DNA Computing and Molecular Programming
17th International Conference, DNA 17, Pasadena, CA, USA, September 19-23, 2011, Proceedings
Published on 15. September 2011
X, 217 pages
978-3-642-23638-9 (ISBN)
Description
This book constitutes the refereed proceedings of the 17th International Conference on DNA Computing and Molecular Programming, DNA17, held in Pasadena, CA, USA, in September 2011.
The 12 revised full papers presented together with 5 invited talks were carefully selected from numerous submissions. Research in DNA computing and molecular programming draws together mathematics, computer science, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. This annual meeting is the premier forum where scientists with diverse backgrounds come together with the common purpose of advancing the engineering and science of biology and chemistry from the point of view of computer science, physics, and mathematics.
The 12 revised full papers presented together with 5 invited talks were carefully selected from numerous submissions. Research in DNA computing and molecular programming draws together mathematics, computer science, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. This annual meeting is the premier forum where scientists with diverse backgrounds come together with the common purpose of advancing the engineering and science of biology and chemistry from the point of view of computer science, physics, and mathematics.
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Luca Cardelli | William Shih
DNA Computing and Molecular Programming
17th International Conference, DNA 17, Pasadena, CA, USA, September 19-23, 2011, Proceedings
Book
09/2011
1st Edition
Springer
€53.49
Shipment within 7-9 days
Content
- Title
- Preface
- Organization
- Table of Contents
- Invited Talks
- Cooperative Assembly Systems
- The Cooperative Assembly Model
- Equilibrium
- Energy, Entropy
- Cooperativity
- Bond Displacement
- A Rough Estimate of B(x) given A(x)
- Simulations
- Deterministic Equilibrium for A(x)
- Fragmentation
- Additional Assumption
- Deterministic Steady State
- Criticality
- References
- The Computer Science of Molecular Programming
- An Autonomous DNA Nanodevice Captures pH Maps of Living Cells in Culture and in Vivo
- Introduction
- Materials and Methods
- Sample Preparation
- In cellulo Studies
- In vivo Studies
- Results
- Design of the I-Switch
- I-Switch and Endocytosis in Drosophila Hemocytes
- I-Switch and Endocytosis in Caenorhabditis elegans Coelomocytes
- Discussion
- References
- Cooperation in an All-RNA Network
- References
- Designer DNA Architectures for Bionanotechnology
- Contributed Papers
- An Improved DNA-Sticker Addition Algorithm and Its Application to Logarithmic Arithmetic
- Introduction
- Prior Algorithms
- Novel Algorithm
- Example
- Adding Constants
- Logarithmic Number System
- Conclusions
- References
- Graph-Theoretic Formalization of Hybridization in DNA Sticker Complexes
- Introduction
- Related Work
- The Sticker-Complex Data Model
- Hybridization
- Deciding Termination
- Complexity Issues
- Conclusion
- References
- Localized Hybridization Circuits
- Introduction
- Local versus Global MC
- Motivation for Local MC
- Our Contribution and Paper Organization
- Prior Work
- Design of DNA Hybridization Circuits on Addressable DNA Substrates
- Design of Logical Gates
- Compiling Boolean Circuits into DNA Hybridization Circuits
- Assembly of DNA Hybridization Circuits on Addressable DNA Nanostructures
- Reusing Sequences in Spatially Separated Circuits
- Functional Units and Architectures
- Modeling and Simulations of Tethered Systems
- A Biophysical Model of Tethered Hybridization
- Simulations of Tethered Hybridization Circuits using Visual DSD
- Discussion
- Refined Modeling and Simulations of Tethered Systems
- Optimizations
- Synchronous Computation and Nanomanufacture
- Possible Errors and Techniques to Mitigate Them
- Conclusions
- References
- Less Haste, LessWaste: On Recycling and Its Limits in Strand Displacement Systems
- Introduction
- On the Potential for Strand Recycling
- On the Limits of Strand Recycling
- Related Work
- GRAY: A Binary Reflecting Gray Code Counter
- Chemical Reaction System for the GRAY Counter
- Strand Displacement Implementation of the GRAY Counter
- Correctness
- Waste and Haste Analysis of the GRAY Counter
- A Fixed Order Implementation of the GRAY Counter
- The QSW Counter
- Limits on Strand Recycling for Multiple-Copy Systems
- Conclusions
- References
- One-Dimensional Staged Self-assembly
- Introduction
- Context-Free Grammars
- Staged Self-assembly
- Equivalence between RCFGs and SSASs
- Converting RCFGs to SSASs
- Converting SSASs to RCFGs
- Approximation Equivalence
- Separation Between SASs and RCFGs
- A Set of Strings S$_k$
- A SAS Upper Bound for S$_k$
- An RCFG Lower Bound for S$_k$
- Asymptotic Separation of SASs and RCFGs for S$_k$
- Upper Bounds for Separation of SASs and RCFGs
- References
- Computing Maximal Kleene Closures That Are Embeddable in a Given Constrained DNA Language
- Introduction
- Basic Notation and Background
- Words, Languages, Codes
- Automata, Graphs, Cycles
- The Subword Closure S and the DFA Trie(S)
- Characterizing Maximal D's with D*S
- Connection with a Previous Method
- Algorithmic Considerations for Maximal D's with D*S
- Algorithm ASP1(T,Q,X) for (SP1), and the 2D Array BQ
- Algorithm ASP2(T,Q,Z,Y) for (SP2)
- Algorithm ASP3(T,Q,X,Y) for (SP3)
- Algorithm for Problem (P1)
- Algorithm for Problem (P2)
- Concluding Remarks
- References
- Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems
- Introduction
- Polymers in DSD
- Stochastic Simulation of Polymerising Systems
- Modelling Stack Machines in DSD
- A Variant Stack Encoding
- Implementing a Stack Machine in DNA
- DSD Stack Machine Example: Ripple Carry Adder
- Stochastic Simulation
- Model Checking
- Related Work
- Discussion
- References
- Synthesizing Small and Reliable Tile Sets for Patterned DNA Self-assembly
- Introduction
- The PATS Problem and the PS-BB Algorithm
- The Abstract Tile Assembly Model RoWi00,Winf98b
- The PATS Problem
- The PS-BB Algorithm
- A New Algorithm for Small Tile Sets
- Reliability of Tile Sets
- Conclusion
- References
- Multivalent Random Walkers -A Model for Deoxyribozyme Walkers
- Introduction
- The Multivalent Random Walker Model
- The State Space of the Walker and the Environment
- State Transitions
- The Equilibrium Body Distribution
- Leg-Site Interactions
- Effect of Forces on Walkers
- Simulation
- Monte Carlo Simulation
- The Kinetic Monte Carlo Algorithm
- Metropolis-Hastings Distributions
- Preliminary Results
- Mechanism of Superdiffusive Motion
- Discussion
- References
- Exact Shapes and Turing Universality at Temperature 1 with a Single Negative Glue
- Introduction
- Preliminaries
- The Abstract Tile Assembly Model
- Restricted Glue and Zig-Zag Tile Assembly Systems and Path Simulation
- Exact Shapes
- Turing Universality
- References
- Autonomous Resolution Based on DNA Strand Displacement
- Introduction
- Principles of the Model
- Autonomous Resolution Using DNA
- Boolean Satisfiability Problem (SAT)
- Conclusions and Future Works
- References
- Multiple Molecular Spiders with a Single Localized Source-The One-Dimensional Case
- Introduction
- Molecular Spiders
- The Antal-Krapivsky Model
- Superdiffusive Motion of Single AK Spiders
- Multiple Spiders Model
- Simulation Results for Multiple Spiders
- Comparison of a Single AK Model Spider with a Single Spider of the Current Model
- Multiple Spiders Simulations
- Discussion
- References
- Author Index
