Reducing control alphabet size for the control of right linear grammars with unknown behaviors

Abstract This paper deals with the control problem of right linear grammars with unknown behaviors (RLUBs, for short) in which derivation behavior is not determined completely. In particular, we discuss on the size of control alphabets of control systems which regulate RLUBs in order to generate a target string only. We contribute to the reduction of control alphabet size from O ( l ) to O ( log ⁡ l ) , where l is a parameter related to reaction conditions under which RLUBs are chemically implemented.

[1]  Y. Yoshimura,et al.  Ultrafast reversible photo-cross-linking reaction: toward in situ DNA manipulation. , 2008, Organic letters.

[2]  Seymour Ginsburg,et al.  Control sets on grammars , 1968, Mathematical systems theory.

[3]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[4]  Masayuki Yamamura,et al.  Quantitative design and experimental validation for a single-molecule DNA nanodevice transformable among three structural states , 2010, Nucleic acids research.

[5]  Jehoshua Bruck,et al.  Neural network computation with DNA strand displacement cascades , 2011, Nature.

[6]  G. Seelig,et al.  DNA as a universal substrate for chemical kinetics , 2010, Proceedings of the National Academy of Sciences.

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

[8]  Erik Winfree,et al.  Universal computation via self-assembly of DNA: Some theory and experiments , 1996, DNA Based Computers.

[9]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[10]  Kenzo Fujimoto,et al.  RNA fluorescence in situ hybridization using 3-cyanovinylcarbazole modified oligodeoxyribonucleotides as photo-cross-linkable probes. , 2016, Bioorganic & medicinal chemistry letters.

[11]  Sinem K. Saka,et al.  Super-resolution labelling with Action-PAINT , 2019, Nature Chemistry.

[12]  Arto Salomaa,et al.  Periodically Time-Variant Context-Free Grammars , 1970, Inf. Control..

[13]  K. Fujimoto,et al.  DNA Photo-cross-linking Using Pyranocarbazole and Visible Light. , 2018, Organic letters.

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

[15]  Daniel J. Rosenkrantz,et al.  Programmed Grammars and Classes of Formal Languages , 1969, JACM.

[16]  Torsten Waldminghaus,et al.  RNA thermometers. , 2006, FEMS microbiology reviews.

[17]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[18]  Satoshi Kobayashi,et al.  Monotonically controlling right linear grammars with unknown behaviors to output a target string , 2019, Theor. Comput. Sci..

[19]  T. Head Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. , 1987, Bulletin of mathematical biology.

[20]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[21]  Kenzo Fujimoto,et al.  Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo‐crosslinking , 2017, Chembiochem : a European journal of chemical biology.

[22]  John A. Rose,et al.  Engineering multistate DNA molecules: a tunable thermal band-pass filter , 2016 .

[23]  V. Manoharan,et al.  Programming colloidal phase transitions with DNA strand displacement , 2014, Science.

[24]  Masayuki Yamamura,et al.  Experimental validation and optimization of signal dependent operation in whiplash PCR , 2010, Natural Computing.

[25]  Andrzej Ehrenfeucht,et al.  Reaction Systems , 2007, Fundam. Informaticae.