DNA Computing and Molecular Programming

Name: DNA Computing and Molecular Programming | 16th International Conference, DNA 16, Hong Kong, China, June 14-17, 2010, Revised Selected Papers
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16th International Conference, DNA 16, Hong Kong, China, June 14-17, 2010, Revised Selected Papers

Yasubumi Sakakibara Yongli Mi(Herausgeber*in)

Springer (Verlag)

Erschienen am 21. Januar 2011

X, 187 Seiten

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978-3-642-18305-8 (ISBN)

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Inhalt

Title
Preface
Organization
Table of Contents
Improving Efficiency of 3-SAT-Solving Tile Systems
Introduction
Tile Assembly Model
Solving 3-SAT Efficiently with Tiles
Notations and Definitions
Clause Examination (Region II)
Assignment Selection (Region III)
Clause Rotation (Region IV)
Assignment Preparation (Region V)
Formula Simplification (Region VI)
Solving 3-SAT
Contributions
References
Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-assembly Systems
Introduction
Two Tile Assembly Models
Minimizing the Error Rate
Simulation Results for Theorem 1
Minimizing the Expected Assembly Time
Further Research
References
Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement
Introduction
Construction
Design of Abstract Chemical Reactions for Gates
Implementation of Abstract Reactions with DNA Strand Displacement
References
Negative Interactions in Irreversible Self-assembly
Introduction
Abstract Tile Assembly Model
Limitation of Tile Reuse with Irreversible Reactions
Turing Machine Simulation
Conclusion
References
Search and Validation of Short Genome-Wide Biomarkers for Bacterial Biological Phylogenies
Introduction
Genome-Wide Methods in Phylogenesis
Biomarkers for Phylogeny
Phylogeny by Noncrosshybridizing Sets
Scalability of Genomic Signatures
Conclusions and Future Work
References
High-Fidelity DNA Hybridization Using Programmable Molecular DNA Devices
Introduction
Motivation
Problem Statement: High-Fidelity DNA Hybridization
Our Results: Protocols for High-Fidelity DNA Hybridization Using DNA Devices
Notation
First Protocol for High-Fidelity Hybridization
Second Protocol for High-Fidelity Hybridization
Potential Applications of High-Fidelity DNA Hybridization
Simulation of Deterministic Finite Automata
Theoretical Analysis of Protocol Kinetics
Conclusion
Experimental Verification
Discussion
References
Synthesizing Minimal Tile Sets for Patterned DNA Self-assembly
Introduction
Preliminaries
The Abstract Tile Assembly Model
The PATS Problem
A Branch-and-Bound Algorithm
The Search Space
Determining Constructibility
An Initial Search DAG
Pruning the DAG to a Search Tree
The Bounding Function
Results
Conclusion
References
Operation of a DNA-Based Autocatalytic Network in Serum
Introduction
Autocatalytic Network
Network Operation in Serum
Conclusion
References
Triangular Tile Self-assembly Systems
Introduction
Definitions
Shape Complexity
Computational Complexity
Self-assembly of Triangles
Conclusion
References
Randomized Self Assembly of Rectangular Nano Structures
Introduction
Basics of the Tile Assembly Model
Probabilistic Self Assembly
Our Results
Randomized Self Assembly with a Sum of Geometric Distributions
Supertile to Encode a Binary String
New Idea of Staircase Sampling
Discussion on the Tileset for Staircase Sampling
Generalization of Staircase Sampling with Multiple Variables
Conclusion
Future Work
References
Design of a Functional Nanomaterial with Recognition Ability for Constructing Light-Driven Nanodevices
Introduction
Results and Discussion
Conclusions
Experimental Section
References
Efficient Turing-Universal Computation with DNA Polymers
Introduction
Irreversible and Reversible Chemical Reaction Networks
A Reversible Polymer Addition Primitive
Irreversible Stack Machine Implementation
Definition of Stack Machines
Reactions Corresponding to the Transition Rules
Reversible Stack Machine Implementation
Simulating a Reversible Turing Machine
Conclusions
References
Reversible Transition of Photonic DNA Automaton Using Hairpin-DNA Responding to a Single Kind of Photonic Signal
Introduction
Reaction Schemes
Experiments
Conclusions
References
Simple Evolution of Complex Crystal Species
Introduction
DNA Tile Crystal Replication and Evolution
Binary Zig-Zag CA Tile Sets
Predicting the Fitness of Zig-Zag CA Crystals
Evolution of Binary Zig-Zag CA Crystals
Evolution of Logically Reversible Zig-Zag CA Crystals
Kinetic Simulation of an Evolution Process
Conclusions and Open Questions
References
Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions
Introduction
Considerations
Implementation
User Interactivity
Discussion
References
DNA-Based Fixed Gain Amplifiers and Linear Classifier Circuits
Introduction
Fixed Gain Amplifiers: Lowering Catalytic Turnover
Fixed Gain Amplifiers: Increasing Catalytic Turnover
A Linear Classifier
Conclusions
References
Author Index

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