Algorithmic bioprocesses

Arto Salomaa (auth.), Anne Condon, David Harel, Joost N. Kok, Arto Salomaa, Erik Winfree (eds.)3540888683, 9783540888680

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.

Table of contents :
Front Matter….Pages I-XX
Front Matter….Pages 1-1
Grzegorz Rozenberg: A Magical Scientist and Brother….Pages 3-11
Front Matter….Pages 13-13
Monotony and Surprise….Pages 15-29
Information Content of Sets of Biological Sequences Revisited….Pages 31-42
Duplication in DNA Sequences….Pages 43-61
Sequence and Structural Analyses for Functional Non-coding RNAs….Pages 63-79
Front Matter….Pages 81-81
Strategies for RNA-Guided DNA Recombination….Pages 83-98
Reality-and-Desire in Ciliates….Pages 99-115
Template-Guided Recombination: From Theory to Laboratory….Pages 117-137
Front Matter….Pages 139-139
DNA Cages with Icosahedral Symmetry in Bionanotechnology….Pages 141-158
Applying Symmetric Enumeration Method to One-Dimensional Assembly of Rotatable Tiles….Pages 159-183
A Self-assembly Model of Time-Dependent Glue Strength….Pages 185-204
The Perils of Polynucleotides Revisited….Pages 205-214
Algorithmic Control: The Assembly and Operation of DNA Nanostructures and Molecular Machinery….Pages 215-225
Front Matter….Pages 227-227
On Nonuniversal Symport/Antiport P Systems….Pages 229-272
Spiking Neural P Systems. Recent Results, Research Topics….Pages 273-291
Membrane Computing Schema: A New Approach to Computation Using String Insertions….Pages 293-309
Front Matter….Pages 311-311
Finite Splicing: Generative Capacity, New Models and Complexity Aspects….Pages 313-329
Formal Models of the Calyx of Held ….Pages 331-366
Understanding Network Behavior by Structured Representations of Transition Invariants….Pages 367-389
Quantitative Verification Techniques for Biological Processes….Pages 391-409
Front Matter….Pages 311-311
A New Mathematical Model for the Heat Shock Response….Pages 411-425
Front Matter….Pages 427-427
Artificial Biochemistry….Pages 429-462
Process Calculi Abstractions for Biology….Pages 463-486
Deriving Differential Equations from Process Algebra Models in Reagent-Centric Style….Pages 487-504
Programmable DNA-Based Finite Automata….Pages 505-516
Front Matter….Pages 517-517
A Multi-volume Approach to Stochastic Modeling with Membrane Systems….Pages 519-542
Programmability of Chemical Reaction Networks….Pages 543-584
Log-gain Principles for Metabolic P Systems….Pages 585-605
Hybrid Method for Simulating Small-Number Molecular Systems….Pages 607-620
Front Matter….Pages 621-621
On Involutions Arising from Graphs….Pages 623-630
Parallel Computing by Xeroxing on Transparencies….Pages 631-637
Some Undecidable Dynamical Properties for One-Dimensional Reversible Cellular Automata….Pages 639-660
On Using Divide and Conquer in Modeling Natural Systems….Pages 661-674
No Molecule Is an Island: Molecular Evolution and the Study of Sequence Space….Pages 675-704
Niching Methods: Speciation Theory Applied for Multi-modal Function Optimization….Pages 705-729
On the Concept of Cis -regulatory Information: From Sequence Motifs to Logic Functions….Pages 731-742