Research papers on automata

Thus, repeated stimulation by smaller charges are counted and summed up to induce the closure of the leaves. The states allowed in M 1 are represented by circles, and the transitions are represented by the arrows.


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The initial state is shown by the double arrow and the final state is shown with the double circle. Input can be accepted thus, closure induced only after repeated stimuli. While the Venus flytrap model Fig. In order to construct a library of interchangeable parts, further search for putative molecules behaving as automata is required. Furthermore, molecules encoded by specific genes, thus proteins, are preferable. In the below sections, the nature and the molecular basis for the abstract sequential machines or automata naturally equipped in living plants, as the interchangeable parts for synthetic biology are discussed.

In electriccal computing models, the Mealy machines and Moore machines are considered to be equivalent, thus these machines can be interchangeable. Here, this review propose a view that most of individual signaling molecules found in biological systems including plants can be categorized as the Moore machines or derived FSA. In contrast, a Moore machine may consecutively emit signals once the transition to the active state is manifested upon receiving an effective input signal. Thus, the input signal can be amplified by the output through Moore-type signaling molecules.

In case of action plants and locomotive cells of green algae, cytoskeletons and motor protein complexes controlled under signaling events can be considered as the Moore machines too. In the above models, intermediate signals such as phosphorylating events and releases of secondary messengers such as cyclic AMP and calcium ions can be considered both as the input and output signals for individual Moore machines or FSA involved in cellular signal transduction.

Despite the above section focused on the signal amplifying roles for the Moore-type signaling molecules, it should be also noted that plant enzymes are rich sources for the Mealy-type molecules. The given xamples with the roles of plant peroxidases in the plant signaling events involving salicylic acid SA , aromatic monoamines AMAs and indoleacetic acid IAA , brought in the below section clearly suggest that this type of molecules can participate the signaling pathways in plants, thus deserve being listed in additions to the Moore-type molecules and FSA from plants. Numbers in the small brackets indicate the formal oxidation states of the heme.

In the reactions above, SA behaves as an e - donor while H 2 O 2 acts as the e - acceptor.


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  • In the hourglass model Fig. Compounds I and II of plant enzymes are considered to possess the hemes at ferryl states with and without additional porphyrin radicals, respectively. Behavior of plant peroxidase as a redox-active mealy machine M 2. A The hourglass model summarizing the superoxide generating reactions catalyzed by plant peroxidases responsive to both salicylic acid SA, a model substrate for peroxidase cycle , aromatic monoamines AMA and indoleacetic acid IAA, a model substrate for oxygenation cycle. Metabolism of IAA, the principal form of auxin in higher plants, is of great interest to plant biologists.

    Plant peroxidases are considered to be involved in the metabolism of IAA, by oxidizing IAA via two different mechanisms: a conventional H 2 O 2 -dependent pathway and one that requires O 2 but not H 2 O 2. IAA can be oxidized by plant peroxidases chiefly by HRP in model experiments by this mechanism but there is no strict substrate specificity in this conventional H 2 O 2 -dependent peroxidase cycle.

    Interestingly, the transitions among different oxidation states in plant peroxidases can be interpreted as the actions of Mealy machines. The models involving IAA Fig. Not like the Moore machines, the members of the Mealy machines require highly repeated inputs for performing the substantially available levels of outputs by consecutively repeating the input-output cycles. Discussion in the above section suggested that many of plant enzymes such as peroxidases can be considered as natural Mealy machines.

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    However, the use of speficic inhibitors targetting the enzymes may behave as the inputs for the Moore machines when dark logic was employed. For an instance, by considering the presence of active enzyme as 0 and loss of activity as 1 thus, dark logic , addition of plant peroxidase inhibitors such as salicylhydroxamic acid or binding of carbon monooxide to heme pockets of the enzymes results in the loss of catalytic activity.

    Therefore, the output from the inactivated state can be considered as 1. Above sections have indicated that the similarity between the computational digital data processing and plant decision-making processes by defining the actions states and transition functions of the natural automata in plant systems. Today, our approaches for synthetic biology targeting the bio-inspired computing and robotics have yet started. The idea of constructing plantoids named after analogy to androids and humanoids was proposed by the group of Prof. Mancuso Univ. Florence, Italy. The plantoids are by definition, the plant-inspired robots proposed for the investigation of both biological and technological issues.

    It is also challenging to develop the intelligent plant-inspired or plant-related robots equipped with plant-derived automata, by connecting computer and natural or artificial plant cellular networks, for enhanced data processing. At present, we merely assume that the operational performance of plantoids can be designed based on the designs of abstract sequential machines or automata, thus, the plantoids may possibly function after installing the interchangeable parts derived from plant molecules or cells.

    Proposed models for plantoids, cells, and molecules functioning as automata. A A model of plantoid produced by Prof. B Image of an electro-physiologically monitored cell Prof. Bouteau, Univ. C An artificial enzyme behaving as a plant peroxidase mimic. In the present article, we have focused on the finding and defining the natural automata acting in living plants.

    Our ongoing study also suggests that natural automata such as Moore-type automata or FSA can be found and defined in living cells of protozoa. To many of cell biology researchers, Paramecium species are very familiar laboratory tools for cell biological and environmental studies.

    It is well known that Paramecium species including the photosynthetic species, green paramecia Paramecium bursaria , migrate toward the anodic electrode when exposed to an electric field in a medium. In fact, over a century ago, it has been known that Paramecium species exhibit galvanotaxis in which the ciliate cells align with an electric field or voltage gradient and swim toward the anode if the electric field is sufficiently strong.

    In fact, the galvanotactic responsiveness observed in Paramecium species particularly P. Lastly, the authors wish to discuss the difference between the deterministic finite automata DFA and nondeterministic finite automata NFA to be applied in designing the plantoids or study in the in vivo cellular robotics. Many of readers with biological backgrounds may wonder if the biological systems function as machines for informatics.

    Automata theory and application

    Can every events and outcomes observed in the biological systems be considered clearly as the series of digitalized information expressed with 1 or 0, as discussed in the above sections? In fact, the answer is yes with some cautions. It is apparently obvious that the applications of automata in the biological topics require special cautions in order to reproduce the real biological phenomena.

    The latter model Fig.


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    • This type of lowered stringency could be achieved by involvement of multiple cells or molecules in the signaling events, thus the resultant performance of the automata would be much closer to the naturally observable phenomena. Previously published online: www. National Center for Biotechnology Information , U. Journal List Commun Integr Biol v.

      Commun Integr Biol. Author information Copyright and License information Disclaimer.

      The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited. This article has been cited by other articles in PMC. Abstract The automata theory is the mathematical study of abstract machines commonly studied in the theoretical computer science and highly interdisciplinary fields that combine the natural sciences and the theoretical computer science. Keywords: aqueous computing, automaton, plant signaling, plant enzyme. Introduction Natural computing is the recently growing field of research that investigates models and computational techniques inspired by nature and, dually, attempts to understand the world around us in terms of information processing.

      Part 1: Primary Papers

      Handling and manipulating the life As natural computing studies attempt to understand the world including the biological systems arrond us, some approaches may be similar to the those taken by synthetic biologists. Computing with Biological Materials One of the aims in synthetic biology is the creation of intelligence based on the biological bricks. Mealy Machines and Moore Machines: Two Different Types of Sequential Machines in vivo As the machine meets an input, it makes a jump to another state, according to the transition functions defined.

      Open in a separate window. Volatile Memory and FSA in Plants By considering an intact plant as an individual sequential machine, the signal processing perception and transduction in inside the living plant can be attributed to the automaton-like decision-making processes. Signaling Molecules as Moore Machines or Derived FSA In electriccal computing models, the Mealy machines and Moore machines are considered to be equivalent, thus these machines can be interchangeable.

      Plant Peroxidase as Redox-Mealy Machines Despite the above section focused on the signal amplifying roles for the Moore-type signaling molecules, it should be also noted that plant enzymes are rich sources for the Mealy-type molecules. Dark logic models using inhibitors converts the biological Mealy machines into Moore machine Discussion in the above section suggested that many of plant enzymes such as peroxidases can be considered as natural Mealy machines. In vivo cellular computing and plantoids Above sections have indicated that the similarity between the computational digital data processing and plant decision-making processes by defining the actions states and transition functions of the natural automata in plant systems.

      Possible natural automata for robotic application found in other biological systems In the present article, we have focused on the finding and defining the natural automata acting in living plants. Perspectives: Deterministic finite automata DFA and nondeterministic finite automata NFA Lastly, the authors wish to discuss the difference between the deterministic finite automata DFA and nondeterministic finite automata NFA to be applied in designing the plantoids or study in the in vivo cellular robotics. Footnotes Previously published online: www. References 1. Kari L. The many facets of natural computing.

      Commun ACM. Tomita Y, Yokomori T. Automata and formal language. Amos M. Genesis machines. New science of biocomputing. Atlantic Books ; London. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol. Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA. Nat Chem. Nandagopal N, Elowitz MB.

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      PARALLEL COMMUNICATING PUSHDOWN AUTOMATA SYSTEMS

      Synthetic biology: integrated gene circuits. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. Brown J.