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Anne Condon, David Harel, Joost N. Kok, Arto Salomaa and Erik Winfree
I-XX
Front matter
3-11
Part 1 / Tribute
Grzegorz Rozenberg: A Magical Scientist and Brother
15-79
Part 2 / Sequence Discovery, Generation, and Analysis
15-29
Monotony and Surprise
31-42
Information Content of Sets of Biological Sequences Revisited
43-61
Duplication in DNA Sequences
63-79
Sequence and Structural Analyses for Functional Non-coding RNAs
83-137
Part 3 / Gene Assembly in Ciliates
83-98
Strategies for RNA-Guided DNA Recombination
99-115
Reality-and-Desire in Ciliates
117-137
Template-Guided Recombination: From Theory to Laboratory
141-225
Part 4 / Nanoconstructions and Self-assembly
141-158
DNA Cages with Icosahedral Symmetry in Bionanotechnology
159-183
Applying Symmetric Enumeration Method to One-Dimensional Assembly of Rotatable Tiles
185-204
A Self-assembly Model of Time-Dependent Glue Strength
205-214
The Perils of Polynucleotides Revisited
215-225
Algorithmic Control: The Assembly and Operation of DNA Nanostructures and Molecular Machinery
229-309
Part 5 / Membrane Computing
229-272
On Nonuniversal Symport/Antiport P Systems
273-291
Spiking Neural P Systems. Recent Results, Research Topics
293-309
Membrane Computing Schema: A New Approach to Computation Using String Insertions
313-425
Part 6 / Formal Models and Analysis
313-329
Finite Splicing: Generative Capacity, New Models and Complexity Aspects
331-366
Formal Models of the Calyx of Held
367-389
Understanding Network Behavior by Structured Representations of Transition Invariants
391-409
Quantitative Verification Techniques for Biological Processes
411-425
A New Mathematical Model for the Heat Shock Response
429-516
Part 7 / Process Calculi and Automata
429-462
Artificial Biochemistry
463-486
Process Calculi Abstractions for Biology
487-504
Deriving Differential Equations from Process Algebra Models in Reagent-Centric Style
505-516
Programmable DNA-Based Finite Automata
519-620
Part 8 / Biochemical Reactions
519-542
A Multi-volume Approach to Stochastic Modeling with Membrane Systems
543-584
Programmability of Chemical Reaction Networks
585-605
Log-gain Principles for Metabolic P Systems
607-620
Hybrid Method for Simulating Small-Number Molecular Systems
623-742
Part 9 / Broader Perspective
623-630
On Involutions Arising from Graphs
631-637
Parallel Computing by Xeroxing on Transparencies
639-660
Some Undecidable Dynamical Properties for One-Dimensional Reversible Cellular Automata
661-674
On Using Divide and Conquer in Modeling Natural Systems
675-704
No Molecule Is an Island: Molecular Evolution and the Study of Sequence Space
705-729
Niching Methods: Speciation Theory Applied for Multi-modal Function Optimization
731-742
On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions
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