Visions of DNA Nanotechnology at 40 for the Next 40 : : A Tribute to Nadrian C. Seeman.

Visions of DNA Nanotechnology at 40 for the Next 40 : : A Tribute to Nadrian C. Seeman.

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Bibliographic Details
Superior document:Natural Computing Series
:
Jonoska, Natasa.
TeilnehmendeR:
Winfree, Erik.
Place / Publishing House:Singapore : : Springer,, 2023.
©2023.
Year of Publication:2023
Edition:1st ed.
Language:English
Series:Natural Computing Series
Online Access:
Physical Description:1 online resource (442 pages)
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Table of Contents:
  • Intro
  • In Memoriam
  • Preface
  • Contents
  • Perspectives
  • Beyond Watson-Crick: The Next 40 Years of Semantomorphic Science
  • 1 A Brief Retrospective
  • 2 A Science Allegory
  • 3 A Roadmap
  • 3.1 DNA Semantics: Schrödinger Crystals Versus Seeman Crystals
  • 3.2 DNA Syntax-Information Bundles and Secondary Structures
  • 3.3 Nucleic Acid Operating Systems: XNA and Beyond
  • 4 Beyond Watson-Crick: A Call to Action
  • References
  • DNA Nanotechnology Out of Equilibrium
  • 1 DNA Nanotechnology: A Personal Account
  • 2 Designing and Programming with DNA
  • 2.1 DNA-A Programmable Molecule
  • 2.2 Learning by Building
  • 2.3 Challenges and Limitations
  • 3 From Self-Assembly to Non-equilibrium Dynamics and Self-Organization
  • 3.1 Molecular Machines
  • 3.2 Non-equilibrium Chemical Dynamics and Self-Assembly
  • 3.3 Robots
  • 4 What Lies Ahead?
  • References
  • The Evolution of DNA-Based Molecular Computing
  • 1 A Brief History of DNA Computing
  • 2 Opportunities and Challenges
  • 2.1 Bridge Between Matter and Information
  • 2.2 Massive Parallelism
  • 2.3 Scalability
  • 3 Directions for Future Development and Potential Approaches
  • 3.1 Scaling-Up
  • 3.2 Updating and Reusing
  • 4 Summary
  • References
  • DNA Nanotechnology Research in Japan
  • 1 Introduction
  • 2 How the Author Got Involved in DNA Nanotechnology
  • 3 The Evolution of Projects in Japan
  • 3.1 The 1980s and 1990s
  • 3.2 The 2000s
  • 3.3 The 2010s
  • 3.4 Current Research
  • 4 Summary
  • References
  • Reminiscences from the Trenches: The Early Years of DNA Nanotech
  • 1 Discovering DNA Computing
  • 2 Connections to Broader Scientific Themes
  • 3 Ned Seeman: Founder of the Field
  • 4 Personal Milestones
  • 5 The End of the Early years
  • References
  • Chemistry and Physics
  • Beyond DNA: New Digital Polymers
  • 1 New Polymer 1 (NP1)
  • 2 New Polymer 2 (NP2)
  • 3 New Polymer 3 (NP3).
  • 4 Example Applications
  • 5 Conclusions
  • References
  • Controlling Single Molecule Conjugated Oligomers and Polymers with DNA
  • 1 Modular Self-Assembly of Molecular Components
  • 2 Conjugated Polymers on DNA Origami
  • 3 Work from Other Groups
  • 4 Conclusion
  • References
  • Organizing Charge Flow with DNA
  • 1 Origami's Rise
  • 2 Making DNA Nanostructures Conductive Through Metallization
  • 3 Decorating Origami
  • 3.1 DNA Scaffolding for Conductive Metals
  • 3.2 DNA Scaffolds for Conductive Polymers
  • 3.3 DNA Scaffolds for Carbon Nanotubes
  • 3.4 Highly Ordered, Three-Dimensional DNA-CNT Arrays
  • 4 The Future of DNA-Organized Electronics
  • 4.1 Making DNA More Electronic
  • 4.2 Scaffolding Biocompatible Electronic Materials
  • References
  • DNA Assembly of Dye Aggregates-A Possible Path to Quantum Computing
  • 1 Introduction
  • 2 The Mathematical Structure of Reality
  • 3 Quantum Computers
  • 3.1 The Controlled NOT Gate
  • 3.2 Quantum Parallelism
  • 4 The Frenkel Exciton Hamiltonian
  • 5 Energy Eigenvalues of a Homodimer Dye Aggregate and Davydov Splitting
  • 6 Coherent Exciton Hopping
  • 7 Exciton Transmission Lines
  • 8 Representation of an Exciton Qubit
  • 9 Basis Change Gates
  • 10 Phase Gates
  • 11 An Exciton Interferometer
  • 12 A Controlled Phase Shift
  • 13 A CNOT Gate
  • 14 Exciton-Based Quantum Computer Architecture
  • 15 But Isn't a Quantum Computer Just an Analog Computer?
  • 16 Molecular Vibrations
  • 17 Conclusion
  • References
  • Structures
  • Building with DNA: From Curiosity-Driven Research to Practice
  • 1 Introduction
  • 2 Engineering Cell-Sized DNA Structures
  • 2.1 Challenges
  • 2.2 Opportunities
  • 3 Building Designer DNA Crystals with Atomic Resolutions
  • 3.1 Challenges
  • 3.2 Opportunities
  • 4 Transferring to RNA Structural Design
  • 4.1 Challenges
  • 4.2 Opportunities
  • 5 At the End
  • References.
  • From Molecules to Mathematics
  • 1 Introduction
  • 2 Flexible Tiles and New Graph Invariants
  • 3 DNA Strand Routing and Topological Graph Theory
  • 4 DNA Origami and New Algebraic Structures
  • 5 DNA Origami and Origami Knots
  • 6 Where Next?
  • References
  • Origami Life
  • 1 Origami Molecules
  • 2 Origami Design Algorithms
  • 3 Origami Folding Pathways
  • 4 Folded Origins
  • References
  • Ok: A Kinetic Model for Locally Reconfigurable Molecular Systems
  • 1 Introduction
  • 2 Molecular Reconfiguration: Oritatami and Nubots
  • 3 The Ok model
  • 3.1 Reconfiguration Events
  • 3.2 Reconfiguration Distributions and Events Rates
  • 3.3 Implementing the Ok model
  • 4 Conclusion
  • References
  • Implementing a Theoretician's Toolkit for Self-Assembly with DNA Components
  • 1 Introduction
  • 2 Definitions and Notation
  • 3 Metrics
  • 4 Monomer Reuse: Hard-Coded Versus Algorithmic
  • 5 Inputs
  • 5.1 Seed Assemblies
  • 5.2 Tile Subsets
  • 5.3 Monomer Concentrations
  • 5.4 Programmed Temperature Fluctuations
  • 5.5 Staged Assembly
  • 6 Dynamics
  • 6.1 Cooperativity
  • 6.2 Single Tile or Hierarchical Growth
  • 6.3 Activatable/Deactivatable Glues
  • 6.4 Tile Removal and Breaking of Assemblies
  • 6.5 Reconfiguration Via Flexibility
  • 6.6 Assembly Growth Controlled by CRNs
  • 7 Conclusion
  • References
  • Reasoning As If
  • 1 Introduction
  • 2 The Snapshot Algorithm
  • 3 Local Determinism
  • 4 The Future of As If
  • References
  • Biochemical Circuits
  • Scaling Up DNA Computing with Array-Based Synthesis and High-Throughput Sequencing
  • 1 Introduction
  • 1.1 Scaling up DNA Computing for Molecular Diagnostics
  • 1.2 Scaling up DNA Computing for DNA Data Storage
  • 1.3 Limitations of Current Approaches to DNA Computing
  • 2 A Vision for the Future
  • 3 Results
  • 3.1 Nicked Double-Stranded DNA Gates Reaction Mechanism
  • 3.2 Gate Design.
  • 3.3 Making ndsDNA Gates from Array-Synthesized DNA
  • 3.4 Characterizing Gate Kinetics
  • 3.5 Reading Out DNA Computation with Next-Generation DNA Sequencing
  • 3.6 Reading Pools of Array-Derived Gates
  • 4 Discussion
  • References
  • Sequenceable Event Recorders
  • 1 Introduction
  • 2 Occurrence Recorder
  • 2.1 Yes Gate
  • 2.2 Occurrence Recorder Algorithm
  • 3 Coincidence Recorder
  • 3.1 Join Gate
  • 3.2 Coincidence Recorder Algorithm
  • 4 Preorder Recorder
  • 4.1 Choice Gate Specification
  • 4.2 Preorder Recorder Algorithm
  • 4.3 Crosstalking Choice Gate
  • 4.4 A ``Proper'' Choice Gate
  • 5 Conclusions
  • References
  • Computational Design of Nucleic Acid Circuits: Past, Present, and Future
  • 1 Past
  • 1.1 Visual DSD Origins
  • 1.2 Visual DSD Evolution
  • 1.3 Visual DSD Analysis
  • 2 Present
  • 2.1 Logic Programming Framework
  • 2.2 Related Work
  • 3 Future
  • 3.1 Computational Tool Integration
  • 3.2 Experiment Integration
  • 3.3 Computational Design for Practical Applications
  • References
  • Spatial Systems
  • Parallel Computations with DNA-Encoded Chemical Reaction Networks
  • 1 Harnessing Parallelization in Chemical Reaction Networks
  • 1.1 D(R)NA-Based Deterministic Chemical Reaction Networks
  • 1.2 CRNs Run on Inherently Parallel Processes
  • 2 Creating Sub-Computations
  • 2.1 No-Diffusion (Leak-Tight) Compartments
  • 2.2 Compartment-Free Approaches
  • 2.3 Intermediate Cases: Some Species Diffuse, Some Do Not
  • 3 Discussion and Applications
  • 3.1 Independent Compartments Containing an Identical Circuit but Receiving Different Inputs
  • 3.2 Independent Compartments Containing Different Circuits, All Working on the Same Inputs
  • 3.3 Cross-Talking Compartments Collaborating to Compute a Global Response
  • References
  • Social DNA Nanorobots
  • 1 Introduction
  • 1.1 Motivation
  • 1.2 Summary of Our Results
  • 1.3 Organization.
  • 2 Sociobiology
  • 3 Prior DNA Nanorobots
  • 3.1 Prior DNA Walkers
  • 3.2 Prior Programmable DNA Nanorobots
  • 3.3 Prior Autonomous DNA Walkers that Do Molecular Cargo-Sorting on a 2D Nanostructure
  • 4 Design and Simulation of Social DNA Nanorobots
  • 4.1 Social DNA Nanorobot Behaviors Designed and Simulated
  • 4.2 Software for Stochastic Simulations of the Social DNA Nanorobots Behaviors
  • 4.3 A Prior DNA Nanorobot that Autonomously Walks
  • 4.4 Prior Demonstrated Technique for Hybridization Inhibition of Short Sequences Within the Hairpin Loops
  • 4.5 A Novel DNA Nanorobot that Executes a Self-Avoiding Walk
  • 4.6 Flocking: Novel DNA Nanorobots that Follow a Leader
  • 4.7 Novel DNA Nanorobots that Vote by Assassination
  • 5 Discussion
  • 5.1 Further Development of Simulation Software for Social Nanorobots
  • 5.2 Experimental Demonstrations of Social DNA Nanorobots
  • 5.3 Further Social DNA Nanorobot Behaviors
  • 5.4 Communication Between Distant Social Nanorobots
  • References
  • Models of Gellular Automata
  • 1 Introduction: Why Cellular Automata?
  • 1.1 Computation by Molecules
  • 1.2 Smart Materials
  • 1.3 Why Discrete?
  • 2 Implementation of Cellular Automata
  • 2.1 Molecular Level
  • 2.2 Reaction-Diffusion Systems
  • 3 Gellular Automata
  • 3.1 Gellular Automata with Holes
  • 3.2 Boolean Total and Non-Camouflage Gellular Automata
  • 3.3 Three-Dimensional Gellular Automata That Learn Boolean Circuits
  • 4 Supervised Learning of Boolean Circuits
  • 4.1 Assumption
  • 4.2 States
  • 4.3 Algorithm
  • 5 Concluding Remark
  • References
  • Patterning DNA Origami on Membranes Through Protein Self-Organization
  • 1 Introduction
  • 2 DNA Origami as a Tool to Elucidate Molecular Mechanisms
  • 3 Stable DNA Origami Patterns on Lipid Membranes
  • 4 Challenges and Opportunities
  • 5 Materials and Methods
  • References.

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