DNA Computing and Molecular Programming 19th International Conference DNA 19 Tempe AZ USA September 22 27 2013 Proceedings 1st Edition by Mark Arnold, David Soloveichik, Bernard Yurke 3319019277 9783319019277

DNA Computing and Molecular Programming 19th International Conference DNA 19 Tempe AZ USA September 22 27 2013 Proceedings 1st Edition by Mark G. Arnold, David Soloveichik, Bernard Yurke – Ebook PDF Instant Download/DeliveryISBN:  3319019277, 9783319019277 

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ISBN-10 :  3319019277 

ISBN-13 :  9783319019277

Author:  Mark G. Arnold, David Soloveichik, Bernard Yurke 

This book constitutes the refereed proceedings of the 19th International Conference on DNA Computing and Molecular Programming, DNA 19, held in Tempe, AZ, USA, in September 2013. The 14 full papers presented were carefully selected from 29 submissions. The papers are organized in many disciplines (including mathematics, computer science, physics, chemistry, material science and biology) to address the analysis, design, and synthesis of information-based molecular systems.

 

DNA Computing and Molecular Programming 19th International Conference DNA 19 Tempe AZ USA September 22 27 2013 Proceedings 1st Table of contents:

Extending DNA-Sticker Arithmetic to Arbitrary Size Using Staples
1 Introduction
2 Simple Sticker System
3 Novel Extended Sticker System
4 Log-Time Summation
4.1 Algorithm Trace
4.2 Complexity
4.3 Macro, Micro and Hybrid Implementation
4.4 Stray Substrands
5 Conclusions
References
Parallel Computation Using Active Self-assembly
1 Introduction
1.1 Previous Work on Active Self-assembly with Movement
1.2 Our Results
Theorem 1.
1.3 Future Work and Open Questions
2 The Nubots Model and Other Definitions
2.1 Nubots and Decision Problems
Definition 1.
2.2 Boolean Circuits and the Class NC
3 Proof Overview of Theorem 1
3.1 Circuit Generation
3.2 Circuit Simulation
References
DNAWalker Circuits: Computational Potential, Design, and Verification
1 Introduction
2 Computational Potential of DNA Walker Circuits
2.1 A Model of Computation for DNA Walker Circuits
2.2 Reporting Output in DNA Walker Circuits
2.3 Deterministic Fork and Join Gates in DNA Walker Circuits
2.4 Evaluating Boolean Formulas with DNA Walker Circuits
3 Design and Verification of DNA Walker Circuits
3.1 Model Results
4 Conclusions
References
Leaderless Deterministic Chemical Reaction Networks
1 Introduction
2 Preliminaries
2.1 Chemical Reaction Networks
2.2 Stable Decidability of Predicates
2.3 Stable Computation of Functions
2.4 Kinetic Model
3 Leaderless CRCs Can Compute Semilinear Functions
4 Conclusion
References
DNA Sticky End Design and Assignmentfor Robust Algorithmic Self-assembly
1 Introduction
2 Theoretical Model
2.1 Uniformity
2.2 Orthogonality
2.3 Sticky End Sensitivity
3 Sequence Design and Assignment
3.1 Sequence Design
3.2 Sequence Assignment
4 Conclusions and Discussion
References
DNA Reservoir Computing: A Novel Molecular Computing Approach
1 Introduction
2 Reservoir Computing
3 Reservoir Computing Using Deoxyribozyme Oscillators
4 Task Solving Using a Deoxyribozyme Reservoir Computer
5 Discussion and Related Work
6 Conclusion and Future Work
References
Signal Transmission across Tile Assemblies: 3D Static Tiles Simulate Active Self-assembly by 2D Sign
1 Introduction
2 Preliminaries
2.1 Informal Definition of the 2HAM
2.2 Informal Description of the STAM
2.3 Informal Definitions for Simulation
3 Transforming STAM+ Systems from Arbitrary to Bounded Signal Complexity
3.1 Impossibility of Eliminating Both Fan-Out and Mutual Activation at
3.2 Eliminating Either Fan-Out or Mutual Activation
3.3 Summary of Results
4 A 3D 2HAM Tile Set Which Is IU for the STAM+
4.1 Construction Overview
5 Conclusion
References
3-Color Bounded Patterned Self-assembly
1 Introduction
2 Rectilinear Tile Assembly Systems
3 NP-Hardness of
4 NP-Hardness of 3-
5 Conclusions
References
Exponential Replication of Patterns in the Signal Tile Assembly Model
1 Introduction
1.1 Outline of Paper
2 Definitions
2.1 Basic Definitions
2.2 Signal Tile Model
2.3 Exponential Replication
3 Replication of 2D Patterns in Two Dimensions
4 Future Work
References
Modular Verification of DNA Strand Displacement Networks via Serializability Analysis
1 Introduction
2 Preliminaries
3 Two-Domain DNA Strand Displacement Gates
4 Modular Chemical Reaction Encodings
5 Soundness of CRN Encodings
6 Verification Example
7 Discussion
References
Iterative Self-assembly with Dynamic Strength Transformation and Temperature Control
1 Introduction
2 Overview of the Approach
3 Formal Definition of the Extended Hexagonal TAS
3.1 A Formal Expression
3.2 Tile Types
3.3 The Procedure of the Iterative Approach
3.4 Proposed Implementation of the Operations
4 Constructing an Equilateral Triangle from Size 4 to 6
5 Equilateral Triangle Is the Only Stable Final Shape
6 Conclusion and Future Work
References
Probabilistic Reasoning with an Enzyme-Driven DNA Device
1 Introduction
2 ExampleofBayesianInference
3 Encoding Input Evidences
4 Encoding Prior Probabilities
5 Encoding Conditional Probabilities
6 Inference Process
6.1 Inference Steps
6.2 Modeling the Inference
7 Discussion
8 Conclusions and Future Work
References
Staged Self-assembly and Polyomino Context-Free Grammars
1 Introduction
2 Staged Self-assembly
3 Polyomino Context-Free Grammars
4 SAS over PCFG Separation Lower Bound
5 SAS over PCFG Separation upper Bound
6 PCFG over SAS and SSAS Separation Lower Bound
6.1 General Shapes
6.2 Rectangles
6.3 Squares
6.4 Constant-Glue Constructions
7 Conclusion
References
Functional Analysis of Large-Scale DNA Strand Displacement Circuits
1 Introduction
2 SMT Analysis of Chemical Reaction Networks
3 SMT Analysis of DNA Strand Displacement Circuits
3.1 Identification of Inactive Reactions
3.2 Encoding Generalization
3.3 Implementation of Methods in Visual DSD
4 Functional Analysis of a 4-bit Square Root Circuit
5 Discussion

 

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