LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

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Preface Molecular Computing is a fast-emerging area of Natural Computing. On the one hand, it is concerned with the use of (bio)molecules for the purpose of computing while on the other hand it tries to understand the computational nature of the molecular processes going on in living cells. The paper “Molecular computation of solutions to combinatorial problems” by L. Adleman, which describes a laboratory experiment and was published in Science in November 1994, was an important milestone for the area of molecular computing, as it provided a “proof-of-principle” that one can indeed perform computations in a biolab using biomolecules and their processing using biomolecular operations. However, research concerning the computational nature of biomolecular operations dates back to before 1994. In particular, a pioneering work concerning the mathematical theory of biooperations is the paper “Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors,” authored by Tom Head in 1987, which appeared in the Bulletin of Mathematical Biology. The paper uses the framework of formal language theory to formulate and investigate the computational effects of biomolecular operations carried out by restriction enzymes. This paper has influenced research in both molecular computing and formal language theory. In molecular computing it has led to a clear computational understanding of important biomolecular operations occurring in nature, and it has also stimulated the design of a number of laboratory experiments utilizing Tom’s ideas for the purpose of human-designed DNA computing. In formal language theory it has led to a novel, interesting and challenging research area, originally called “splicing systems” and then renamed “H systems” in honor of Tom (“H” stands for “Head”). Many papers stimulated by the pioneering ideas presented by Tom in his seminal paper were written by researchers from all over the world. Adleman’s paper was a great event in Tom’s life: it has confirmed his conviction that biooperations can be used for the purpose of computing, but more importantly it has stimulated his interest in experimental research. One can safely say that since 1994 most of Tom’s research has been focused on the design of experiments related to DNA computing. Also on this research path he remained highly innovative and original, combining his great talent for modeling with a passsion for experimental biology. A good manifestation of this line of Tom’sresearchisaqueouscomputing–areallyelegantbutalsoexperimentally feasible model of molecular computing invented by him. An example of the recognition of Tom’s research within the molecular computing community is the “DNA Scientist of the Year” award that Tom received in 2003. Tom’s multidisciplinary talents and interests become even more evident when one realizes that his original training and passion was mathematics, and in particular algebra. He moved from there to formal language theory. It is also im-
VIII Preface portant to keep in mind that his work on formal models for biology started long before his 1987 paper, as he was a very active and productive researcher in the area of Lindenmayer systems that model the development of simple multicellular organisms, not on the molecular but rather on the cellular level. With this volume, presenting many aspects of research in (or stimulated by) molecular computing, we celebrate a scientist who has been a source of inspiration to many researchers, and to us a mentor, a scientific collaborator, and a warm and caring friend. HAPPY BIRTHDAY, Tom! November 2003 Nataˇsa Jonoska Gheorghe Păun Grzegorz Rozenberg
Page 1 and 2: Lecture Notes in Computer Science 2
Page 3 and 4: Nata˘sa Jonoska Gheorghe Păun Grz
Page 5: Thomas J. Head
Page 9 and 10: X Table of Contents Formal Properti
Page 11 and 12: Solving Graph Problems by P Systems
Page 25 and 26: where Solving Graph Problems by P S
Page 33 and 34: Writing Information into DNA Masano
Page 35 and 36: Writing Information into DNA 25 Ham
Page 37 and 38: Writing Information into DNA 27 Fig
Page 39 and 40: Writing Information into DNA 29 Dea
Page 41 and 42: 5 Results 5.1 DNA Code for the Engl
Page 43 and 44: Writing Information into DNA 33 3.
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Page 47 and 48: Balance Machines: Computing = Balan
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1 Balance Machines: Computing = Bal
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Eilenberg P Systems with Symbol-Obj
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2 Definitions Definition 1. A strea
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5 Conclusions Eilenberg P Systems w
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Molecular Tiling and DNA Self-assem
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3 Molecular Self-assembly Processes
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8 Hierarchical Tiling Molecular Til
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References Molecular Tiling and DNA
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On Some Classes of Splicing Languag
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ˆxa ˆby ✬ ✩✬ ✩ a b x y
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The Power of Networks of Watson-Cri
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Fixed Point Approach to Commutation
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Here the last one holds if and only
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� � � � � Fixed Point App
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Remarks on Relativisations and DNA
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Splicing Test Tube Systems and Thei
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Splicing Test Tube Systems 141 the
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Splicing Test Tube Systems 143 to a
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Splicing Test Tube Systems 145 6. R
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Splicing Test Tube Systems 147 (c)
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I0 Ai i Splicing Test Tube Systems
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Splicing Test Tube Systems 151 4. J
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Digital Information Encoding on DNA
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DNA-based Cryptography Ashish Gehan
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DNA-based Cryptography 169 concern.
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DNA-based Cryptography 171 The one-
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DNA-based Cryptography 173 of DNA t
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DNA-based Cryptography 175 Fig. 3.
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DNA-based Cryptography 177 the comp
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DNA-based Cryptography 179 can be c
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DNA-based Cryptography 181 4.4 DNA-
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DNA-based Cryptography 183 Fig. 7.
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DNA-based Cryptography 185 offer li
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DNA-based Cryptography 187 30. C. M
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Splicing to the Limit Elizabeth Goo
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Splicing to the Limit 191 molecular
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Splicing to the Limit 193 Discussio
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Example 9. The splicing rules are S
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−2α � kNNk = −2αMN, k α
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Finally we define the limit languag
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6 Conclusion Splicing to the Limit
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Formal Properties of Gene Assembly
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(a) (b) Formal Properties of Gene A
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n-Insertion on Languages Masami Ito
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n-Insertion on Languages 215 3. ∀
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n-Insertion on Languages 217 Theore
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Transducers with Programmable Input
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1 01 s 0 Transducers with Programma
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order β l Transducers with Program
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start tile Transducers with Program
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Methods for Constructing Coded DNA
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u u Methods for Constructing Coded
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On the Universality of P Systems wi
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An Algorithm for Testing Structure
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Definition 1. Define the relation
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280 Manfred Kudlek Definition 5. Co
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On Languages of Cyclic Words 283 Th
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On Languages of Cyclic Words 285 No
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On Languages of Cyclic Words 287 Th
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A DNA Algorithm for the Hamiltonian
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Formal Languages Arising from Gene
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A Proof of Regularity for Finite Sp
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--- ◦ ❄ ⊗ γ ✲ A Proof of R
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The Duality of Patterning in Molecu
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The Duality of Patterning in Molecu
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Membrane Computing: Some Non-standa
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where: Membrane Computing: Some Non
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where: Membrane Computing: Some Non
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The P Versus NP Problem Through Cel
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Realizing Switching Functions Using
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Realizing Switching Functions Using
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AND Gate Realizing Switching Functi
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NOR Gate Realizing Switching Functi
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Plasmids to Solve #3SAT Rani Siromo
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Plasmids to Solve #3SAT 363 A comme
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Plasmids to Solve #3SAT 365 from th
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Communicating Distributed H Systems
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Proof Communicating Distributed H S
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Books: Publications by Thomas J. He
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Publications by Thomas J. Head 387
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Publications by Thomas J. Head 389
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LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

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