Algorithmic Bioprocesses

by Condon, Anne; Harel, David; Kok, Joost N.; Salomaa, Arto; Winfree, Erik

• ISBN13: 9783540888680
• ISBN10: 3540888683
• Format: Hardcover
• Copyright: 2009-09-03
• Publisher: Springer-Verlag New York Inc

Summary

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 bioprocesses on our understanding of computation.

Author Biography

The editors and contributors include most of the key researchers working on these topics worldwide.

Table of Contents

Tribute
Grzegorz Rozenberg: A Magical Scientist and Brother	p. 3
Sequence Discovery, Generation, and Analysis
Monotony and Surprise	p. 15
Information Content of Sets of Biological Sequences Revisited	p. 31
Duplication in DNA Sequences	p. 43
Sequence and Structural Analyses for Functional Non-coding RNAs	p. 63
Gene Assembly in Ciliates
Strategies for RNA-Guided DNA Recombination	p. 83
Reality-and-Desire in Ciliates	p. 99
Template-Guided Recombination: From Theory to Laboratory	p. 117
Nanoconstructions and Self-assembly
DNA Cages with Icosahedral Symmetry in Bionanotechnology	p. 141
Applying Symmetric Enumeration Method to One-Dimensional Assembly of Rotatable Tiles	p. 159
A Self-assembly Model of Time-Dependent Glue Strength	p. 185
The Perils of Polynucleotides Revisited	p. 205
Algorithmic Control: The Assembly and Operation of DNA Nanostructures and Molecular Machinery	p. 215
Membrane Computing
On Nonuniversal Symport/Antiport P Systems	p. 229
Spiking Neural P Systems. Recent Results, Research Topics	p. 273
Membrane Computing Schema: A New Approach to Computation Using String Insertions	p. 293
Formal Models and Analysis
Finite Splicing: Generative Capacity, New Models and Complexity Aspects	p. 313
Formal Models of the Calyx of Held	p. 331
Understanding Network Behavior by Structured Representations of Transition Invariants	p. 367
Quantitative Verification Techniques for Biological Processes	p. 391
A New Mathematical Model for the Heat Shock Response	p. 411
Process Calculi and Automata
Artificial Biochemistry	p. 429
Process Calculi Abstractions for Biology	p. 463
Deriving Differential Equations from Process Algebra Models in Reagent-Centric Style	p. 487
Programmable DNA-Based Finite Automata	p. 505
Biochemical Reactions
A Multi-volume Approach to Stochastic Modeling with Membrane Systems	p. 519
Programmability of Chemical Reaction Networks	p. 543
Log-gain Principles for Metabolic P Systems	p. 585
Hybrid Method for Simulating Small-Number Molecular Systems	p. 607
On Involutions Arising from Graphs	p. 623
Parallel Computing by Xeroxing on Transparencies	p. 631
Some Undecidable Dynamical Properties for One-Dimensional Reversible Cellular Automata	p. 639
On Using Divide and Conquer in Modeling Natural Systems	p. 661
No Molecule Is an Island: Molecular Evolution and the Study of Sequence Space	p. 675
Niching Methods: Speciation Theory Applied for Multi-modal Function Optimization	p. 705
On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions	p. 731
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