DNA Computing and Molecular Programming

Name: DNA Computing and Molecular Programming | 25th International Conference, DNA 25, Seattle, WA, USA, August 5-9, 2019, Proceedings
Brand: Springer
Price: 60.98 EUR
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25th International Conference, DNA 25, Seattle, WA, USA, August 5-9, 2019, Proceedings

Chris Thachuk Yan Liu(Editor)

Springer (Publisher)

Published on 30. July 2019

XII, 237 pages

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978-3-030-26807-7 (ISBN)

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Content

Intro
Preface
Organization
Contents
Chemical Reaction Networks and Stochastic Local Search
1 Introduction
2 Stochastic Chemical Reaction Networks
3 Evaluating and Satisfying Circuits
4 Formula Satisfiability
5 Recognizing and Generating Patterns
6 Sudoku
7 Discussion
References
Implementing Arbitrary CRNs Using Strand Displacing Polymerase*-12pt
1 Introduction
1.1 Motivation for Our Work
1.2 Our Contribution
1.3 Paper Organization
2 Strand Displacement with DNA Polymerase
3 Implementation of Arbitrary Reactions
3.1 Arbitrary Unimolecular Reactions
3.2 Arbitrary Bimolecular Reactions
4 Scaling Reaction Systems for Practicality
5 Applications
5.1 Generalized Autocatalytic Amplifier
5.2 Molecular-Scale Consensus Network
5.3 Molecular-Scale Dynamic Oscillator
6 Discussion
6.1 Experimental Demonstration and Considerations
6.2 Replenishing Supporting Gates with Buffered Reaction
7 Conclusion
References
Real-Time Equivalence of Chemical Reaction Networks and Analog Computers*-12pt
1 Introduction
2 Preliminaries
3 Real-Time Equivalence of CRNs and GPACs
4 e and Are Real-Time Computable by CRNs
5 Conclusion
References
A Reaction Network Scheme Which Implements Inference and Learning for Hidden Markov Models
1 Introduction
2 Hidden Markov Models and the Baum Welch Algorithm
3 Chemical Baum-Welch Algorithm
3.1 Reaction Networks
3.2 Baum-Welch Reaction Network
4 Analysis and Simulations
5 Related Work
6 Discussion
A Appendix
A.1 Comparing Points of Equilibria
A.2 Rate of Convergence Analysis
References
Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains
1 Introduction
1.1 Mean First Passage Time Estimation
1.2 Parameter Estimation
2 Preliminaries
2.1 The Multistrand Kinetic Simulator
2.2 Gillespie's Stochastic Simulation Algorithm
3 Methodology
3.1 Mean First Passage Time Estimation
3.2 Parameter Estimation
4 Experiments
4.1 Dataset
4.2 Mean First Passage Time Estimation
4.3 Parameter Estimation
5 Discussion
References
New Bounds on the Tile Complexity of Thin Rectangles at Temperature-1
1 Introduction
1.1 Main Results of This Paper
1.2 Comparison with Related Work
2 Preliminaries
3 Lower Bound
3.1 Window Movie Lemmas
3.2 Counting Procedure for Undirected Self-assembly in 2D
3.3 Lower Bound for Undirected Self-assembly in 2D: Theorem 1
4 Upper Bound
5 Future Work
References
Non-cooperatively Assembling Large Structures
1 Introduction
2 Definitions and Preliminaries
2.1 Abstract Tile Assembly Model
2.2 Paths and Non-cooperative Self-assembly
3 The Tile Assembly System
3.1 Definition of the Tile Assembly System
3.2 Basic Properties
3.3 Analysis of the Prefixes
3.4 Analysis of the Tile Assembly System
3.5 Conclusion of the Proof
4 Open Questions
A Make Your Own Large Paths
References
Simulation of Programmable Matter Systems Using Active Tile-Based Self-Assembly*-12pt
1 Introduction
2 The Tile Automata Model
2.1 Wire Transmission
3 The Amoebot Model
4 Simulating Amoebot Systems with Tile Automata
4.1 Defining Simulation
4.2 Construction Definitions
4.3 Simulation Overview
5 Simulation of Movement
5.1 handover
5.2 Attachment Sites
6 Conclusion
References
Combined Amplification and Molecular Classification for Gene Expression Diagnostics
1 Introduction
2 A Molecular Classifier with Built-In Amplification
3 Computational Design of Sparsely Featured Diagnostic Classifiers
4 Simulating the Accuracy of a Molecular Classifier
5 Scaling up Weights to Reduce Bias Variation
6 Classifier Calibration by Screening Probes
7 Encoding Weights in Probe Concentration
8 Discussion
References
Reversible Computation Using Swap Reactions on a Surface
1 Introduction
2 Computing Paradigm
3 Building Logic Circuits with Swaps
3.1 NOT, AND, OR
3.2 Fanout, Wirecross
3.3 Compiling a Feedforward Circuit to a Surface Layout
3.4 4-Bit Square Root Circuit
4 Proving Circuit Correctness
5 Kinetics and Entropics
6 Future Directions
References
Error-Free Stable Computation with Polymer-Supplemented Chemical Reaction Networks*-10pt
1 Introduction
1.1 Contributions and Highlights
1.2 Related Work
2 Polymer-Supplemented Chemical Reaction Networks
3 Stable, Turing-Universal Computation by Sequential PsCRNs with Leader Polymers
4 Faster Computation of Square by Threaded psCRNs with Anonymous Polymers
5 psCRN Time Complexity Analysis and Simulation
6 Conclusions and Future Work
References
SIMD||DNA: Single Instruction, Multiple Data Computation with DNA Strand Displacement Cascades
1 Introduction
2 SIMD||DNA
2.1 Encoding Data
2.2 Instructions
2.3 Programs
3 Programs for Binary Counting and Rule 110
3.1 Cellular Automaton Rule 110
3.2 Counting
4 Discussion and Future Work
4.1 Data Preparation
4.2 Experimental Feasibility and Error Handling
4.3 Data Density
4.4 Uniform Versus Non-uniform Instructions
4.5 Determinism and Nondeterminism
4.6 Running Time
4.7 Universal Computation
4.8 Space-Efficient Computation
4.9 Equalizing Encodings
References
Author Index

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DNA Computing and Molecular Programming

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