diff --git a/bib/hdr_noverlan.bib b/bib/hdr_noverlan.bib new file mode 100644 index 0000000..8851723 --- /dev/null +++ b/bib/hdr_noverlan.bib @@ -0,0 +1,673 @@ +% This file was created with JabRef 2.6. +% Encoding: Cp1252 + +@STRING{HFL = {Handbook of Formal Languages, 3 volumes}} + +@STRING{Springer = {Springer Verlag, Berlin, Heidelberg, New York}} + +@STRING{TCS = {Theoretical Computer Science}} + +@ARTICLE{Adleman94, + author = {Leonard M. Adleman}, + title = {Molecular Computation of Solutions to Combinatorial Problems}, + journal = {Science}, + year = {1994}, + volume = {266}, + pages = {1021-1024}, + month = nov # {~11,}, + abstract = {{\textbf{Abstract:} The tools of molecular biology were used to solve + an instance of the directed Hamiltonian path problem. A small graph + was encoded in molecules of {DNA}, and the "operations" of the computation + were performed with standard protocols and enzymes. This experiment + demonstrates the feasibility of carrying out computations at the + molecular level. }}, + url = {\url{ftp://ftp.krl.caltech.edu/pub/users/brown/adleman.ps.gz}} +} + +@BOOK{alberts02molecular, + title = {Molecular Biology of the Cell, Fourth Edition}, + publisher = {Garland}, + year = {2002}, + author = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Raff, + Martin and Roberts, Keith and Walter, Peter}, + abstract = {...covers every important aspect in the field, from experimental techniques + and basic concepts to reviews... excellent university course resource.}, + howpublished = {Hardcover}, + isbn = {0815332181}, + keywords = {ref-corpus, ref-transloc}, + posted-at = {2006-06-09 22:44:14}, + priority = {2}, + url = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20&path=ASIN/0815332181} +} + +@BOOK{Benne93, + title = {{RNA}-Editing: The Alteration of Protein Coding Sequences of {RNA}}, + publisher = {Ellis Horwood, Chichester, West Sussex}, + year = {1993}, + author = {Robert Benne}, + owner = {ver}, + timestamp = {2009.10.27} +} + +@ARTICLE{CPPP07, + author = {Gabriel Ciobanu and Linqiang Pan and Gheorghe P\u{a}un and Mario + J. P\'erez-Jim\'enez}, + title = {P systems with minimal parallelism}, + journal = {Theoretical Computer Science}, + year = {2007}, + volume = {378}, + pages = {117 - 130}, + number = {1}, + doi = {DOI: 10.1016/j.tcs.2007.03.044}, + issn = {0304-3975}, + keywords = {Membrane computing}, + url = {http://www.sciencedirect.com/science/article/B6V1G-4NCJCYC-6/2/504442139c4d241b7de81f444297452f} +} + +@ARTICLE{CockMin64, + author = {John Cocke and Marvin Minsky}, + title = {Universality of Tag Systems with {P}=2}, + journal = {Journal of the ACM}, + year = {1964}, + volume = {11}, + pages = {15--20}, + number = {1} +} + +@ARTICLE{CD90, + author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and J{\"u}rgen Dassow}, + title = {On Cooperating/Distributed Grammar Systems}, + journal = {Elektronische Informationsverarbeitung und Kybernetik}, + year = {1990}, + volume = {26}, + pages = {49-63}, + number = {1/2}, + bibsource = {DBLP, http://dblp.uni-trier.de} +} + +@INPROCEEDINGS{CVS97, + author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and Arto Salomaa}, + title = {Networks of Parallel Language Processors}, + booktitle = {New Trends in Formal Languages}, + year = {1997}, + editor = {Gheorghe P\u{a}un and Arto Salomaa}, + volume = {1218}, + series = {Lecture Notes in Computer Science}, + pages = {299-318}, + publisher = {Springer}, + isbn = {3-540-62844-4} +} + +@ARTICLE{CsuhajEA96A, + author = { Erzsebet Csuhaj-Varj{\'{u}} and Lila Kari and Gheorghe P\u{a}un}, + title = {Test Tube Distributed Systems Based on Splicing}, + journal = {Computers and Artificial Intelligence}, + year = {1996}, + volume = {15}, + pages = {211-232}, + number = {2--3}, + url = {\url{http://www.csd.uwo.ca/~lila/dnapcgs.ps}} +} + +@INPROCEEDINGS{DKGS99, + author = {Mark Daley and Lila Kari and Greg Gloor and Rani Siromoney}, + title = {Circular Contextual Insertions/Deletions with Applications to Biomolecular + Computation}, + booktitle = {SPIRE/CRIWG}, + year = {1999}, + pages = {47-54}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://computer.org/proceedings/spire/0268/02680047abs.htm} +} + +@ARTICLE{DO04, + author = {Michael Domaratzki and Alexander Okhotin}, + title = {Representing Recursively Enumerable Languages by Iterated Deletion}, + journal = {Theoretical Computer Science}, + year = {2004}, + volume = {314}, + pages = {451-457}, + number = {3}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1016/j.tcs.2004.01.002} +} + +@INPROCEEDINGS{FIPY05, + author = {Rudolf Freund and Oscar H. Ibarra and Gheorghe P\u{a}un and Hsu-Chun Yen}, + title = {Matrix Languages, Register Machines, Vector Addition Systems}, + booktitle = {Proceedings of the Third Brainstorming Week on Membrane Computing}, + year = {2005}, + editor = {M.A. Guti\'errez-Naranjo and A. Riscos-N\'u\~nez and F.J. Romero Campero + and D. Sburlan}, + pages = {155--168}, + publisher = {University of Sevilla}, + owner = {ver}, + timestamp = {2009.10.27} +} + +@INPROCEEDINGS{FP02, + author = {Rudolf Freund and Andrei P\u{a}un}, + title = {Membrane Systems with Symport/Antiport Rules: Universality Results}, + booktitle = {Membrane Computing, International Workshop, WMC-CdeA 2002, Curtea + de Arges, Romania, August 19-23, 2002, Revised Papers}, + year = {2002}, + editor = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto Salomaa and Claudio + Zandron}, + volume = {2597}, + series = {Lecture Notes in Computer Science}, + pages = {270-287}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://link.springer.de/link/service/series/0558/bibs/2597/25970270.htm} +} + +@ARTICLE{FW96, + author = {Rudolf Freund and F. Wachtler}, + title = {Universal Systems with Operations Related to Splicing}, + journal = {Computers and Artificial Intelligence}, + year = {1996}, + volume = {15}, + pages = {273-294}, + number = {4}, + bibsource = {DBLP, http://dblp.uni-trier.de} +} + +@INPROCEEDINGS{FH02, + author = {Pierluigi Frisco and Hendrik Jan Hoogeboom}, + title = {Simulating Counter Automata by {P} Systems with Symport/Antiport}, + booktitle = {Membrane Computing, International Workshop, WMC-CdeA 2002, Curtea + de Arges, Romania, August 19-23, 2002, Revised Papers}, + year = {2002}, + editor = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto Salomaa and Claudio + Zandron}, + volume = {2597}, + series = {Lecture Notes in Computer Science}, + pages = {288-301}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://link.springer.de/link/service/series/0558/bibs/2597/25970288.htm} +} + +@ARTICLE{Galiuk81, + author = {Boris S. Galiukschov}, + title = {Semicontextual Grammars}, + journal = {Matematicheskaya Logica i Matematicheskaya Lingvistika}, + year = {1981}, + volume = { }, + pages = {38-50}, + note = {Tallin University, (in russian)} +} + +@BOOK{goto, + title = {A Minimum Time Solution of the Firing Squad Problem}, + publisher = {Harvard University}, + year = {1962}, + author = {E. Goto}, + volume = {298}, + series = {Course Notes for Applied Mathematics}, + owner = {ver}, + timestamp = {2010.05.08} +} + +@ARTICLE{GFB96, + author = {F. Guarnieri and M. Fliss and C. Bacroft}, + title = {Making {DNA} Add}, + journal = {Science}, + year = {1996}, + volume = {273}, + pages = {220--223}, + number = {12}, + owner = {ver}, + timestamp = {2010.07.21} +} + +@PHDTHESIS{Haussler82, + author = {David Haussler}, + title = {Insertion and Iterated Insertion as Operations on Formal Languages}, + school = {University of Colorado at Boulder}, + year = {1982}, + owner = {ver}, + timestamp = {2009.10.27} +} + +@ARTICLE{Haussler83, + author = {David Haussler}, + title = {Insertion Languages}, + journal = {Information Sciences}, + year = {1983}, + volume = {31}, + pages = {77-89}, + number = {1}, + owner = {ver}, + timestamp = {2009.10.27} +} + +@ARTICLE{head87, + author = {T. Head}, + title = {Formal Language Theory and {DNA}: an Analysis of the Generative Capacity + of Specific Recombinant Behaviors.}, + journal = {Bulletin of Mathematical Biology}, + year = {1987}, + volume = {49}, + pages = {737--759}, + number = {6}, + abstract = { {\textbf{Abstract:} A new manner of relating formal language theory + to the study of informational macromolecules is initiated. A language + is associated with each pair of sets where the first set consists + of double-stranded {DNA} molecules and the second set consists of + the recombinational behaviors allowed by specified classes of enzymatic + activities. The associated language consists of strings of symbols + that represent the primary structures of the {DNA} molecules that + may potentially arise from the original set of {DNA} molecules under + the given enzymatic activities. + + Attention is focused on the potential effect of sets of restriction + enzymes and a ligase that allow {DNA} molecules to be cleaved and + reassociated to produce further molecules. The associated languages + are analyzed by means of a new generative formalism called a splicing + system. A significant subclass of these languages, which we call + the persistent splicing languages, is shown to coincide with a class + of regular languages which have been previously studied in other + context: the strictly locally testable languages. + + This study initiates the formal analysis of the generative power + of recombinational behaviors in general. The splicing system formalism + allows observations to be made concerning the generative power of + general recombination and also of sets of enzymatic activities that + include general recombination. } }, + owner = {ver}, + timestamp = {2010.06.12}, + www = {\url{http://math.binghamton.edu/tom/index.html}} +} + +@INPROCEEDINGS{head97, + author = {Tom Head}, + title = {Splicing Languages Generated with One Sided Context}, + booktitle = {Computing with Bio-Molecules. Theory and Experiments}, + year = {1998}, + pages = {158--181}, + abstract = { {\textbf{Abstract:} The splicing system concept was created in 1987 + to allow the convenient representation in formal language theoretic + terms of recombinant actions of certain sets of enzymes on double + stranded {DNA} molecules. Characterizations are given here for those + regular languages that are generated by splicing systems having splicing + rules that test context on only one side. An algorithm is given for + deciding whether any arbitrary regular language can be generated + by a splicing system in which all splicing rules test context on + the same side. Schutzenberger's concept of a constant relative to + a language provides the tool for constructing the required splicing + rules. To provide a potential biochemical example, the formal generative + capacity of the restriction enzyme {BpmI} in the company of a ligase + is discussed. Experimental investigation is suggested. } }, + annotate = { Part of \cite{HeadEA97}. }, + keywords = { Splicing systems, H-Systems, {DNA}-computing, biocomputing, bioinformatics, + regular languages, finite automata. }, + owner = {ver}, + timestamp = {2010.06.12} +} + +@BOOK{HML, + title = {Introduction to Automata Theory, Languages, and Computation}, + publisher = {Addison-Wesley, Reading, Mass.}, + year = {2001}, + author = {J.E. Hopcroft and R. Motwani and J.D. Ullman}, + edition = {2nd}, + owner = {ver}, + timestamp = {2010.06.12} +} + +@PHDTHESIS{KariPhD, + author = {Lila Kari}, + title = {On Insertion and Deletion in Formal Languages}, + school = {University of Turku}, + year = {1991}, + owner = {ver}, + timestamp = {2009.10.27} +} + +@INPROCEEDINGS{KPTY97, + author = {Lila Kari and Gheorghe P\u{a}un and Gabriel Thierrin and Sheng Yu}, + title = {At the Crossroads of DNA Computing and Formal Languages: Characterizing + {RE} Using Insertion-Deletion Systems}, + booktitle = {Proc. of 3rd DIMACS Workshop on DNA Based Computing}, + year = {1997}, + pages = {318-333}, + publisher = {Philadelphia}, + owner = {ver}, + timestamp = {2009.10.27} +} + +@ARTICLE{KT96, + author = {Lila Kari and Gabriel Thierrin}, + title = {Contextual Insertions/Deletions and Computability}, + journal = {Information and Computation}, + year = {1996}, + volume = {131}, + pages = {47-61}, + number = {1}, + bibsource = {DBLP, http://dblp.uni-trier.de} +} + +@INPROCEEDINGS{KKK01, + author = {Yevgenia Khodor and Julia Khodor and Thomas F. Knight Jr.}, + title = {Experimental Conformation of the Basic Principles of Length-only + Discrimination}, + booktitle = {DNA Computing, 7th International Workshop on DNA-Based Computers, + DNA7, Tampa, Florida, USA, June 10-13, 2001, Revised Papers}, + year = {2001}, + editor = {Natasa Jonoska and Nadrian C. Seeman}, + volume = {2340}, + series = {Lecture Notes in Computer Science}, + pages = {223-230}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://link.springer.de/link/service/series/0558/bibs/2340/23400223.htm} +} + +@ARTICLE{Kitano, + author = {H. Kitano}, + title = {A Graphical Notation for Biochemical Networks}, + journal = {Biosilico}, + year = {2003}, + volume = {1}, + pages = {169-176}, + owner = {ver}, + timestamp = {2010.07.19} +} + +@INCOLLECTION{Kleene56, + author = {Stephen Cole Kleene}, + title = {Representation of Events in Nerve Nets and Finite Automata}, + booktitle = {Automata Studies}, + publisher = {Princeton University Press}, + year = {1956}, + editor = {Claude Shannon and John McCarthy}, + pages = {3--41}, + address = {Princeton, NJ} +} + +@ARTICLE{Kohn, + author = {K. W. Kohn}, + title = {Molecular Interaction Map of the Mammalian Cell Cycle Control and + {DNA} Repair Systems}, + journal = {Molecular Biology of the Cell}, + year = {1999}, + volume = {10}, + pages = {2703-2734}, + owner = {ver}, + timestamp = {2010.07.19} +} + +@ARTICLE{Korec, + author = {Ivan Korec}, + title = {Small Universal Register Machines}, + journal = {Theoretical Computer Science}, + year = {1996}, + volume = {168}, + pages = {267-301}, + number = {2}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1016/S0304-3975(96)00080-1} +} + +@ARTICLE{Marcus69, + author = {Solomon Marcus}, + title = {Contextual Grammars}, + journal = {Revue Roumaine de Math\' ematiques Pures et Appliqu\' ees}, + year = {1969}, + volume = {14}, + pages = {1525-1534}, + owner = {ver}, + timestamp = {2009.10.26} +} + +@ARTICLE{MR99, + author = {Maurice Margenstern and Yurii Rogozhin}, + title = {A Universal Time-Varying Distributed {H} System of Degree 2}, + journal = {Biosystems}, + year = {1999}, + volume = {52}, + pages = {73--80} +} + +@ARTICLE{MVPS98, + author = {Carlos Mart\'{\i}n-Vide and Gheorghe P\u{a}un and Arto Salomaa}, + title = {Characterizations of Recursively Enumerable Languages by Means of + Insertion Grammars}, + journal = {Theoretical Computer Science}, + year = {1998}, + volume = {205}, + pages = {195-205}, + number = {1-2}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1016/S0304-3975(97)00079-0} +} + +@ARTICLE{mazoyer87, + author = {Jacques Mazoyer}, + title = {A Six-State Minimal Time Solution to the Firing Squad Synchronization + Problem}, + journal = {Theoretical Computer Science}, + year = {1987}, + volume = {50}, + pages = {183-238}, + bibsource = {DBLP, http://dblp.uni-trier.de} +} + +@BOOK{minsky67, + title = {Computations: Finite and Infinite Machines}, + publisher = {Prentice Hall, Englewood Cliffts, NJ}, + year = {1967}, + author = {Marvin Minsky} +} + +@ARTICLE{Paun96, + author = {Gheorghe P\u{a}un}, + title = {Regular Extended {H} Systems are Computationally Universal}, + journal = {Journal of Automata, Languages and Combinatorics}, + year = {1996}, + volume = {1}, + pages = {27-36}, + number = {1}, + bibsource = {DBLP, http://dblp.uni-trier.de} +} + +@BOOK{PaunKluwer97, + title = {Marcus Contextual Grammars}, + publisher = {Kluwer Academic Publishers}, + year = {1997}, + author = {Gheorghe P\u{a}un}, + address = {Norwell, MA, USA}, + isbn = {0792347838} +} + +@BOOK{Pbook, + title = {Membrane Computing. An Introduction}, + publisher = {Springer--Verlag}, + year = {2002}, + author = {Gheorghe P\u{a}un}, + owner = {ver}, + timestamp = {2009.10.27} +} + +@BOOK{Phandbook, + title = {The Oxford Handbook Of Membrane Computing}, + publisher = {Oxford University Press}, + year = {2009}, + author = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto Salomaa}, + owner = {ver}, + timestamp = {2010.05.08} +} + +@BOOK{PRSbook, + title = {{DNA} Computing: New Computing Paradigms}, + publisher = {Springer}, + year = {1998}, + author = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Aarto Salomaa}, + isbn = {3-540-64196-3}, + key = {PaunG} +} + +@ARTICLE{Post43, + author = {Emil Post}, + title = {Formal Reductions of the General Combinatorial Decision Problem}, + journal = {American Journal of Mathematics}, + year = {1943}, + volume = {65}, + pages = {197--215}, + number = {2}, + owner = {ver}, + timestamp = {2010.07.25} +} + +@ARTICLE{Rogozhin96, + author = {Yurii Rogozhin}, + title = {Small Universal {T}uring Machines}, + journal = {Theoretical Computer Science}, + year = {1996}, + volume = {168}, + pages = {215-240}, + number = {2}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1016/S0304-3975(96)00077-1} +} + +@BOOK{HFL, + title = HFL, + publisher = Springer, + year = {1997}, + editor = { }, + author = {G. Rozenberg and A. Salomaa}, + owner = {ver}, + timestamp = {2010.06.12} +} + +@INPROCEEDINGS{worsch, + author = {Hubert Schmid and Thomas Worsch}, + title = {The Firing Squad Synchronization Problem with Many Generals For One-Dimensional + CA}, + booktitle = {Exploring New Frontiers of Theoretical Informatics, IFIP 18th World + Computer Congress, TC1 3rd International Conference on Theoretical + Computer Science (TCS2004), 22-27 August 2004, Toulouse, France}, + year = {2004}, + editor = {Jean-Jacques L{\'e}vy and Ernst W. Mayr and John C. Mitchell}, + pages = {111-124}, + publisher = {Kluwer}, + bibsource = {DBLP, http://dblp.uni-trier.de} +} + +@INPROCEEDINGS{Smith96, + author = {Warren D. Smith}, + title = {{DNA} Computers in Vitro and in Vivo}, + booktitle = {Proceedings of DIMACS Workshop on DNA Based Computers}, + year = {1996}, + editor = {R.J. Lipton and E.B. Baum}, + series = {DIMACS Series in Discrete Mathematicts and Theoretical Computer Science}, + pages = {121-185}, + publisher = {American Mathematical Society}, + owner = {ver}, + timestamp = {2009.10.27} +} + +@ARTICLE{spellman, + author = {PT. Spellman and G. Sherlock}, + title = {Reply Whole-Cell Synchronization -- Effective Tools for Cell Cycle + Studies}, + journal = {Trends in Biotechnology}, + year = {2004}, + volume = {22}, + pages = {270-273}, + number = {6}, + owner = {ver}, + timestamp = {2010.05.08} +} + +@ARTICLE{TY-NC, + author = {Akihiro Takahara and Takashi Yokomori}, + title = {On the Computational Power of Insertion-Deletion Systems}, + journal = {Natural Computing}, + year = {2003}, + volume = {2}, + pages = {321-336}, + number = {4}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1023/B:NACO.0000006769.27984.23} +} + +@INPROCEEDINGS{TY02, + author = {Akihiro Takahara and Takashi Yokomori}, + title = {On the Computational Power of Insertion-Deletion Systems}, + booktitle = {DNA Computing, 8th International Workshop on DNA Based Computers, + DNA8, Sapporo, Japan, June 10-13, 2002, Revised Papers}, + year = {2002}, + editor = {Masami Hagiya and Azuma Ohuchi}, + volume = {2568}, + series = {Lecture Notes in Computer Science}, + pages = {269-280}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://link.springer.de/link/service/series/0558/bibs/2568/25680269.htm} +} + +@INPROCEEDINGS{umeo, + author = {Hiroshi Umeo and Masashi Maeda and Norio Fujiwara}, + title = {An Efficient Mapping Scheme for Embedding Any One-Dimensional Firing + Squad Synchronization Algorithm onto Two-Dimensional Arrays}, + booktitle = {Cellular Automata, 5th International Conference on Cellular Automata + for Research and Industry, ACRI 2002, Geneva, Switzerland, October + 9-11, 2002, Proceedings}, + year = {2002}, + editor = {Stefania Bandini and Bastien Chopard and Marco Tomassini}, + volume = {2493}, + series = {Lecture Notes in Computer Science}, + pages = {69-81}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://link.springer.de/link/service/series/0558/bibs/2493/24930069.htm} +} + +@BOOK{Wolfram02, + title = {A New Kind of Science}, + publisher = {Wolfram Media Inc}, + year = {2002}, + author = {Stephen Wolfram}, + owner = {ver}, + timestamp = {2010.07.20} +} + +@ARTICLE{yunes, + author = {Jean-Baptiste Yun{\`e}s}, + title = {Seven-State Solutions to the Firing Squad Synchronization Problem}, + journal = {Theoretical Computer Science}, + year = {1994}, + volume = {127}, + pages = {313-332}, + number = {2}, + bibsource = {DBLP, http://dblp.uni-trier.de} +} + +@BOOK{applP, + title = {Applications of Membrane Computing}, + publisher = {Springer}, + year = {2006}, + editor = {Gabriel Ciobanu and Mario J. P{\'e}rez-Jim{\'e}nez and Gheorghe P\u{a}un}, + series = {Natural Computing Series}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + booktitle = {Applications of Membrane Computing}, + isbn = {978-3-540-25017-3} +} + +@OTHER{Ppage, + key = {ZZZ}, + owner = {ver}, + timestamp = {2010.07.19}, + title = {The {P} systems Web Page: \texttt{http://ppage.psystems.eu/}} +} + +@comment{jabref-meta: selector_publisher:} + +@comment{jabref-meta: selector_author:} + +@comment{jabref-meta: selector_journal:} + +@comment{jabref-meta: selector_keywords:} + diff --git a/bib/hdr_verlan.bib b/bib/hdr_verlan.bib new file mode 100644 index 0000000..b253243 --- /dev/null +++ b/bib/hdr_verlan.bib @@ -0,0 +1,494 @@ +% This file was created with JabRef 2.6. +% Encoding: Cp1252 + +@STRING{TCS = {Theoretical Computer Science}} + +@INCOLLECTION{FARV09, + author = {R. Freund and A. Alhazov and Y. Rogozhin and S. Verlan}, + title = {Communication {P} Systems}, + booktitle = {The Oxford Handbook of Membrane Computing}, + publisher = {Oxford University Press}, + year = {2009}, + editor = {Gh. P\u{a}un and G. Rozenberg and A. Salomaa}, + pages = {118--143}, + crossref = {Paun:2010:OHM:1738939}, + owner = {ver}, + timestamp = {2010.06.14}, + url = {05-Paun-C05.pdf} +} + +@INCOLLECTION{VF09, + author = {S. Verlan and P. Frisco}, + title = {Splicing {P} systems}, + booktitle = {The Oxford Handbook of Membrane Computing}, + publisher = {Oxford University Press}, + year = {2009}, + editor = {Gh. P\u{a}un and G. Rozenberg and A. Salomaa}, + pages = {198--226}, + crossref = {Phandbook}, + owner = {ver}, + timestamp = {2010.06.14}, + url = {08-Paun-C08.pdf} +} + +@INPROCEEDINGS{AFOV07, + author = {Artiom Alhazov and Rudolf Freund and Marion Oswald and Sergey Verlan}, + title = {Partial Halting in {P} Systems Using Membrane Rules with Permitting + Contexts}, + booktitle = {Machines, Computations, and Universality, 5th International Conference, + MCU 2007, Orl{\'e}ans, France, September 10-13, 2007, Proceedings}, + year = {2007}, + editor = {J{\'e}r{\^o}me Olivier Durand-Lose and Maurice Margenstern}, + volume = {4664}, + series = {Lecture Notes in Computer Science}, + pages = {110-121}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1007/978-3-540-74593-8_10}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {phaltMCU_LNCS.pdf} +} + +@INPROCEEDINGS{AKRV09, + author = {Artiom Alhazov and Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan}, + title = {P Systems with Minimal Insertion and Deletion}, + booktitle = {Proceedings of Seventh Brainstorming Week on Membrane Computing Sevilla, + February 2--6, 2009}, + year = {2009}, + editor = {Rosa Guti\'errez-Escudero and Miguel Angel Guti\'errez-Naranjo and + Gheorghe P\u{a}un and Ignacio P\'erez-Hurtado and Agust\'in Riscos-Nunez}, + volume = {I}, + pages = {9--21}, + publisher = {F\'enix Editora, Sevilla}, + note = {Also accepted to \emph{Theoretical Computer Science}.}, + timestamp = {2009.07.02}, + url = {mInsDel_tcs4_v1.pdf} +} + +@INBOOK{AKRV10-chapter, + chapter = {1}, + pages = {459--524}, + title = {New Trends in Formal Language Theory + + Inspired by Natural Computing: + + Small Size Insertion and Deletion Systems}, + publisher = {Imperial College Press}, + year = {2010}, + author = {Artiom Alhazov and Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan}, + series = {Mathematics, Computing, Language, and Life: Frontiers in Mathematical + Linguistics and Language Theory}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {book_main.pdf} +} + +@INBOOK{AKRV10-chapter-pub, + chapter = {1}, + pages = {459--524}, + title = {Small Size Insertion and Deletion Systems}, + publisher = {World Scientific}, + booktitle = {Scientific Applications of Language Methods. Mathematics, Computing, Language, and Life: Frontiers in Mathematical Linguistics and Language Theory}, + year = {2010}, + volume = {228}, + author = {Artiom Alhazov and Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan}, + series = {Mathematics, Computing, Language, and Life: Frontiers in Mathematical + Linguistics and Language Theory}, +} + +@INPROCEEDINGS{AMV08, + author = {Artiom Alhazov and Maurice Margenstern and Sergey Verlan}, + title = {Fast Synchronization in {P} Systems}, + booktitle = {Membrane Computing - 9th International Workshop, WMC 2008, Edinburgh, + UK, July 28-31, 2008, Revised Selected and Invited Papers}, + year = {2008}, + editor = {David W. Corne and Pierluigi Frisco and Gheorghe P\u{a}un and Grzegorz + Rozenberg and Arto Salomaa}, + volume = {5391}, + series = {Lecture Notes in Computer Science}, + pages = {118-128}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + comment = {DBLP:conf/membrane/AlhazovMV08}, + ee = {http://dx.doi.org/10.1007/978-3-540-95885-7_9}, + isbn = {978-3-540-95884-0}, + owner = {ver}, + timestamp = {2010.05.08}, + url = {fastSyncLNCS.pdf} +} + +@ARTICLE{ARV07, + author = {Artiom Alhazov and Yurii Rogozhin and Sergey Verlan}, + title = {Minimal Cooperation in Symport/Antiport Tissue {P} Systems}, + journal = {International Journal of Foundations of Computer Science}, + year = {2007}, + volume = {18}, + pages = {163-180}, + number = {1}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1142/S0129054107004619}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {mincoIJFCS.pdf} +} + +@TECHREPORT{AV08, + author = {Artiom Alhazov and Sergey Verlan}, + title = {Minimization Strategies for Maximally Parallel Multiset Rewriting + Systems}, + institution = {TUCS}, + year = {2008}, + number = {862}, + note = {Also accepted to \emph{Theoretical Computer Science}}, + owner = {ver}, + timestamp = {2010.05.08}, + url = {tiny_symanti_tcs_v2.pdf} +} + +@ARTICLE{BGMV07, + author = {Francesco Bernardini and Marian Gheorghe and Maurice Margenstern + and Sergey Verlan}, + title = {How to Synchronize the Activity of All Components of a {P} System?}, + journal = {International Journal of Foundations of Computer Science.}, + year = {2008}, + volume = {19}, + pages = {1183-1198}, + number = {5}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + comment = {DBLP:journals/ijfcs/BernardiniGMV08}, + ee = {http://dx.doi.org/10.1142/S0129054108006224}, + owner = {ver}, + timestamp = {2010.07.19}, + url = {syncIJFCS.pdf} +} + +@ARTICLE{CMVV07, + author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and Maurice Margenstern and Gy{\"o}rgy + Vaszil and Sergey Verlan}, + title = {On Small Universal Antiport {P} Systems}, + journal = TCS, + year = {2007}, + volume = {372}, + pages = {152-164}, + number = {2-3}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1016/j.tcs.2006.11.023}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {smallsantiTCS.pdf} +} + +@ARTICLE{CV08, + author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and Sergey Verlan}, + title = {On Length-Separating Test Tube Systems}, + journal = {Natural Computing}, + year = {2008}, + volume = {7}, + pages = {167-181}, + number = {2}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + comment = {DBLP:journals/nc/Csuhaj-VarjuV08}, + ee = {http://dx.doi.org/10.1007/s11047-007-9034-z}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {lensepNC.pdf} +} + +@ARTICLE{CV10, + author = {E. Csuhaj-Varj{\'u} and S. Verlan}, + title = {On Generalized Communicating {P} Systems with Minimal Interaction + Rules}, + journal = {Theoretical Computer Science}, + year = {2010}, + note = {2010. In press.}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {min-int-revised-v8.pdf} +} + +@INPROCEEDINGS{FKV09, + author = {Rudolf Freund and Marian Kogler and Sergey Verlan}, + title = {P Automata with Controlled Use of Minimal Communication Rules}, + booktitle = {Workshop on Non-Classical Models of Automata and Applications, NCMA + 2009, Wroclaw, Poland}, + year = {2009}, + editor = {H. Bordihn and R. Freund and M. Holzer and M. Kutrib and F. Otto}, + pages = {107--120}, + publisher = {Oesterreichische Computer Gesellschaft}, + owner = {ver}, + timestamp = {2009.10.08}, + url = {NCMAfreundetal.pdf} +} + +@INPROCEEDINGS{FreundVerlan07, + author = {Rudolf Freund and Sergey Verlan}, + title = {A Formal Framework for Static (Tissue) {P} Systems}, + booktitle = {Membrane Computing, 8th International Workshop, WMC 2007, Thessaloniki, + Greece, June 25-28, 2007 Revised Selected and Invited Papers}, + year = {2007}, + editor = {George Eleftherakis and Petros Kefalas and Gheorghe P\u{a}un and + Grzegorz Rozenberg and Arto Salomaa}, + volume = {4860}, + series = {Lecture Notes in Computer Science}, + pages = {271-284}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1007/978-3-540-77312-2_17}, + isbn = {978-3-540-77311-5}, + owner = {ver}, + timestamp = {2009.11.18}, + url = {formFrameworkLNCS.pdf} +} + +@INPROCEEDINGS{FV08, + author = {R. Freund and S. Verlan}, + title = {P Systems Working in the k-Restricted Minimally Parallel Mode}, + booktitle = {International Workshop on Computing with Biomolecules, August 27th, + 2008, Wien, Austria}, + year = {2008}, + editor = {Erzs�bet Csuhaj-Varj� and Rudolf Freund and Marion Oswald and Kai + Salomaa}, + volume = {244}, + pages = {43--52}, + publisher = {Oesterreichische Computer Gesellschaft}, + owner = {ver}, + timestamp = {2009.07.02}, + url = {minmaxkfin.pdf} +} + +@INPROCEEDINGS{KRV08, + author = {Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan}, + title = {Further Results on Insertion-Deletion Systems with One-Sided Contexts}, + booktitle = {Language and Automata Theory and Applications, Second International + Conference, LATA 2008, Tarragona, Spain, March 13-19, 2008. Revised + Papers}, + year = {2008}, + editor = {Carlos Mart\'{\i}n-Vide and Friedrich Otto and Henning Fernau}, + volume = {5196}, + series = {Lecture Notes in Computer Science}, + pages = {333-344}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + comment = {DBLP:conf/lata/KrassovitskiyRV08}, + ee = {http://dx.doi.org/10.1007/978-3-540-88282-4_31}, + isbn = {978-3-540-88281-7}, + url = {furtherInsDelLNCS.pdf} +} + +@INPROCEEDINGS{KRV08b, + author = {Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan}, + title = {One-Sided Insertion and Deletion: Traditional and {P} Systems Case}, + booktitle = {International Workshop on Computing with Biomolecules, August 27th, + 2008, Wien, Austria}, + year = {2008}, + editor = {Erzs\'ebet Csuhaj-Varj\'u and Rudolf Freund and Marion Oswald and + Kai Salomaa}, + pages = {53--64}, + publisher = {Druckerei Riegelnik}, + comment = {http://www.emcc.at/CBM2008/CBM2008.pdf}, + timestamp = {2009.07.02}, + url = {insdelMemf1.pdf} +} + +@INPROCEEDINGS{KRV08c, + author = {Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan}, + title = {Computational Power of {P} Systems with Small Size Insertion and + Deletion Rules}, + booktitle = {Proceedings International Workshop on The Complexity of Simple Programs, + Cork, Ireland, 6-7th December 2008}, + year = {2009}, + editor = {Turlough Neary and Damien Woods and Anthony Karel Seda and Niall + Murphy}, + volume = {1}, + series = {EPTCS}, + pages = {108-117}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://arxiv.org/abs/0906.3119}, + owner = {ver}, + timestamp = {2010.06.14}, + url = {pinsdel-final.pdf} +} + +@UNPUBLISHED{KRV09-NC, + author = {Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan}, + title = {Computational Power of Insertion-Deletion ({P}) Systems with Rules + of Size Two}, + note = {Accepted to \emph{Natural Computing}. 2010, in publication.}, + owner = {ver}, + timestamp = {2009.10.28}, + url = {insdel_110_nc-v6.pdf} +} + +@ARTICLE{MPRV05, + author = {Maurice Margenstern and Gheorghe P\u{a}un and Yurii Rogozhin and + Sergey Verlan}, + title = {Context-Free Insertion-Deletion Systems}, + journal = TCS, + year = {2005}, + volume = {330}, + pages = {339-348}, + number = {2}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1016/j.tcs.2004.06.031}, + url = {cfInsDelTCS.pdf} +} + +@INPROCEEDINGS{MRV07, + author = {Artiom Matveevici and Yurii Rogozhin and Sergey Verlan}, + title = {Insertion-Deletion Systems with One-Sided Contexts}, + booktitle = {Machines, Computations, and Universality, 5th International Conference, + MCU 2007, Orl{\'e}ans, France, September 10-13, 2007, Proceedings}, + year = {2007}, + editor = {J{\'e}r{\^o}me Olivier Durand-Lose and Maurice Margenstern}, + volume = {4664}, + series = {Lecture Notes in Computer Science}, + pages = {205-217}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1007/978-3-540-74593-8_18}, + url = {insdeloneM_LNCS.pdf} +} + +@INPROCEEDINGS{RV05, + author = {Yurii Rogozhin and Sergey Verlan}, + title = {On the Rule Complexity of Universal Tissue {P} Systems}, + booktitle = {Membrane Computing, 6th International Workshop, WMC 2005, Vienna, + Austria, July 18-21, 2005, Revised Selected and Invited Papers}, + year = {2005}, + editor = {Rudolf Freund and Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto + Salomaa}, + volume = {3850}, + series = {Lecture Notes in Computer Science}, + pages = {356-362}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1007/11603047_24}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {ruleComplLNCS.pdf} +} + +@INCOLLECTION{Verlan04a, + author = {Sergey Verlan}, + title = {Communicating Distributed {H} Systems with Alternating Filters}, + booktitle = {Aspects of Molecular Computing. Essays Dedicated to Tom Head on the + Occasion of His 70th Birthday}, + publisher = {Springer}, + year = {2004}, + editor = {N. Jonoska and Gh. P\u{a}un and G. Rozenberg}, + volume = {2950}, + series = {Lecture Notes in Computer Science}, + pages = {367--384}, + doi = {http://dx.doi.org/10.1007/b94864}, + url = {ttH_LNCS.pdf} +} + +@ARTICLE{Verlan07, + author = {Sergey Verlan}, + title = {On Minimal Context-Free Insertion-Deletion Systems}, + journal = {Journal of Automata, Languages and Combinatorics}, + year = {2007}, + volume = {12}, + pages = {317-328}, + number = {1-2}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + comment = {DBLP:journals/jalc/Verlan07}, + url = {http://lacl.univ-paris12.fr/verlan/data/articles/insdel22_jalc2.pdf} +} + +@PHDTHESIS{VerlanPhD, + author = {Sergey Verlan}, + title = {Head Systems and Applications to Bioinformatics}, + school = {University of Metz}, + year = {2004}, + owner = {ver}, + timestamp = {2010.07.25}, + url = {http://lacl.univ-paris12.fr/verlan/data/thesis-en.pdf} +} + +@INPROCEEDINGS{VerlanWMC09, + author = {Sergey Verlan}, + title = {Look-Ahead Evolution for {P} Systems}, + booktitle = {Membrane Computing, 10th International Workshop, WMC 2009, Curtea + de Arges, Romania, August 24-27, 2009. Revised Selected and Invited + Papers}, + year = {2009}, + editor = {Gheorghe P\u{a}un and Mario J. P{\'e}rez-Jim{\'e}nez and Agustin + Riscos-N{\'u}{\~n}ez and Grzegorz Rozenberg and Arto Salomaa}, + volume = {5957}, + series = {Lecture Notes in Computer Science}, + pages = {479-485}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1007/978-3-642-11467-0_32}, + isbn = {978-3-642-11466-3}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {Look-aheadP.pdf} +} + +@INPROCEEDINGS{VBGM06, + author = {Sergey Verlan and Francesco Bernardini and Marian Gheorghe and Maurice + Margenstern}, + title = {Computational Completeness of Tissue {P} Systems with Conditional + Uniport}, + booktitle = {Membrane Computing, 7th International Workshop, WMC 2006, Leiden, + The Netherlands, July 17-21, 2006, Revised, Selected, and Invited + Papers}, + year = {2006}, + editor = {Hendrik Jan Hoogeboom and Gheorghe P\u{a}un and Grzegorz Rozenberg + and Arto Salomaa}, + volume = {4361}, + series = {Lecture Notes in Computer Science}, + pages = {521-535}, + publisher = {Springer}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + ee = {http://dx.doi.org/10.1007/11963516_33}, + owner = {ver}, + timestamp = {2010.06.11}, + url = {condUniport.pdf} +} + +@ARTICLE{VBGM08, + author = {Sergey Verlan and Francesco Bernardini and Marian Gheorghe and Maurice + Margenstern}, + title = {Generalized Communicating {P} Systems}, + journal = TCS, + year = {2008}, + volume = {404}, + pages = {170-184}, + number = {1-2}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + comment = {DBLP:journals/tcs/VerlanBGM08}, + ee = {http://dx.doi.org/10.1016/j.tcs.2008.04.008}, + owner = {ver}, + timestamp = {2010.05.08}, + url = {genComm.pdf} +} + +@INPROCEEDINGS{VR09, + author = {Sergey Verlan and Yurii Rogozhin}, + title = {New Choice for Small Universal Devices: Symport/Antiport {P} Systems}, + booktitle = {Proceedings International Workshop on The Complexity of Simple Programs, + Cork, Ireland, 6-7th December 2008}, + year = {2008}, + editor = {Turlough Neary and Damien Woods and Anthony Karel Seda and Niall + Murphy}, + volume = {1}, + series = {EPTCS}, + pages = {235-241}, + bibsource = {DBLP, http://dblp.uni-trier.de}, + owner = {ver}, + timestamp = {2010.06.14}, + url = {symantiov.pdf} +} + +@comment{jabref-meta: selector_publisher:} + +@comment{jabref-meta: selector_author:} + +@comment{jabref-meta: selector_journal:} + +@comment{jabref-meta: selector_keywords:} + diff --git a/bib/insdel.bib b/bib/insdel.bib new file mode 100644 index 0000000..5955035 --- /dev/null +++ b/bib/insdel.bib @@ -0,0 +1,726 @@ +@article{Biegler2007, + author = {Biegler, Franziska and Burrell, Michael J. and Daley, Mark}, + title = {Regulated {RNA} Rewriting: Modelling {RNA} Editing with Guided Insertion}, + journal = {Theoretical Computer Science}, + issue_date = {2007}, + volume = {387}, + number = {2}, + month = nov, + year = {2007}, + issn = {0304-3975}, + pages = {103--112}, + numpages = {10}, + url = {http://dx.doi.org/10.1016/j.tcs.2007.07.030}, + doi = {10.1016/j.tcs.2007.07.030}, + acmid = {1297474}, + publisher = {Elsevier Science Publishers Ltd.}, + address = {Essex, UK}, + keywords = {Formal languages, Kinetoplasts, RNA editing, Regulated rewriting}, +} + +@article{MPMV98, + author = {Marcus, Solomon and P\u{a}un, Gheorghe and Mart\'{\i}n-Vide, Carlos}, + title = {Contextual Grammars As Generative Models of Natural Languages}, + journal = {Computational Linguistics}, + issue_date = {June 1998}, + volume = {24}, + number = {2}, + month = jun, + year = {1998}, + issn = {0891-2017}, + pages = {245--274}, + numpages = {30}, + url = {http://dl.acm.org/citation.cfm?id=972732.972735}, + acmid = {972735}, + publisher = {MIT Press}, + address = {Cambridge, MA, USA}, +} + +@incollection{KMM97, +year={1997}, +isbn={978-3-540-63386-0}, +booktitle={Fundamentals of Computation Theory}, +volume={1279}, +series={Lecture Notes in Computer Science}, +editor={Chlebus, Bogdan S. and Czaja, Ludwik}, +doi={10.1007/BFb0036190}, +title={Contextual grammars with distributed catenation and shuffle}, +url={http://dx.doi.org/10.1007/BFb0036190}, +publisher={Springer Berlin Heidelberg}, +author={Kudlek, Manfred and Marcus, Solomon and Mateescu, Alexandru}, +pages={269-280}, +language={English} +} + +@article{Domosi20084877, +title = "Marcus contextual languages consisting of primitive words ", +journal = "Discrete Mathematics ", +volume = "308", +number = "21", +pages = "4877 - 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61", +year = "2005", +note = "", +issn = "0304-3975", +doi = "http://dx.doi.org/10.1016/j.tcs.2004.09.038", +url = "http://www.sciencedirect.com/science/article/pii/S0304397504006863", +author = "Lila Kari and Petr Sosík" +} + +@article {PPJY2008, + title = {Representations and characterizations of languages in {C}homsky hierarchy by means of insertion-deletion systems}, + journal = {International Journal of Foundations of Computer Science}, + volume = {19}, + year = {2008}, + pages = {859-871}, + publisher = {World Scientific}, + address = {London, U.K.}, + keywords = {Insertion-deletion systems; Recursively enumerable languages; Context-free languages; Regular languages; 68Q42 (AMSC); 68Q45 (AMSC); 68Q50 (AMSC)}, + issn = {0129-0541}, + doi = {10.1142/S0129054108006005}, + url = {http://dx.doi.org/10.1142/S0129054108006005}, + author = {Gheorghe P\u{a}un and Mario J. 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Inf.}, + issue_date = {August 2006}, + volume = {71}, + number = {2,3}, + month = feb, + year = {2006}, + issn = {0169-2968}, + pages = {279--308}, + numpages = {30}, + url = {http://dl.acm.org/citation.cfm?id=1227505.1227513}, + acmid = {1227513}, + publisher = {IOS Press}, + address = {Amsterdam, The Netherlands, The Netherlands}, + keywords = {Spiking neurons, Turing computability, membrane computing, semilinear set}, +} + +@article{Frisco2005, + author = {Pierluigi Frisco}, + title = {About {P} systems with symport/antiport}, + journal = {Soft Computing}, + volume = {9}, + number = {9}, + pages = {664--672}, + year = {2005}, + url = {http://dx.doi.org/10.1007/s00500-004-0396-1}, + doi = {10.1007/s00500-004-0396-1}, + timestamp = {Fri, 27 Jan 2006 08:38:29 +0100}, + biburl = {http://dblp.uni-trier.de/rec/bib/journals/soco/Frisco05}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@incollection{FLMPVZ2014, +year={2014}, +isbn={978-3-642-54238-1}, +booktitle={Membrane Computing}, +volume={8340}, +series={Lecture Notes in Computer Science}, +editor={Alhazov, Artiom and Cojocaru, Svetlana and Gheorghe, Marian and Rogozhin, Yurii and Rozenberg, Grzegorz and Salomaa, Arto}, +doi={10.1007/978-3-642-54239-8_13}, +title={Flattening in (Tissue) {P} Systems}, +url={http://dx.doi.org/10.1007/978-3-642-54239-8_13}, +publisher={Springer Berlin Heidelberg}, +author={Freund, Rudolf and Leporati, Alberto and Mauri, Giancarlo and Porreca, Antonio E. and Verlan, Sergey and Zandron, Claudio}, +pages={173-188}, +language={English} +} + +@incollection{AS2005, +year={2005}, +isbn={978-3-540-25080-7}, +booktitle={Membrane Computing}, +volume={3365}, +series={Lecture Notes in Computer Science}, +editor={Mauri, Giancarlo and P\u{a}un, Gheorghe and P\'erez-Jim\'enez, Mario J. and Rozenberg, Grzegorz and Salomaa, Arto}, +doi={10.1007/978-3-540-31837-8_10}, +title={Ultimately Confluent Rewriting Systems. Parallel Multiset-Rewriting with Permitting or Forbidding Contexts}, +url={http://dx.doi.org/10.1007/978-3-540-31837-8_10}, +publisher={Springer Berlin Heidelberg}, +author={Alhazov, Artiom and Sburlan, Drago\c{s}}, +pages={178-189}, +language={English} +} + +@article{CPPPJ2007117, +title = "P systems with minimal parallelism ", +journal = "Theoretical Computer Science ", +volume = "378", +number = "1", +pages = "117 - 130", +year = "2007", +note = "", +issn = "0304-3975", +doi = "http://dx.doi.org/10.1016/j.tcs.2007.03.044", +url = "http://www.sciencedirect.com/science/article/pii/S0304397507002459", +author = "Gabriel Ciobanu and Linqiang Pan and Gheorghe P\u aun and Mario J. P\'erez-Jim\'enez", +keywords = "Membrane computing", +keywords = "P System", +keywords = "Universality", +keywords = "\{SAT\} Problem " +} + +@incollection{Freund2005, +year={2005}, +isbn={978-3-540-25080-7}, +booktitle={Membrane Computing}, +volume={3365}, +series={Lecture Notes in Computer Science}, +editor={Mauri, Giancarlo and Păun, Gheorghe and Pérez-Jiménez, MarioJ. and Rozenberg, Grzegorz and Salomaa, Arto}, +doi={10.1007/978-3-540-31837-8_3}, +title={Asynchronous {P} Systems and {P} Systems Working in the Sequential Mode}, +url={http://dx.doi.org/10.1007/978-3-540-31837-8_3}, +publisher={Springer Berlin Heidelberg}, +author={Freund, Rudolf}, +pages={36-62}, +language={English} +} + +@inproceedings{CS2004, + author = {Matteo Cavaliere and + Drago\c{s} Sburlan}, + title = {Time-Independent {P} Systems}, + booktitle = {Membrane Computing, 5th International Workshop, {WMC} 2004, Milan, + Italy, June 14-16, 2004, Revised Selected and Invited Papers}, + pages = {239--258}, + year = {2004}, + crossref = {DBLP:conf/membrane/2004}, + url = {http://dx.doi.org/10.1007/978-3-540-31837-8_14}, + doi = {10.1007/978-3-540-31837-8_14}, + timestamp = {Mon, 08 Aug 2011 15:22:15 +0200}, + biburl = {http://dblp.uni-trier.de/rec/bib/conf/membrane/CavaliereS04}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@proceedings{DBLP:conf/membrane/2004, + editor = {Giancarlo Mauri and + Gheorghe P\u{a}un and + Mario J. P{\'{e}}rez{-}Jim{\'{e}}nez and + Grzegorz Rozenberg and + Arto Salomaa}, + title = {Membrane Computing, 5th International Workshop, {WMC} 2004, Milan, + Italy, June 14-16, 2004, Revised Selected and Invited Papers}, + series = {Lecture Notes in Computer Science}, + volume = {3365}, + publisher = {Springer}, + year = {2005}, + isbn = {3-540-25080-8}, + timestamp = {Mon, 21 Feb 2005 10:04:47 +0100}, + biburl = {http://dblp.uni-trier.de/rec/bib/conf/membrane/2004}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@incollection{Ivanov2012, +year={2012}, +isbn={978-3-642-28023-8}, +booktitle={Membrane Computing}, +volume={7184}, +series={Lecture Notes in Computer Science}, +editor={Gheorghe, Marian and P\u{u}un, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto and Verlan, Sergey}, +doi={10.1007/978-3-642-28024-5_16}, +title={Basic Concurrency Resolution in Clock-Free {P} Systems}, +url={http://dx.doi.org/10.1007/978-3-642-28024-5_16}, +publisher={Springer Berlin Heidelberg}, +author={Ivanov, Sergiu}, +pages={226-242}, +language={English} +} + +@article{Ivanov2013, +author = {Ivanov, Sergiu}, +title = {A formal framework for clock-free networks of cells}, +journal = {International Journal of Computer Mathematics}, +volume = {90}, +number = {4}, +pages = {776-788}, +year = {2013}, +doi = {10.1080/00207160.2012.743652} +} + +@incollection{Freund2010, +year={2010}, +isbn={978-3-642-11466-3}, +booktitle={Membrane Computing}, +volume={5957}, +series={Lecture Notes in Computer Science}, +editor={P\u{a}un, Gheorghe and P\'erez-Jim\'enez, Mario J. and Riscos-N\'u\~nez, Agust\'in and Rozenberg, Grzegorz and Salomaa, Arto}, +doi={10.1007/978-3-642-11467-0_3}, +title={Transition and Halting Modes in (Tissue) {P} Systems}, +url={http://dx.doi.org/10.1007/978-3-642-11467-0_3}, +publisher={Springer Berlin Heidelberg}, +author={Freund, Rudolf}, +pages={18-29}, +language={English} +} + +@article{Ibarra2004379, +title = "Catalytic P systems, semilinear sets, and vector addition systems ", +journal = "Theoretical Computer Science ", +volume = "312", +number = "2–3", +pages = "379 - 399", +year = "2004", +note = "", +issn = "0304-3975", +doi = "http://dx.doi.org/10.1016/j.tcs.2003.10.028", +url = "http://www.sciencedirect.com/science/article/pii/S0304397503005735", +author = "Oscar H. Ibarra and Zhe Dang and Omer Egecioglu", +keywords = "Membrane computing", +keywords = "Catalytic system", +keywords = "Semilinear set", +keywords = "Vector addition system", +keywords = "Reachability problem " +} + +@Article{Turing1936, + Title = {On Computable Numbers, with an Application to the {E}ntscheidungsproblem}, + Author = {Alan M. Turing}, + Journal = {Proceedings of the London Mathematical Society}, + Year = {1936}, + Number = {2}, + Pages = {230--265}, + Volume = {42}, + + Owner = {ver}, + Publisher = {London Mathematical Society}, + Timestamp = {2013.09.16} +} + +@article{Wang:1957, + author = {Wang, Hao}, + title = {A Variant to {T}uring's Theory of Computing Machines}, + journal = {Journal of the ACM}, + issue_date = {Jan. 1957}, + volume = {4}, + number = {1}, + month = jan, + year = {1957}, + issn = {0004-5411}, + pages = {63--92}, + numpages = {30}, + url = {http://doi.acm.org/10.1145/320856.320867}, + doi = {10.1145/320856.320867}, + acmid = {320867}, + publisher = {ACM}, + address = {New York, NY, USA}, +} + +@article{Minsky1961, +author = {Minsky, Marvin}, +title = {Recursive unsolvability of {P}ost's problem of “Tag” and other topics in the theory of {T}uring machines}, +journal = {Annals of Mathematics, second series}, +volume = {74}, +year = {1961}, +pages = {437--455}, +} + +@incollection{Paun2001, +year={2001}, +isbn={978-1-85233-415-4}, +booktitle={Unconventional Models of Computation, UMC'2K}, +series={Discrete Mathematics and Theoretical Computer Science}, +editor={Antoniou, I. and Calude, C.S. and Dinneen, M.J.}, +doi={10.1007/978-1-4471-0313-4_7}, +title={Computing with Membranes: Attacking {NP}-Complete Problems}, +url={http://dx.doi.org/10.1007/978-1-4471-0313-4_7}, +publisher={Springer London}, +author={P\u{a}un, Gheorghe}, +pages={94-115}, +language={English} +} + +@article{Baker1974315, +title = "Reversal-bounded multipushdown machines ", +journal = "Journal of Computer and System Sciences ", +volume = "8", +number = "3", +pages = "315 - 332", +year = "1974", +note = "", +issn = "0022-0000", +doi = "http://dx.doi.org/10.1016/S0022-0000(74)80027-9", +url = "http://www.sciencedirect.com/science/article/pii/S0022000074800279", +author = "Brenda S. Baker and Ronald V. Book" +} + +@incollection{ARV2011, +year={2011}, +isbn={978-3-642-18122-1}, +booktitle={Membrane Computing}, +volume={6501}, +series={Lecture Notes in Computer Science}, +editor={Gheorghe, Marian and Hinze, Thomas and Păun, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto}, +doi={10.1007/978-3-642-18123-8_10}, +title={A Small Universal Splicing P System}, +url={http://dx.doi.org/10.1007/978-3-642-18123-8_10}, +publisher={Springer Berlin Heidelberg}, +author={Alhazov, Artiom and Rogozhin, Yurii and Verlan, Sergey}, +pages={95-102}, +language={English} +} + +@Article{Shannon, + Title = {A Universal {T}uring Machine with Two Internal States}, + Author = {Claude E. Shannon}, + Journal = {Automata Studies, Annals of Mathematics Studies}, + Year = {1956}, + Pages = {157--165}, + Volume = {34}, + + Owner = {ver}, + Timestamp = {2013.09.17} +} + +@InProceedings{Minsky62, + Title = {Size and structure of universal {T}uring machines using tag systems}, + Author = {Marvin Minsky}, + Booktitle = {Recursive Function Theory: Proceedings, Symposium in Pure Mathematics, Provelence}, + Year = {1962}, + Pages = {229-238}, + Volume = {5}, + + Owner = {ver}, + Timestamp = {2013.09.17} +} + +@Article{Watanabe61, + Title = {5-symbol 8-state and 5-symbol 6-state universal {T}uring machines}, + Author = {Shinichi Watanabe}, + Journal = {Journal of the ACM}, + Year = {1961}, + Number = {4}, + Pages = {476--483}, + Volume = {8}, + + Owner = {ver}, + Timestamp = {2013.09.17} +} + +@inproceedings{IPV2014a, + author = {Sergiu Ivanov and + Elisabeth Pelz and + Sergey Verlan}, + title = {Small Universal Non-deterministic {P}etri Nets with Inhibitor Arcs}, + booktitle = {Descriptional Complexity of Formal Systems - 16th International Workshop, + {DCFS} 2014, Turku, Finland, August 5-8, 2014. Proceedings}, + pages = {186--197}, + year = {2014}, + crossref = {DBLP:conf/dcfs/2014}, + url = {http://dx.doi.org/10.1007/978-3-319-09704-6_17}, + doi = {10.1007/978-3-319-09704-6_17}, + timestamp = {Mon, 14 Jul 2014 13:19:05 +0200}, + biburl = {http://dblp.uni-trier.de/rec/bib/conf/dcfs/0001PV14}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@proceedings{DBLP:conf/dcfs/2014, + editor = {Helmut J{\"{u}}rgensen and + Juhani Karhum{\"{a}}ki and + Alexander Okhotin}, + title = {Descriptional Complexity of Formal Systems - 16th International Workshop, + {DCFS} 2014, Turku, Finland, August 5-8, 2014. Proceedings}, + series = {Lecture Notes in Computer Science}, + volume = {8614}, + publisher = {Springer}, + year = {2014}, + url = {http://dx.doi.org/10.1007/978-3-319-09704-6}, + doi = {10.1007/978-3-319-09704-6}, + isbn = {978-3-319-09703-9}, + timestamp = {Mon, 14 Jul 2014 13:14:30 +0200}, + biburl = {http://dblp.uni-trier.de/rec/bib/conf/dcfs/2014}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@InProceedings{IPV2014b, + Title = {Small Universal {P}etri Nets with Inhibitor Arcs}, + Author = {Sergiu Ivanov and + Elisabeth Pelz and + Sergey Verlan}, + Booktitle = {Computability in Europe}, + Year = {2014}, + + Ee = {http://arxiv.org/abs/1312.4414}, + Journal = {arXiv, CoRR} +} + +@INCOLLECTION{detpelz, + author = {Elisabeth Pelz}, + title = {Closure Properties of Deterministic {P}etri nets}, + booktitle = {Symposium on Theoretical Aspects of Computer Science, STACS '87}, + volume = {247}, + series = {Lecture Notes in Computer Science}, + pages = {371--382}, + publisher = {Springer}, + year = 1986 +} + +@article{Koiran:1999, + author = {Koiran, Pascal and Moore, Cristopher}, + title = {Closed-form Analytic Maps in One and Two Dimensions Can Simulate Universal {T}uring Machines}, + journal = {Theoretical Computer Science}, + issue_date = {Jan. 6, 1999}, + volume = {210}, + number = {1}, + month = jan, + year = {1999}, + issn = {0304-3975}, + pages = {217--223}, + numpages = {7}, + url = {http://dx.doi.org/10.1016/S0304-3975(98)00117-0}, + doi = {10.1016/S0304-3975(98)00117-0}, + acmid = {292115}, + publisher = {Elsevier Science Publishers Ltd.}, + address = {Essex, UK}, +} + +@Misc{gurobi, + Title = {Gurobi Optimizer Reference Manual}, + + Author = {Gurobi Optimization{, }Inc.}, + Year = {2014}, + + Url = {http://www.gurobi.com} +} + +@Book{AMPL, + Title = {AMPL: A Modeling Language for Mathematical Programming}, + Author = {Robert Fourer and David M. Gay and Brian W. Kernighan}, + Publisher = {Duxbury Press, Brooks/Cole Publishing Company}, + Year = {2002}, + Edition = {2nd}, + + ISBN = {0-534-38809-4} +} + +@inproceedings{LerouxS14, + author = {J{\'{e}}r{\^{o}}me Leroux and + Philippe Schnoebelen}, + title = {On Functions Weakly Computable by Petri Nets and Vector Addition Systems}, + booktitle = {Reachability Problems - 8th International Workshop, {RP} 2014, Oxford, + UK, September 22-24, 2014. Proceedings}, + pages = {190--202}, + year = {2014}, + crossref = {DBLP:conf/rp/2014}, + url = {http://dx.doi.org/10.1007/978-3-319-11439-2_15}, + doi = {10.1007/978-3-319-11439-2_15}, + timestamp = {Tue, 28 Oct 2014 18:50:19 +0100}, + biburl = {http://dblp.uni-trier.de/rec/bib/conf/rp/LerouxS14}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@proceedings{DBLP:conf/rp/2014, + editor = {Jo{\"{e}}l Ouaknine and + Igor Potapov and + James Worrell}, + title = {Reachability Problems - 8th International Workshop, {RP} 2014, Oxford, + UK, September 22-24, 2014. Proceedings}, + series = {Lecture Notes in Computer Science}, + volume = {8762}, + publisher = {Springer}, + year = {2014}, + url = {http://dx.doi.org/10.1007/978-3-319-11439-2}, + doi = {10.1007/978-3-319-11439-2}, + isbn = {978-3-319-11438-5}, + timestamp = {Mon, 15 Sep 2014 12:50:50 +0200}, + biburl = {http://dblp.uni-trier.de/rec/bib/conf/rp/2014}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@inproceedings{DufordJS99, + author = {Catherine Dufourd and + Petr Jancar and + Philippe Schnoebelen}, + title = {Boundedness of Reset {P/T} Nets}, + booktitle = {Automata, Languages and Programming, 26th International Colloquium, + ICALP'99, Prague, Czech Republic, July 11-15, 1999, Proceedings}, + pages = {301--310}, + year = {1999}, + crossref = {DBLP:conf/icalp/99}, + url = {http://dx.doi.org/10.1007/3-540-48523-6_27}, + doi = {10.1007/3-540-48523-6_27}, + timestamp = {Sun, 20 Sep 2009 11:17:52 +0200}, + biburl = {http://dblp.uni-trier.de/rec/bib/conf/icalp/DufordJS99}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@proceedings{DBLP:conf/icalp/99, + editor = {Ji\v{r}{\'{\i}} Wiedermann and + Peter van Emde Boas and + Mogens Nielsen}, + title = {Automata, Languages and Programming, 26th International Colloquium, + ICALP'99, Prague, Czech Republic, July 11-15, 1999, Proceedings}, + series = {Lecture Notes in Computer Science}, + volume = {1644}, + publisher = {Springer}, + year = {1999}, + isbn = {3-540-66224-3}, + timestamp = {Mon, 21 Jan 2002 15:41:36 +0100}, + biburl = {http://dblp.uni-trier.de/rec/bib/conf/icalp/99}, + bibsource = {dblp computer science bibliography, http://dblp.org} +} + +@article{Araki197685, +title = "Some decision problems related to the reachability problem for {P}etri nets ", +journal = "Theoretical Computer Science ", +volume = "3", +number = "1", +pages = "85 - 104", +year = "1976", +note = "", +issn = "0304-3975", +doi = "http://dx.doi.org/10.1016/0304-3975(76)90067-0", +url = "http://www.sciencedirect.com/science/article/pii/0304397576900670", +author = "Toshiro Araki and Tadao Kasami", +} diff --git a/bib/psystems.bib b/bib/psystems.bib new file mode 100644 index 0000000..962a9ce --- /dev/null +++ b/bib/psystems.bib @@ -0,0 +1,147 @@ +% psystems.bib +% +% A reference database for P systems. + +@String{j-jucs = "Journal of Universal Computer Science"} + +@incollection{AI2011, +year={2011}, +isbn={978-3-642-18122-1}, +booktitle={Membrane Computing}, +volume={6501}, +series={Lecture Notes in Computer Science}, +editor={Gheorghe, Marian and Hinze, Thomas and P\u{a}un, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto}, +doi={10.1007/978-3-642-18123-8_9}, +title={Polymorphic {P} Systems}, +url={http://dx.doi.org/10.1007/978-3-642-18123-8_9}, +publisher={Springer Berlin Heidelberg}, +author={Alhazov, Artiom and Ivanov, Sergiu and Rogozhin, Yurii}, +pages={81-94} +} + +@book{DBLP:books/daglib/0011126, + author = {John E. Hopcroft and + Rajeev Motwani and + Jeffrey D. Ullman}, + title = {Introduction to automata theory, languages, and computation + - international edition (2. ed)}, + publisher = {Addison-Wesley}, + year = {2003}, + isbn = {978-0-321-21029-6}, + pages = {I-XIV, 1-521}, + bibsource = {DBLP, http://dblp.uni-trier.de} +} + +@incollection{CPP2006, +year={2006}, +isbn={978-3-540-25017-3}, +booktitle={Applications of Membrane Computing}, +series={Natural Computing Series}, +editor={Ciobanu, Gabriel and P\u{a}un, Gheorghe and P\'{e}rez-Jim\{e}nez, Mario J.}, +doi={10.1007/3-540-29937-8_1}, +title={Introduction to Membrane Computing}, +url={http://dx.doi.org/10.1007/3-540-29937-8_1}, +publisher={Springer Berlin Heidelberg}, +author={P\u{a}un, Gheorghe}, +pages={1-42}, +language={English} +} + +@ARTICLE{Paun98computingwith, + author = {Gheorghe P\u{a}un}, + title = {Computing with Membranes}, + journal = {Journal of Computer and System Sciences}, + year = {1998}, + volume = {61}, + pages = {108--143} +} + +@MISC{Freund_matrixlanguages, + author = {Rudolf Freund and Oscar H. Ibarra and Gheorghe P\u{a}un and Hsu-chen Yen}, + title = {Matrix Languages, Register Machines, Vector Addition Systems}, + year = {} +} + +@misc{ppage, + title = {The {P} systems web page}, + howpublished = {\url{http://ppage.psystems.eu/}} +} + +@book{păun2002membrane, + title={Membrane Computing: An Introduction}, + author={P{\u{a}}un, Gheorghe}, + isbn={9783540436010}, + lccn={2002075730}, + series={Natural Computing Series Natural Computing}, + url={https://encrypted.google.com/books?id=8CE3BZ7y\_kIC}, + year={2002}, + publisher={Springer} +} + +@Article{Dassow:jucs_5_2:on_the_power_of, + author = {J\"{u}rgen Dassow and Gheorghe P\u{a}un"}, + title = "On the Power of Membrane Computing", + abstract = " + +We continue the investigation of the power of the computability models introduced in [12] under the name of transition super-cell systems. We compare these systems with classic mechanisms in formal language theory, context-free and matrix grammars, E0L and ET0L systems, interpreted as generating mechanisms of number relations (we take the Parikh image of the usual language generated by these mecha- nisms rather than the language). Several open problems are also formulated. +", + journal = j-jucs, + year = "1999", + volume = "5", + number = "2", + pages = "33--49", + date = "1999-02-28", + month = "feb", + note = "\url|http://www.jucs.org/jucs_5_2/on_the_power_of|"} + +@book{Paun:2010:OHM:1738939, + author = {P\u{a}un, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto}, + title = {The Oxford Handbook of Membrane Computing}, + year = {2010}, + isbn = {0199556679, 9780199556670}, + publisher = {Oxford University Press, Inc.}, + address = {New York, NY, USA}, +} + +@incollection{FV2007, +year={2007}, +isbn={978-3-540-77311-5}, +booktitle={Membrane Computing}, +volume={4860}, +series={Lecture Notes in Computer Science}, +editor={Eleftherakis, George and Kefalas, Petros and P\u{a}un, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto}, +doi={10.1007/978-3-540-77312-2_17}, +title={A Formal Framework for Static (Tissue) {P} Systems}, +url={http://dx.doi.org/10.1007/978-3-540-77312-2_17}, +publisher={Springer Berlin Heidelberg}, +author={Freund, Rudolf and Verlan, Sergey}, +pages={271-284} +} + +@book{Rozenberg:1997:HFL:267871, + editor = {Rozenberg, Grzegorz and Salomaa, Arto}, + title = {Handbook of Formal Languages, Vol. 3: Beyond Words}, + year = {1997}, + isbn = {3-540-60649-1}, + publisher = {Springer-Verlag New York, Inc.}, + address = {New York, NY, USA}, +} + +@article{Porreca:2011:PSA:1968992.1969023, + author = {Porreca, Antonio E. and Leporati, Alberto and Mauri, Giancarlo and Zandron, Claudio}, + title = {P Systems with Active Membranes: Trading Time for Space}, + issue_date = {March 2011}, + volume = {10}, + number = {1}, + month = mar, + year = {2011}, + issn = {1567-7818}, + pages = {167--182}, + numpages = {16}, + url = {http://dx.doi.org/10.1007/s11047-010-9189-x}, + doi = {10.1007/s11047-010-9189-x}, + acmid = {1969023}, + publisher = {Kluwer Academic Publishers}, + address = {Hingham, MA, USA}, + keywords = {Computational complexity, Membrane computing, Register machines} +}