Modelling in Molecular Biology

1. Front Matter

   Pages I-X

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2. Stoichiometric Foundation of Large-Scale Biochemical System Analysis

   • Daniel A. Beard, Hong Qian, James B. Bassingthwaighte

   Pages 1-19

3. Modelling Stochastic Clonal Interference

   • Paulo RA Campos, Christoph Adami, Claus O. Wilke

   Pages 21-38

4. Software Verification of Biomolecular Systems

   • Gabriel Ciobanu

   Pages 39-57

5. Kinetic Modelling as a Modern Technology to Explore and Modify Living Cells

   • Oleg V. Demin, Galina V. Lebedeva, Alex G. Kolupaev, E. A. Zobova, T. Yu. Plyusnina, A. I. Lavrova et al.

   Pages 59-103

6. Modelling Gene Assembly in Ciliates

   • Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescott, Grzegorz Rozenberg

   Pages 105-124

7. Towards Molecular Programming — a Personal Report on DNA8 and Molecular Computing

   • Masami Hagiya

   Pages 125-140

8. Molecular Information Theory: Solving the Mysteries of DNA

   • Sungchul Ji

   Pages 141-150

9. Formal Modelling of C. elegans Development. A Scenario-Based Approach

   • Na’aman Kam, David Harel, Hillel Kugler, Rami Marelly, Amir Pnueli, Jane Albert Hubbard et al.

   Pages 151-173

10. P Systems with Symport/Antiport Rules. A Survey

    • Carlos Martín-Vide, Gheorghe Păun

    Pages 175-192

11. Mathematical Modelling of the Immune System

    • Santo Motta, Vladimir Brusic

    Pages 193-218

12. The π-calculus as an Abstraction for Biomolecular Systems

    • Aviv Regev, Ehud Shapiro

    Pages 219-266

13. The Topology of Evolutionary Biology

    • Bärbel M. R. Stadler, Peter F. Stadler

    Pages 267-286

14. Models of Genome Evolution

    • Yi Zhou, Bud Mishra

    Pages 287-304

15. Back Matter

    Pages 305-305

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This volume is based on the workshop“Modelling in Molecular Biology” that tookplacein2002inSingapore. Themaingoaloftheworkshopwastopresent models/methods used in solving some fundamental problems in biosciences. The volume consists of a selection of papers presented at the workshop as well as of some other papers that are included so that the presentation of the theme of the workshop is broader and more balanced. As a matter of fact we feel that the collection of papers comprising this volume represents a wide spectrum of quite diverse ideas and trends. The paper by D. A. Beard et al. explores the common thesis that und- standingthebehaviouroflargeinteractingsystemsofmanyenzymesandre- tants underlies the modelling and simulation of whole-cell systems. Moreover, the models need to represent the basic stoichiometry, with balanced che- cal reactions and the conservation of mass, energy and charge. The authors discuss the stoichiometric and then kinetic details of approaches to modelling and simulation of biochemical systems. P. R. A. Campos et al. are concerned with models of evolution and adaptation (which is essential for precise - derstanding of molecular phylogeny). In particular, their paper is concerned with the rate of adaptation of asexual organisms(which is important because it in?uences the speed of the assumed molecular clock). It is known that for such organisms the rate of adaptation does not steadily increase with the - creasing rate of advantageous mutations, and this paper studies the mutual interference of two advantageous mutants that are each initially present in only a single organism.

• Cell Biology
• DNA
• Evolution
• Evolutionary Biology
• Gene Assembly
• Genome Evolution
• Molecular Programming
• Process Algebra
• Protein-DNA Interactions
• Protein-protein Interactions
• genes
• genome
• molecular biology
• software verification
• verification

• Institute of Computer Science, Romanian Academy of Sciences, Iasi, Romania

  Gabriel Ciobanu

• Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands

  Grzegorz Rozenberg

G. Ciobanu is Professor at the Romanian Academy, Institute of Computer Science and has received the first "Grigore Moisil" award for theoretical computer science offered by the Romanian Academy. Over 60 papers published in international journals.

G. Rozenberg is multiple Springer author and editor of books and series (EATCS, NCS).

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