochastic choice between alternative computation paths, in a cumbersome way. Biomolecular computers use a different computational paradigm and hence afford novel designs. We constructed a stochastic molecular automaton in which stochastic choice is realized by means of competition between a...

Multidimensional fuzzy finite tree automata

This paper introduces the notion of multidimensional fuzzy finite tree automata (MFFTA) and investigates its closure properties from the area of automata and language theory. MFFTA are a superclass of fuzzy tree automata whose behavior is generalized to adapt to multidimensional fuzzy sets. An MFFTA recognizes a multidimensional fuzzy tree language which is a regular tree language so that for e...

Cellular Automata Modeling of Biomolecular Networks