Particular Biomolecular Processes as Computing Paradigms.

The research on alternative computation paradigms has been initiated mainly because of the apparent limits induced by the nature of the materials and the methods used in current computing technologies. Due to the above observation, various bio-inspired computing methods have already been proposed and studied, both in practice and theory. In this paper, a review of such models is outlined with emphasis on biomolecular forms of computing. In addition, a novel biomolecular model of computation based on P systems is proposed inspired by the structure of mitochondria, namely, the mitochondria P systems and automata.

[1]  Peter Dittrich,et al.  Chemical Computing , 2004, UPP.

[2]  Tetsuya Asai,et al.  Reaction-diffusion computers , 2005 .

[3]  S. Archer.  Mitochondrial dynamics--mitochondrial fission and fusion in human diseases. , 2013, The New England journal of medicine.

[4]  D. Chan,et al.  Mitochondrial dynamics–fusion, fission, movement, and mitophagy–in neurodegenerative diseases , 2009, Human molecular genetics.

[5]  Andrew Adamatzky,et al.  Towards slime mould chemical sensor: Mapping chemical inputs onto electrical potential dynamics of Physarum Polycephalum , 2013, ArXiv.

[6]  Herbert Jaeger,et al.  Reservoir computing approaches to recurrent neural network training , 2009, Comput. Sci. Rev..

[7]  Andrew Adamatzky,et al.  Developing Proximity Graphs by Physarum polycephalum: Does the Plasmodium Follow the Toussaint Hierarchy? , 2009, Parallel Process. Lett..

[8]  Fernando Arroyo,et al.  Biocircuit design through engineering bacterial logic gates , 2011, Natural Computing.

[9]  Y. Hatefi.  The mitochondrial electron transport and oxidative phosphorylation system. , 1985, Annual review of biochemistry.

[10]  Erzsébet Csuhaj-Varjú,et al.  P Automata or Purely Communicating Accepting P Systems , 2002, WMC-CdeA.

[11]  H. McBride,et al.  Mitochondria: More Than Just a Powerhouse , 2006, Current Biology.

[12]  Leandro Nunes de Castro,et al.  Fundamentals of natural computing: an overview , 2007 .

[13]  Mario J. Pérez-Jiménez,et al.  A Model of the Quorum Sensing System in Vibrio fischeri Using P Systems , 2008, Artificial Life.

[14]  Dana S. Scott,et al.  Finite Automata and Their Decision Problems , 1959, IBM J. Res. Dev..

[15]  Erzsébet Csuhaj-Varjú.  P Automata: Concepts, Results, and New Aspects , 2009, Workshop on Membrane Computing.

[16]  Bruce Alberts,et al.  Essential Cell Biology , 1983 .

[17]  Erzsébet Csuhaj-Varjú,et al.  (Mem)brane automata , 2008, Theor. Comput. Sci..

[18]  Stephen Wolfram,et al.  Cellular automata as models of complexity , 1984, Nature.

[19]  Jirí Wiedermann.  Nanomachine Computing by Quorum Sensing , 2011, Computation, Cooperation, and Life.

[20]  Cristian S. Calude.  Unconventional Computing: A Brief Subjective History , 2017 .

[21]  Julian Francis Miller,et al.  Evolution-in-materio: evolving computation in materials , 2014, Evolutionary Intelligence.

[22]  Grzegorz Rozenberg,et al.  The many facets of natural computing , 2008, Commun. ACM.

[23]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[24]  Erzsébet Csuhaj-Varjú.  P and dP Automata: Unconventional versus Classical Automata , 2012, Developments in Language Theory.

[25]  Rolf Landauer.  Information is inevitably physical , 1999 .

[26]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[27]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[28]  Marian Gheorghe,et al.  Deterministic and stochastic P systems for modelling cellular processes , 2009, Natural Computing.

[29]  Theodore Andronikos,et al.  Mitochondrial fusion through membrane automata. , 2015, Advances in experimental medicine and biology.

[30]  Dana H. Ballard,et al.  Brain Computation as Hierarchical Abstraction , 2015 .

[31]  Oscar H. Ibarra,et al.  Simulating FAS-induced apoptosis by using P systems , 2007 .

[32]  Victoria Coleman.  Embodied Molecular Computation: Potential and Challenges , 2016, Computer.

[33]  R. Feynman.  Simulating physics with computers , 1999 .

[34]  A. Turing.  On Computable Numbers, with an Application to the Entscheidungsproblem. , 1937 .

[35]  Gheorghe Paun,et al.  P automata revisited , 2012, Theor. Comput. Sci..

[36]  A. Adamatzky.  Towards fungal computer , 2018, Interface Focus.

[37]  Theodore Andronikos,et al.  The mechanism of splitting mitochondria in terms of membrane automata , 2015, 2015 IEEE International Symposium on Signal Processing and Information Technology (ISSPIT).

[38]  Gheorghe Paun,et al.  Computing with Membranes , 2000, J. Comput. Syst. Sci..

[39]  Shinnosuke Seki,et al.  Nondeterministic seedless oritatami systems and hardness of testing their equivalence , 2016, Natural Computing.

[40]  Lila Kari,et al.  On the descriptional complexity of Watson-Crick automata , 2009, Theor. Comput. Sci..

[41]  Isaac L. Chuang,et al.  Quantum Computation and Quantum Information (10th Anniversary edition) , 2011 .

[42]  Erik D. Demaine,et al.  Know When to Fold 'Em: Self-Assembly of Shapes by Folding in Oritatami , 2018, DNA.

[43]  Marvin Minsky,et al.  Computation : finite and infinite machines , 2016 .

[44]  Artiom Alhazov,et al.  Computation power of asynchronous spiking neural P systems with polarizations , 2019, Theor. Comput. Sci..

[45]  B. Lang,et al.  Mitochondrial evolution. , 1999, Science.

[46]  Gheorghe Paun,et al.  The Oxford Handbook of Membrane Computing , 2010 .

[47]  Andrei Paun,et al.  The power of communication: P systems with symport/antiport , 2002, New Generation Computing.

[48]  John von Neumann,et al.  The Computer and the Brain , 1960 .

[49]  M. Mitchell Waldrop,et al.  The chips are down for Moore’s law , 2016, Nature.

[50]  Santosh S. Vempala,et al.  Cortical Computation , 2015, PODC.

[51]  Theodore Andronikos,et al.  QM Automata: A New Class of Restricted Quantum Membrane Automata. , 2017, Advances in experimental medicine and biology.

[52]  J. Prudent,et al.  Mitochondrial dynamics: overview of molecular mechanisms , 2018, Essays in biochemistry.

[53]  Alfonso Rodríguez-Patón,et al.  Tissue P systems , 2003, Theor. Comput. Sci..

[54]  J. Taanman,et al.  The mitochondrial genome: structure, transcription, translation and replication. , 1999, Biochimica et biophysica acta.

[55]  Theodore Andronikos,et al.  Membrane automata for modeling biomolecular processes , 2017, Natural Computing.

[56]  R. Wiesner,et al.  Counting target molecules by exponential polymerase chain reaction: copy number of mitochondrial DNA in rat tissues. , 1992, Biochemical and biophysical research communications.

[57]  Mark Burgin,et al.  Unconventional Algorithms: Complementarity of Axiomatics and Construction , 2012, Entropy.