Languages Alive: Essays Dedicated to Jürgen Dassow on the Occasion of His 65th Birthday

299 Pages·2012·5.18 MB·English

by  M. Sakthi Balan

Lecture Notes in Computer Science 7300
CommencedPublicationin1973
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EditorialBoard
DavidHutchison
LancasterUniversity,UK
TakeoKanade
CarnegieMellonUniversity,Pittsburgh,PA,USA
JosefKittler
UniversityofSurrey,Guildford,UK
JonM.Kleinberg
CornellUniversity,Ithaca,NY,USA
AlfredKobsa
UniversityofCalifornia,Irvine,CA,USA
FriedemannMattern
ETHZurich,Switzerland
JohnC.Mitchell
StanfordUniversity,CA,USA
MoniNaor
WeizmannInstituteofScience,Rehovot,Israel
OscarNierstrasz
UniversityofBern,Switzerland
C.PanduRangan
IndianInstituteofTechnology,Madras,India
BernhardSteffen
TUDortmundUniversity,Germany
MadhuSudan
MicrosoftResearch,Cambridge,MA,USA
DemetriTerzopoulos
UniversityofCalifornia,LosAngeles,CA,USA
DougTygar
UniversityofCalifornia,Berkeley,CA,USA
GerhardWeikum
MaxPlanckInstituteforInformatics,Saarbruecken,Germany
Henning Bordihn Martin Kutrib
Bianca Truthe (Eds.)
Languages Alive
Essays Dedicated to Jürgen Dassow
on the Occasion of His 65th Birthday
1 3
VolumeEditors
HenningBordihn
UniversitätPotsdam,InstitutfürInformatik
August-Bebel-Straße89
14482Potsdam,Germany
E-mail:[email protected]
MartinKutrib
UniversitätGiessen,InstitutfürInformatik
Arndtstraße2
35392Giessen,Germany
E-mail:[email protected]
BiancaTruthe
Otto-von-Guericke-UniversitätMagdeburg,FakultätfürInformatik
Universitätsplatz2
39106Magdeburg,Germany
E-mail:[email protected]
CoverillustrationbyBiancaTruthe
©BiancaTruthe
ISSN0302-9743 e-ISSN1611-3349
ISBN978-3-642-31643-2 e-ISBN978-3-642-31644-9
DOI10.1007/978-3-642-31644-9
SpringerHeidelbergDordrechtLondonNewYork
LibraryofCongressControlNumber:2012940987
CRSubjectClassification(1998):F.1,F.2,F.4,G.2.3,I.1.3
LNCSSublibrary:SL1–TheoreticalComputerScienceandGeneralIssues
©Springer-VerlagBerlinHeidelberg2012
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Ju¨rgen Dassow
(painted by his wife Christine)
Preface
This Festschrift is dedicated to Professor Ju¨rgen Dassow on the occasionof his
65th birthday on July 11, 2012.The volume contains articles on recent research
inthetheoryofautomata,formallanguages,biologicallyinspiredcomputations,
and related topics. The contributing authors – leading researchers, colleagues,
and friends – honor Ju¨rgen Dassow with papers covering a wide range of topics
in the field in which he has been very active for many years.
Ju¨rgen Dassow studied mathematics at the University of Rostock. He ob-
tained his doctoral degree (Dr. rer. nat.) with the dissertation U¨ber das Ver-
halten von lokalen Ringen bei monoidalen Transformationen in 1972 and his
habilitation (Dr. rer. nat. habil.) with the habilitationsschrift Ein modifizierter
Vollsta¨ndigkeitsbegriff in einer Algebra von Automatenabbildungen in1978,both
fromthe UniversityofRostock.He startedhis academic careeras a researchas-
sociate in Rostock. In 1980, Ju¨rgen Dassow took a position as a lecturer in
Magdeburg, where he later became a professor of mathematics in 1987 and a
professor of computer science in 1992.
Asascientist,heisparticularlyknownforhisworkonregulatedrewriting and
on cooperating distributed grammar systems. Further main areas of his research
are grammatical picture generation, Lindenmayer systems, and biologically in-
spired formalisms. These five topics have also been chosen for the illustration
appearing on the cover of this book. The green tree in the center of the picture
wasobtainedaftergraphicallyinterpretingastringgeneratedbyaLindenmayer
system. The speech balloons emerging from birds residing in the tree symbolize
the connectionbetween naturaland formallanguages.The picture in the upper
rightcornershowssymbolicallyapartofaDNAstrandthatstandsforthework
inspired by biology, while the one in the upper left corner represents a chain
code picture that emblematizes the work on grammatical picture generation.
Thespeechballooninthelowerleftcornercontainsaderivationtreefromwhich
anunwantedpartistobecut–regulatingarewritingprocess.Thepictureinthe
lower right corner symbolizes a cooperating distributed grammar system which
in turn models some kind of ‘blackboard architecture’ where different agents
performactionstowardacommonsolution.Furtherinterpretationsarewelcome
and left to the reader ...
To date, Ju¨rgen Dassow has been the author/coauthor of more than 200
scientific papers, four monographs, and 18 proceedings. He has given at least
100 lectures at conferences and universities in 18 countries. Moreover, he has
been a very active organizer of scientific exchange. He is the Editor-in-Chief of
the Journal of Automata, Languages and Combinatorics (JALC), the successor
ofthe renownedEastGermanJournal of Information Processing and Cybernet-
ics (EIK), and has organized several international conferences and workshops,
for instance the First International Workshop on Descriptional Complexity of
VIII Preface
Automata, Grammars and Related Structures (DCAGRS), one of the two pre-
decessorsoftheworkshopDescriptionalComplexityofFormalSystems(DCFS),
and the Second International Conference on Developments in Language The-
ory (DLT). In addition, Ju¨rgen Dassow renders outstanding organizing services
withintheGermancommunity.In1992,hewasoneofthefoundersofthespecial
interest group on Automata and Formal Languages of the German Association
ofInformatics(Gesellschaftfu¨rInformatik).For14years,heservedasamember
of its Steering Committee, from 1993to 2003as Chairman.The Theorietag Au-
tomatenundFormaleSprachen,theannualmeetingofthespecialinterestgroup,
was organizedby Ju¨rgenDassow in 1991,2001,and 2011.Moreover,he was the
scientific host to five researchers who spent one or two years at the University
of Magdeburg with a Fellowship from the Alexander von Humboldt Foundation
of Germany. Many other guests were supervised during short-term visits.
Besidehisresearchactivities,Ju¨rgenDassowtookresponsibilityintheadmin-
istration of the University of Magdeburg. He served as the rector and prorector
oftheuniversity,andasdeanoftheDepartmentsofMathematicsandComputer
Science. Last but not least, he has supervised several diploma and PhD theses.
ThevariousauthorsandtheircontributionstothisFestschriftcovermanyar-
eas of automata and language theory and reflect the international reputation of
Ju¨rgen Dassow. This volume contains papers on picture languages,cooperating
distributed systems of automata, quantum automata, grammar systems, online
computation, word equations, biologically motivated formal systems, controlled
derivations, descriptional complexity, as well as on ‘classic’ topics of automata
and language theory. The contributions have been refereed by at least two re-
viewers according to usual standards.
We would like to thank all those who helped to realize this Festschrift, the
authors and the referees for their contributions and for timely cooperation, as
well as Alfred Hofmann and Anna Kramer from Springer for their friendly col-
laboration and help in the preparation of this volume.
Dear Professor Dassow, dear Ju¨rgen, we are grateful for all the ideas and
inspiringworkyousharedwithus.Wewishyoumanymoreyearsfullofpleasure.
Happy Birthday!
April 2012 Henning Bordihn
Martin Kutrib
Bianca Truthe
Table of Contents
Peptide Computers............................................... 1
M. Sakthi Balan and Helmut Ju¨rgensen
On the Power of Randomness versus Advice in Online Computation.... 30
Hans-Joachim Bo¨ckenhauer, Juraj Hromkoviˇc, Dennis Komm,
Richard Kr´aloviˇc, and Peter Rossmanith
Relevance of Entities in Reaction Systems........................... 44
Andrzej Ehrenfeucht, Jetty Kleijn, Maciej Koutny, and
Grzegorz Rozenberg
Generalized Random Context Picture Grammars:
The State of the Art ............................................. 56
Sigrid Ewert and Max Rabkin
Cooperating Distributed Tree Automata ............................ 75
Henning Fernau
A Note on Combined Derivation Modes for Cooperating Distributed
Grammar Systems ............................................... 86
Markus Holzer
Equations in the Partial Semigroup of Words with Overlapping
Products........................................................ 99
Mari Huova and Juhani Karhuma¨ki
On CD-Systems of Stateless Deterministic Two-Phase
RR(1)-Automata ................................................ 111
Martin Kutrib and Friedrich Otto
The Boolean Formula Value Problem as Formal Language............. 138
Klaus-Jo¨rn Lange
Hairpin Lengthening and Shortening of Regular Languages............ 145
Florin Manea, Robert Mercas, and Victor Mitrana
One-Sided Random Context Grammars with Leftmost Derivations ..... 160
Alexander Meduna and Petr Zemek
Earley’s Parsing Algorithm and k-Petri Net Controlled Grammars ..... 174
Taishin Y. Nishida
Descriptional Complexity of Input-Driven Pushdown Automata........ 186
Alexander Okhotin, Xiaoxue Piao, and Kai Salomaa
X Table of Contents
Towards “Fypercomputations” (in Membrane Computing) ............ 207
Gheorghe P˘aun
Undecidability of State Complexities Using Mirror Images............. 221
Arto Salomaa
Asymptotic Subword Complexity .................................. 236
Ludwig Staiger
On Grammars Controlled by Parikh Vectors......................... 246
Ralf Stiebe
On the Nonterminal Complexity of Tree Controlled Grammars......... 265
Gyo¨rgy Vaszil
One-Way Finite Automata with Quantum and Classical States ........ 273
Shenggen Zheng, Daowen Qiu, Lvzhou Li, and Jozef Gruska
Author Index.................................................. 291
Peptide Computers
M. Sakthi Balan1 and Helmut Ju¨rgensen2
1 ECOM Research Lab, Education and Research, Infosys Limited,
Bangalore - 560100, India
sakthi [email protected]
2 Department of ComputerScience, TheUniversity of Western Ontario,
London,Ontario, Canada, N6A 5B7
[email protected]
Abstract. A peptide computer is a formal model for computations
based on peptide-antibody interactions. We provide a rigorous detailed
formal model and prove that this model leads to a well-defined com-
putational behaviour. We review existing results concerning the power
and limitations of peptide computers and the types of non-determinism
arising in such computers on the basis of thisformal model.
1 Introduction
Toconsidertheinteractionsbetweenpeptidesandantibodiesasamodelofcom-
putation was proposedin 2001 by Hug and Schuler [30]. Like a DNA computer,
a peptide computer utilizes the massive parallelism of chemical reactions. Some
of the potential advantages of a peptide computer compared to other biologi-
cally inspiredmodels of computing couldbe the largernumber of basic building
blocks, the different binding affinities, and a potentially greater tolerance to
experimental conditions [30].
The classical model of computation, often referred to as the Turing model,
reliesontheintuitionofwritingsymbolsonasheetofpaper.Severalmodelsrely-
ingonotherperceivedmodesofcomputationhavebeenformulated,forexample,
modelsrelyingonbiologicalorphysicalorchemicalphenomena.The fundamen-
taldiscussionregardingtheessenceofcomputingisfarfromsettled.Evenshortly
aftertheformulationofChurch’sorTuring’stheses,therewerewell-foundedfor-
mal mathematical andphilosophicalargumentsstating thatthe conceptofTur-
ing computability was too wide (P´eter [40]) or too narrow (Kalm´ar [36]). With
ourincreased,butstill andlikelyeverincomplete,understandingofnaturalpro-
cesses, many aspects of computability keep undergoing scrutiny (e.g. [29, 41]).
Natural processes can be modelled as computations at different levels. One
can work at a behavioural level, a phenomenological level or at the actual level
of the respective science involved. For any computing model, some abstraction
is needed.
AformalmathematicalmodelofapeptidecomputerwasintroducedbyBalan
in 2004 [3]. This model involved an ‘agent’ – like a human in a laboratory –
to supervise the process and to evaluate the respective situation. This model
H.Bordihn,M.Kutrib,andB.Truthe(Eds.):DassowFestschrift2012,LNCS7300,pp.1–29,2012.
(cid:2)c Springer-VerlagBerlinHeidelberg2012
2 M.S. Balan and H.Ju¨rgensen
is referred to as look-and-do by us in [8]. A more rigorous, but less intuitive
alternative definition, which does not need such an agent, was indicated by us
brieflyin[8] andalsoin[4]. Certainessentialdetails wereomitted therebecause
ofspacelimitations.Belowweexpandthisdefinitionbyprovidingalldetailsand
we augment it by explanations.
SeveralspecialresultsbyBalan,KrithivasanandSivasubramanyam[2,10–12]
publishedbetween2001and2004concernthesimulationofBooleanfunctionsby
andthecomputationalpowerof,peptidecomputers1.Muchofthisissummarized
inthe survey[9]. Depending onthe details ofthe definition, apeptide computer
is at least as powerful as a Turing machine [7, 8, 10]. In view of the ongoing
discussions regarding the foundations of computability, one could envisage a
modelofpeptide computingwhichisevenmorepowerfulthanTuringmachines.
Whenstudyingcomputingmodelsinspiredbynaturalprocessesonemayhave
several complementary goals, for instance:
– Understand the natural processes.
– Model the processes for simulation.
– Use the processes to perform computations.
– Use the model to understand aspects of computation.
– Use the model to build computers.
– Simulate the model to build computers.
Inthisrespect,peptidecomputersaresimilartoothermodelsofcomputationin-
spiredby naturalphenomena.The mathematical model ofpeptide computing is
anabstractionofthebio-chemicalprocesses,whichattemptstocaptureessential
properties and ignores issues which appear to be less important. As is common
in the literature on computing based on biological, chemical or other processes
occurringinnature,wefocusonthe mathematicalaspects.Itisobviousthat,at
some point, in-vitro experiments would be needed to validate the practicability
of the proposed computations.
Ourfocusisonthemathematicalmodelanditspotential.Forthebio-chemical
background we refer to [17]. In the book Immunological Computation [21] one
finds a much simplified introductionanda huge anduseful, but notquite repre-
sentative, list of references. Also severalinteresting applications including fault-
tolerant computing and intrusion detection are presented there.
1 ThereseemstobearecentbookPeptideComputing,whichwehavenotseenyet[42],
ISBN9786131428623. Wehavenot found thisbook in any library search across the
world. According to the publishers the book “exclusively contains articles from the
free Wikipedia Encyclopedia, which means that we are not able to send a review
copyofthebookbecausethecontentisavailablefreelyontheinternet...”(emailof
9December,2011froml.sabjan atvdm-vsg.de).Thebookisannouncedtohave112
pages. On the internet we found one Wikipedia article on Peptide Computing as a
stub(endofNovember2011)andaboutfiveadditionalpagesonthetopicwhichare
not copyrighted. Accordingto theinformation available, this book is not a relevant
source and will beignored in thesequel.