DNA Computing and Molecular Programming

Name: DNA Computing and Molecular Programming | 17th International Conference, DNA 17, Pasadena, CA, USA, September 19-23, 2011, Proceedings
Brand: Springer
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17th International Conference, DNA 17, Pasadena, CA, USA, September 19-23, 2011, Proceedings

Luca Cardelli William Shih(Herausgeber*in)

Springer (Verlag)

Erschienen am 15. September 2011

X, 217 Seiten

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Inhalt

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

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