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UID:

Format: 1 Online-Ressource.

ISBN: 978-981-19-9891-1

Series Statement: Natural computing series

Additional Edition: Erscheint auch als Druck-Ausgabe, Hardcover ISBN 978-981-19-9890-4

Additional Edition: Erscheint auch als Druck-Ausgabe, Paperback ISBN 978-981-19-9893-5

Language: English

Keywords: Festschrift

DOI: 10.1007/978-981-19-9891-1

URL: Volltext  (kostenfrei)

URL: Volltext  (kostenfrei)

UID:

Format: 1 Online-Ressource.

ISBN: 978-981-19-9891-1

Series Statement: Natural computing series

Additional Edition: Erscheint auch als Druck-Ausgabe, Hardcover ISBN 978-981-19-9890-4

Additional Edition: Erscheint auch als Druck-Ausgabe, Paperback ISBN 978-981-19-9893-5

Language: English

Keywords: Festschrift

DOI: 10.1007/978-981-19-9891-1

URL: Volltext  (kostenfrei)

URL: Volltext  (kostenfrei)

UID:

Format: 1 Online-Ressource.

ISBN: 978-981-19-9891-1

Series Statement: Natural computing series

Additional Edition: Erscheint auch als Druck-Ausgabe, Hardcover ISBN 978-981-19-9890-4

Additional Edition: Erscheint auch als Druck-Ausgabe, Paperback ISBN 978-981-19-9893-5

Language: English

Keywords: Festschrift

DOI: 10.1007/978-981-19-9891-1

URL: Volltext  (kostenfrei)

URL: Volltext  (kostenfrei)

UID:

Format: 1 Online-Ressource

ISBN: 9789811998911

Series Statement: Natural computing series

Additional Edition: Erscheint auch als Druck-Ausgabe, Hardcover ISBN 978-981-19-9890-4

Additional Edition: Erscheint auch als Druck-Ausgabe, Paperback ISBN 978-981-19-9893-5

Language: English

Keywords: Festschrift

DOI: 10.1007/978-981-19-9891-1

URL: Volltext  (kostenfrei)

URL: Volltext  (kostenfrei)

UID:

Format: 1 Online-Ressource (x, 333 Seiten) , 271 Illustrationen, 5 in Farbe

ISBN: 9783030485160

Series Statement: Lecture notes in computer science 12086

Additional Edition: Erscheint auch als Druck-Ausgabe ISBN 978-3-030-48515-3

Additional Edition: Erscheint auch als Druck-Ausgabe ISBN 978-3-030-48517-7

Language: English

Subjects: Computer Science

Keywords: Künstliche Intelligenz ; Logik ; Formale Sprache ; Theoretische Informatik ; Konferenzschrift

DOI: 10.1007/978-3-030-48516-0

URL: Volltext  (URL des Erstveröffentlichers)

UID:

Format: x, 333 Seiten , Illustrationen, Diagramme

ISBN: 9783030485153

Series Statement: Lecture notes in computer science 12086

Additional Edition: Erscheint auch als Online-Ausgabe ISBN 978-3-030-48516-0

Language: English

Subjects: Computer Science

Keywords: Formale Sprache ; Theoretische Informatik ; Künstliche Intelligenz ; Logik ; Konferenzschrift

UID:

Format: 1 online resource (442 pages)

Edition: First edition.

Series Statement: Natural Computing Series.

Note: 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.

Additional Edition: ISBN 981-19-9890-6

Language: English

UID:

Format: 1 online resource (442 pages)

Edition: First edition.

Series Statement: Natural Computing Series.

Note: 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.

Additional Edition: ISBN 981-19-9890-6

Language: English

UID:

Format: 1 online resource (442 pages)

Edition: First edition.

Series Statement: Natural Computing Series.

Note: 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.

Additional Edition: ISBN 981-19-9890-6

Language: English

UID:

Format: 1 online resource (xxviii, 431 pages) : , illustrations (chiefly color).

ISBN: 9789811998911 , 9811998914

Series Statement: Natural computing series

Content: This open access book provides a unique and state-of-the-art view on DNA nanotechnology with an eye toward future developments. Intended as a tribute to Nadrian C. Seeman, who founded the field of DNA nanotechnology, the content is an exciting mixture of technical and non-technical material, reviews, tutorials, perspectives, new findings, and open questions. The book aims to inspire current researchers to sit back and think about the big picture, while also enticing new researchers to enter the field. Most of all, the book captures voices from a unique moment in time: 40 years after the publication of the first paper that envisioned DNA nanotechnology. From this vantage point, what are the untold stories, the unspoken concerns, the underlying fundamental issues, the overlooked opportunities, and the unifying grand challenges? What will help us see more clearly, see more creatively, or see farther? What is transpiring right now that could pave the way for the future? To address these questions, leading researchers have contributed 22 chapters, grouped into five sections: perspectives, chemistry and physics, structures, biochemical circuits, and spatial systems. This book will be an important reference point in the field of DNA nanotechnology, both for established researchers looking to take stock of the field and its future, and for newcomers such as graduate students and researchers in other fields who are beginning to appreciate the power and applicability of its methods.

Note: Beyond Watson-Crick -- DNA nanotechnology out of equilibrium -- The Evolution of DNA-Based Molecular Computing -- DNA Nanotechnology Research in Japan -- Reminiscences from the Trenches -- Beyond DNA -- Controlling single molecule conjugated oligomers and polymers with DNA -- Organizing charge flow with DNA -- DNA Assembly of Dye Aggregates -- Building with DNA -- From Molecules to Mathematics -- Origami Life -- Ok: a kinetic model for locally reconfigurable molecular systems -- Implementing a Theoretician’s Toolkit for Self-Assembly with DNA Components -- Reasoning As If -- Scaling up DNA computing with array-based synthesis and high-throughput sequencing -- Sequenceable Event Recorders -- Computational Design of Nucleic Acid Circuits -- Parallel computations with DNA-encoded chemical reaction networks -- Social DNA Nanorobots -- Models of Gellular Automata -- Patterning DNA origami on membranes through protein self-organization.

Language: English

Keywords: Electronic books. ; Festschriften.

DOI: 10.1007/978-981-19-9891-1

URL: SpringerLink

URL: Click here to view book