Algorithmic Bioprocesses

  • Anne Condon
  • David Harel
  • Joost N. Kok
  • Arto Salomaa
  • Erik Winfree

Part of the Natural Computing Series book series (NCS)

Table of contents

  1. Front Matter
    Pages I-XX
  2. Tribute

    1. Front Matter
      Pages 1-1
  3. Sequence Discovery, Generation, and Analysis

    1. Front Matter
      Pages 13-13
    2. Alberto Apostolico
      Pages 15-29
    3. Alessandra Carbone, Stefan Engelen
      Pages 31-42
    4. Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki
      Pages 43-61
    5. Yasubumi Sakakibara, Kengo Sato
      Pages 63-79
  4. Gene Assembly in Ciliates

    1. Front Matter
      Pages 81-81
    2. Angela Angeleska, Nataša Jonoska, Masahico Saito, Laura F. Landweber
      Pages 83-98
    3. Robert Brijder, Hendrik Jan Hoogeboom
      Pages 99-115
    4. Mark Daley, Michael Domaratzki
      Pages 117-137
  5. Nanoconstructions and Self-assembly

    1. Front Matter
      Pages 139-139
    2. Nataša Jonoska, Anne Taormina, Reidun Twarock
      Pages 141-158
    3. Sudheer Sahu, Peng Yin, John H. Reif
      Pages 185-204
    4. Nadrian C. Seeman
      Pages 205-214
  6. Membrane Computing

    1. Front Matter
      Pages 227-227
    2. Oscar H. Ibarra, Sara Woodworth
      Pages 229-272
    3. Gheorghe Păun, Mario J. Pérez-Jiménez
      Pages 273-291
    4. Mario J. Pérez-Jiménez, Takashi Yokomori
      Pages 293-309
  7. Formal Models and Analysis

    1. Front Matter
      Pages 311-311
    2. Andrea Bracciali, Marcello Brunelli, Enrico Cataldo, Pierpaolo Degano
      Pages 331-366
    3. Marta Kwiatkowska, Gethin Norman, David Parker
      Pages 391-409
    4. Ion Petre, Andrzej Mizera, Claire L. Hyder, Andrey Mikhailov, John E. Eriksson, Lea Sistonen et al.
      Pages 411-425
  8. Process Calculi and Automata

    1. Front Matter
      Pages 427-427
    2. Luca Cardelli
      Pages 429-462
    3. Maria Luisa Guerriero, Davide Prandi, Corrado Priami, Paola Quaglia
      Pages 463-486
    4. Tamar Ratner, Ehud Keinan
      Pages 505-516
  9. Biochemical Reactions

    1. Front Matter
      Pages 517-517
    2. Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
      Pages 519-542
    3. Matthew Cook, David Soloveichik, Erik Winfree, Jehoshua Bruck
      Pages 543-584
    4. Vincenzo Manca
      Pages 585-605
    5. Kazufumi Mizunuma, Masami Hagiya
      Pages 607-620
  10. Broader Perspective

    1. Front Matter
      Pages 621-621
    2. Jurriaan Hage, Tero Harju
      Pages 623-630
    3. Yaki Setty, Irun R. Cohen, Avi E. Mayo, David Harel
      Pages 661-674
    4. Erik A. Schultes, Peter T. Hraber, Thomas H. LaBean
      Pages 675-704

About this book


A fundamental understanding of algorithmic bioprocesses is key to learning how information processing occurs in nature at the cell level. The field is concerned with the interactions between computer science on the one hand and biology, chemistry, and DNA-oriented nanoscience on the other. In particular, this book offers a comprehensive overview of research into algorithmic self-assembly, RNA folding, the algorithmic foundations for biochemical reactions, and the algorithmic nature of developmental processes.

The editors of the book invited 36 chapters, written by the leading researchers in this area, and their contributions include detailed tutorials on the main topics, surveys of the state of the art in research, experimental results, and discussions of specific research goals. The main subjects addressed are sequence discovery, generation, and analysis; nanoconstructions and self-assembly; membrane computing; formal models and analysis; process calculi and automata; biochemical reactions; and other topics from natural computing, including molecular evolution, regulation of gene expression, light-based computing, cellular automata, realistic modelling of biological systems, and evolutionary computing.

This subject is inherently interdisciplinary, and this book will be of value to researchers in computer science and biology who study the impact of the exciting mutual interaction between our understanding of bioprocesses and our understanding of computation.


Algorithmic bioprocesses Algorithmic botany Algorithmic self-assembly Biochemical reactions Bioinformatics Cell biology Developmental processes Grammatical models Information processing Live sequence charts Molecular computing Nanoscience Natu

Editors and affiliations

  • Anne Condon
    • 1
  • David Harel
    • 2
  • Joost N. Kok
    • 3
  • Arto Salomaa
    • 4
  • Erik Winfree
    • 5
  1. 1.Dept. Computer ScienceUniversity of British ColumbiaVancouverCanada
  2. 2.Dept. Applied MathematicsWeizmann Institute of ScienceRehovotIsrael
  3. 3.Leiden Inst. Advanced Computer ScienceLeiden UniversityLeidenNetherlands
  4. 4.Turku Centre for Computer ScienceTurkuFinland
  5. 5.Computer Science, Computation,California Inst. of TechnologyPasadenaU.S.A.

Bibliographic information

  • DOI
  • Copyright Information Springer-Verlag Berlin Heidelberg 2009
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-540-88868-0
  • Online ISBN 978-3-540-88869-7
  • Series Print ISSN 1619-7127
  • Buy this book on publisher's site