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

• Superior document: Natural Computing Series
• Author: 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
• Physical Description: 1 online resource (442 pages)

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.