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Gabriel Ciobanu, Grzegorz Rozenberg, eds.
Modelling in Molecular Biology.
Springer. 2004

This volume consists of papers concerned with models and methods used in solving some fundamental problems of biosciences. They represent a wide spectrum of diverse ideas and trends. In particular, they reflect the genuinely interdisciplinary nature of research on modelling in molecular biology – the inspiration, ideas and techniques presented in this volume come from mathematics, computer science, statistics, chemistry and biology.

Contents

• Daniel A. Beard, Hong Qian, James B. Bassingthwaighte. Stoichiometric foundation of large-scale biochemical system analysis. 2004
• Paulo R. A. Campos, Christoph Adami, Claus O. Wilke. Modelling stochastic clonal interference. 2004
• Gabriel Ciobanu. Software verification of biomolecular systems. 2004
• Oleg V. Demin, Galina V. Lebedeva, Alex G. Kolupaev, E. A. Zobova, T. Yu. Plyusnina, A. I. Lavrova, A. Dubinsky, E. A. Goryacheva, Frank Tobin, Igor I. Goryanin. Kinetic modelling as a modern technology to explore and modify living cells. 2004
• Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescott, Grzegorz Rozenberg. Modelling gene assembly in ciliates. 2004
• Masami Hagiya. Towards molecular programming -- a personal report on DNA8 and Molecular Computing. 2004
• Sungchul Ji. Molecular information theory: solving the mysteries of DNA. 2004
• Na'aman Kam, David Harel, Hillel Kugler, Rami Marelly, Amir Pnueli, E. Jane Albert Hubbard, Michael J. Stern. Formal modelling of C. elegans. development: a scenario-based approach. 2004
• Carlos Martin-Vide, Gheorghe Paun. P Systems with symport/antiport rules: a survey. 2004
• Santo Motta, Vladimir Brusic. Mathematical modelling of the immune system. 2004
• Aviv Regev, Ehud Shapiro. The pi-calculus as an abstraction for biomolecular systems. 2004
• Barbel M. R. Stadler, Peter F. Stadler. The topology of evolutionary biology. 2004
• Yi Zhou, Bud Mishra. Models of genome evolution. 2004

Bogdan Aman, Gabriel Ciobanu.
Mobility in Process Calculi and Natural Computing.
Springer. 2011

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The design of formal calculi in which fundamental concepts underlying interactive systems can be described and studied has been a central theme of theoretical computer science in recent decades, while membrane computing, a rule-based formalism inspired by biological cells, is a more recent field that belongs to the general area of natural computing. This is the first book to establish a link between these two research directions while treating mobility as the central topic.

In the first chapter the authors offer a formal description of mobility in process calculi, noting the entities that move: links (π-calculus), ambients (ambient calculi) and branes (brane calculi). In the second chapter they study mobility in the framework of natural computing. The authors define several systems of mobile membranes in which the movement inside a spatial structure is provided by rules inspired by endocytosis and exocytosis. They study their computational power in comparison with the classical notion of Turing computability and their efficiency in algorithmically solving hard problems in polynomial time. The final chapter deals with encodings, establishing links between process calculi and membrane computing so that researchers can share techniques between these fields.

The book is suitable for computer scientists working in concurrency and in biologically inspired formalisms, and also for mathematically inclined scientists interested in formalizing moving agents and biological phenomena. The text is supported with examples and exercises, so it can also be used for courses on these topics.