Quantum Aspects of Life.

By: Abbott, DerekContributor(s): Davies, Paul C. W | Pati, Arun KumarPublisher: Singapore : Imperial College Press, 2008Copyright date: ©2008Description: 1 online resource (468 pages)Content type: text Media type: computer Carrier type: online resourceISBN: 9781848162556Subject(s): Quantum biochemistry.;Life -- OriginGenre/Form: Electronic books. Additional physical formats: Print version:: Quantum Aspects of LifeDDC classification: 576.83 LOC classification: QP517.Q34 -- Q36 2008ebOnline resources: Click to View
Contents:
Intro -- Contents -- Foreword -- Preface -- Acknowledgments -- Part 1: Emergence and Complexity -- 1. A Quantum Origin of Life? Paul C. W. Davies -- 1.1. Chemistry and Information -- 1.2. Q-life -- 1.3. The Problemof Decoherence -- 1.4. Life as the "Solution" of a Quantum Search Algorithm -- 1.5. Quantum Choreography -- Acknowledgements -- References -- 2. Quantum Mechanics and Emergence Seth Lloyd -- 2.1. Bits -- 2.2. Coin Flips -- 2.3. The Computational Universe -- 2.4. Generating Complexity -- 2.5. A Human Perspective -- 2.6. A QuantumPerspective -- References -- Part 2: Quantum Mechanisms in Biology -- 3. Quantum Coherence and the Search for the First Replicator Jim Al-Khalili and Johnjoe McFadden -- 3.1. When did Life Start? -- 3.2. Where did Life Start? -- 3.3. Where did the Precursors Come From? -- 3.4. What was the Nature of the First Self-replicator? -- 3.5. The RNAWorld Hypothesis -- 3.6. A Quantum Mechanical Origin of Life -- 3.6.1. The dynamic combinatorial library -- 3.6.2. The two-potential model -- 3.6.3. Decoherence -- 3.6.4. Replication as measurement -- 3.6.5. Avoiding decoherence -- 3.7. Summary -- References -- 4. Ultrafast Quantum Dynamics in Photosynthesis Alexandra Olaya Castro, Francesca Fassioli Olsen, Chiu Fan Lee, and Neil F. Johnson -- 4.1. Introduction -- 4.2. A Coherent Photosynthetic Unit (CPSU) -- 4.3. Toy Model: Interacting Qubits with a Spin-star Configuration -- 4.4. A More Detailed Model: Photosynthetic Unit of Purple Bacteria -- 4.5. Experimental Considerations -- 4.6. Outlook -- References -- 5. Modelling Quantum Decoherence in Biomolecules Jacques Bothma, Joel Gilmore, and Ross H. McKenzie -- 5.1. Introduction -- 5.2. Time and Energy Scales -- 5.3. Models for Quantum Baths and Decoherence -- 5.3.1. The spin-bosonmodel -- 5.3.1.1. Independent boson model -- 5.3.2. Caldeira-Leggett Hamiltonian.
5.3.3. The spectral density -- 5.4. The Spectral Density for the Different Continuum Models of the Environment -- 5.5. Obtaining the Spectral Density from Experimental Data -- 5.6. Analytical Solution for the Time Evolution of the Density Matrix -- 5.7. Nuclear Quantum Tunnelling in Enzymes and the Crossover Temperature -- 5.8. Summary -- References -- Part 3: The Biological Evidence -- 6. Molecular Evolution: A Role for Quantum Mechanics in the Dynamics of Molecular Machines that Read and Write DNA Anita Goel -- 6.1. Introduction -- 6.2. Background -- 6.3. Approach -- 6.3.1. The information processing power of a molecularmotor -- 6.3.2. Estimation of decoherence times of the motor-DNA complex -- 6.3.3. Implications and discussion -- References -- 7. Memory Depends on the Cytoskeleton, but is it Quantum? Andreas Mershin and Dimitri V. Nanopoulos -- 7.1. Introduction -- 7.2. Motivation behind Connecting Quantum Physics to the Brain -- 7.3. Three Scales of Testing for Quantum Phenomena in Consciousness -- 7.4. Testing the QCI at the 10 nm-10 µm Scale -- 7.5. Testing for Quantum Effects in Biological Matter Amplified from the 0.1 nm to the 10 nm Scale and Beyond -- 7.6. Summary and Conclusions -- 7.7. Outlook -- Acknowledgements -- References -- 8. Quantum Metabolism and Allometric Scaling Relations in Biology Lloyd Demetrius -- 8.1. Introduction -- 8.2. Quantum Metabolism: Historical Development -- 8.2.1. Quantization of radiation oscillators -- 8.2.2. Quantization of material oscillators -- 8.2.3. Quantization of molecular oscillators -- 8.2.4. Material versus molecular oscillators -- 8.3. Metabolic Energy and Cycle Time -- 8.3.1. The mean energy -- 8.3.2. The total metabolic energy -- 8.4. The Scaling Relations -- 8.4.1. Metabolic rate and cell size -- 8.4.2. Metabolic rate and body mass -- 8.5. Empirical Considerations -- 8.5.1. Scaling exponents.
8.5.2. The proportionality constant -- References -- 9. Spectroscopy of the Genetic Code Jim D. Bashford and Peter D. Jarvis -- 9.1. Background: Systematics of the Genetic Code -- 9.1.1. RNA translation -- 9.1.2. The nature of the code -- 9.1.3. Information processing and the code -- 9.2. Symmetries and Supersymmetries in the Genetic Code -- 9.2.1. sl(6/1) model: UA+S scheme -- 9.2.2. sl(6/1) model: 3CH scheme -- 9.2.3. Dynamical symmetry breaking and third base wobble -- 9.3. Visualizing the Genetic Code -- 9.4. Quantum Aspects of Codon Recognition -- 9.4.1. N(34) conformational symmetry -- 9.4.2. Dynamical symmetry breaking and third base wobble -- 9.5. Conclusions -- Acknowledgements -- References -- 10. Towards Understanding the Origin of Genetic Languages Apoorva D. Patel -- 10.1. The Meaning of It All -- 10.2. Lessons of Evolution -- 10.3. Genetic Languages -- 10.4. Understanding Proteins -- 10.5. Understanding DNA -- 10.6. What Preceded the Optimal Languages? -- 10.7. Quantum Role? -- 10.8. Outlook -- References -- Part 4: Artificial Quantum Life -- 11. Can Arbitrary Quantum Systems Undergo Self-replication? Arun K. Pati and Samuel L. Braunstein -- 11.1. Introduction -- 11.2. Formalizing the Self-replicating Machine -- 11.3. Proof of No-self-replication -- 11.4. Discussion -- 11.5. Conclusion -- Acknowledgments -- References -- 12. A Semi-quantum Version of the Game of Life Adrian P. Flitney and Derek Abbott -- 12.1. Background and Motivation -- 12.1.1. Classical cellular automata -- 12.1.2. Conway's game of life -- 12.1.3. Quantum cellular automata -- 12.2. Semi-quantumLife -- 12.2.1. The idea -- 12.2.2. A first model -- 12.2.3. A semi-quantum model -- 12.2.4. Discussion -- 12.3. Summary -- References -- 13. Evolutionary Stability in Quantum Games Azhar Iqbal and Taksu Cheon -- 13.1. Evolutionary Game Theory and Evolutionary Stability.
13.1.1. Population setting of evolutionary game theory -- 13.2. Quantum Games -- 13.3. Evolutionary Stability in Quantum Games -- 13.3.1. Evolutionary stability in EWL scheme -- 13.3.2. Evolutionary stability in MW quantization scheme -- 13.4. Concluding Remarks -- References -- 14. Quantum Transmemetic Intelligence Edward W. Piotrowski and Jan S ladkowski -- 14.1. Introduction -- 14.2. A QuantumModel of FreeWill -- 14.3. Quantum Acquisition of Knowledge -- 14.4. Thinking as a Quantum Algorithm -- 14.5. Counterfactual Measurement as a Model of Intuition -- 14.6. Quantum Modi.cation of Freud's Model of Consciousness -- 14.7. Conclusion -- Acknowledgements -- References -- Part 5: The Debate -- 15. Dreams versus Reality: Plenary Debate Session on Quantum Computing -- 16. Plenary Debate: Quantum E.ects in Biology: Trivial or Not? -- 17. Nontrivial Quantum Effects in Biology: A Skeptical Physicists' View Howard Wiseman and Jens Eisert -- 17.1. Introduction -- 17.2. A Quantum Life Principle -- 17.2.1. A quantum chemistry principle? -- 17.2.2. The anthropic principle -- 17.3. Quantum Computing in the Brain -- 17.3.1. Nature did everything first? -- 17.3.2. Decoherence as the make or break issue -- 17.3.3. Quantum error correction -- 17.3.4. Uselessness of quantum algorithms for organisms -- 17.4. Quantum Computing in Genetics -- 17.4.1. Quantum search -- 17.4.2. Teleological aspects and the fast-track to life -- 17.5. Quantum Consciousness -- 17.5.1. Computability and free will -- 17.5.2. Time scales -- 17.6. QuantumFreeWill . -- 17.6.1. Predictability and free will -- 17.6.2. Determinism and free will -- Acknowledgements -- References -- 18. That's Life!-The Geometry of π Electron Clouds Stuart Hamero. -- 18.1. What is Life? -- 18.2. Protoplasm: Water, Gels and Solid Non-polar Regions -- 18.3. Van der Waals Forces.
18.4. Kekule's Dream and π Electron Resonance -- 18.5. Proteins-The Engines of Life -- 18.6. Anesthesia and Consciousness -- 18.7. Cytoskeletal Geometry: Microtubules, Cilia and Flagella -- 18.8. Decoherence -- 18.9. Conclusion -- Acknowledgements -- References -- Appendix 1. Quantum Computing in DNA π Electron Stacks -- Appendix 2. Penrose-Hameroff OrchORModel -- Index.
Summary: This book presents the hotly debated question of whether quantum mechanics plays a non-trivial role in biology. In a timely way, it sets out a distinct quantum biology agenda. The burgeoning fields of nanotechnology, biotechnology, quantum technology, and quantum information processing are now strongly converging. The acronym BINS, for Bio-Info-Nano-Systems, has been coined to describe the synergetic interface of these several disciplines. The living cell is an information replicating and processing system that is replete with naturally-evolved nanomachines, which at some level require a quantum mechanical description. As quantum engineering and nanotechnology meet, increasing use will be made of biological structures, or hybrids of biological and fabricated systems, for producing novel devices for information storage and processing and other tasks. An understanding of these systems at a quantum mechanical level will be indispensable.
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Intro -- Contents -- Foreword -- Preface -- Acknowledgments -- Part 1: Emergence and Complexity -- 1. A Quantum Origin of Life? Paul C. W. Davies -- 1.1. Chemistry and Information -- 1.2. Q-life -- 1.3. The Problemof Decoherence -- 1.4. Life as the "Solution" of a Quantum Search Algorithm -- 1.5. Quantum Choreography -- Acknowledgements -- References -- 2. Quantum Mechanics and Emergence Seth Lloyd -- 2.1. Bits -- 2.2. Coin Flips -- 2.3. The Computational Universe -- 2.4. Generating Complexity -- 2.5. A Human Perspective -- 2.6. A QuantumPerspective -- References -- Part 2: Quantum Mechanisms in Biology -- 3. Quantum Coherence and the Search for the First Replicator Jim Al-Khalili and Johnjoe McFadden -- 3.1. When did Life Start? -- 3.2. Where did Life Start? -- 3.3. Where did the Precursors Come From? -- 3.4. What was the Nature of the First Self-replicator? -- 3.5. The RNAWorld Hypothesis -- 3.6. A Quantum Mechanical Origin of Life -- 3.6.1. The dynamic combinatorial library -- 3.6.2. The two-potential model -- 3.6.3. Decoherence -- 3.6.4. Replication as measurement -- 3.6.5. Avoiding decoherence -- 3.7. Summary -- References -- 4. Ultrafast Quantum Dynamics in Photosynthesis Alexandra Olaya Castro, Francesca Fassioli Olsen, Chiu Fan Lee, and Neil F. Johnson -- 4.1. Introduction -- 4.2. A Coherent Photosynthetic Unit (CPSU) -- 4.3. Toy Model: Interacting Qubits with a Spin-star Configuration -- 4.4. A More Detailed Model: Photosynthetic Unit of Purple Bacteria -- 4.5. Experimental Considerations -- 4.6. Outlook -- References -- 5. Modelling Quantum Decoherence in Biomolecules Jacques Bothma, Joel Gilmore, and Ross H. McKenzie -- 5.1. Introduction -- 5.2. Time and Energy Scales -- 5.3. Models for Quantum Baths and Decoherence -- 5.3.1. The spin-bosonmodel -- 5.3.1.1. Independent boson model -- 5.3.2. Caldeira-Leggett Hamiltonian.

5.3.3. The spectral density -- 5.4. The Spectral Density for the Different Continuum Models of the Environment -- 5.5. Obtaining the Spectral Density from Experimental Data -- 5.6. Analytical Solution for the Time Evolution of the Density Matrix -- 5.7. Nuclear Quantum Tunnelling in Enzymes and the Crossover Temperature -- 5.8. Summary -- References -- Part 3: The Biological Evidence -- 6. Molecular Evolution: A Role for Quantum Mechanics in the Dynamics of Molecular Machines that Read and Write DNA Anita Goel -- 6.1. Introduction -- 6.2. Background -- 6.3. Approach -- 6.3.1. The information processing power of a molecularmotor -- 6.3.2. Estimation of decoherence times of the motor-DNA complex -- 6.3.3. Implications and discussion -- References -- 7. Memory Depends on the Cytoskeleton, but is it Quantum? Andreas Mershin and Dimitri V. Nanopoulos -- 7.1. Introduction -- 7.2. Motivation behind Connecting Quantum Physics to the Brain -- 7.3. Three Scales of Testing for Quantum Phenomena in Consciousness -- 7.4. Testing the QCI at the 10 nm-10 µm Scale -- 7.5. Testing for Quantum Effects in Biological Matter Amplified from the 0.1 nm to the 10 nm Scale and Beyond -- 7.6. Summary and Conclusions -- 7.7. Outlook -- Acknowledgements -- References -- 8. Quantum Metabolism and Allometric Scaling Relations in Biology Lloyd Demetrius -- 8.1. Introduction -- 8.2. Quantum Metabolism: Historical Development -- 8.2.1. Quantization of radiation oscillators -- 8.2.2. Quantization of material oscillators -- 8.2.3. Quantization of molecular oscillators -- 8.2.4. Material versus molecular oscillators -- 8.3. Metabolic Energy and Cycle Time -- 8.3.1. The mean energy -- 8.3.2. The total metabolic energy -- 8.4. The Scaling Relations -- 8.4.1. Metabolic rate and cell size -- 8.4.2. Metabolic rate and body mass -- 8.5. Empirical Considerations -- 8.5.1. Scaling exponents.

8.5.2. The proportionality constant -- References -- 9. Spectroscopy of the Genetic Code Jim D. Bashford and Peter D. Jarvis -- 9.1. Background: Systematics of the Genetic Code -- 9.1.1. RNA translation -- 9.1.2. The nature of the code -- 9.1.3. Information processing and the code -- 9.2. Symmetries and Supersymmetries in the Genetic Code -- 9.2.1. sl(6/1) model: UA+S scheme -- 9.2.2. sl(6/1) model: 3CH scheme -- 9.2.3. Dynamical symmetry breaking and third base wobble -- 9.3. Visualizing the Genetic Code -- 9.4. Quantum Aspects of Codon Recognition -- 9.4.1. N(34) conformational symmetry -- 9.4.2. Dynamical symmetry breaking and third base wobble -- 9.5. Conclusions -- Acknowledgements -- References -- 10. Towards Understanding the Origin of Genetic Languages Apoorva D. Patel -- 10.1. The Meaning of It All -- 10.2. Lessons of Evolution -- 10.3. Genetic Languages -- 10.4. Understanding Proteins -- 10.5. Understanding DNA -- 10.6. What Preceded the Optimal Languages? -- 10.7. Quantum Role? -- 10.8. Outlook -- References -- Part 4: Artificial Quantum Life -- 11. Can Arbitrary Quantum Systems Undergo Self-replication? Arun K. Pati and Samuel L. Braunstein -- 11.1. Introduction -- 11.2. Formalizing the Self-replicating Machine -- 11.3. Proof of No-self-replication -- 11.4. Discussion -- 11.5. Conclusion -- Acknowledgments -- References -- 12. A Semi-quantum Version of the Game of Life Adrian P. Flitney and Derek Abbott -- 12.1. Background and Motivation -- 12.1.1. Classical cellular automata -- 12.1.2. Conway's game of life -- 12.1.3. Quantum cellular automata -- 12.2. Semi-quantumLife -- 12.2.1. The idea -- 12.2.2. A first model -- 12.2.3. A semi-quantum model -- 12.2.4. Discussion -- 12.3. Summary -- References -- 13. Evolutionary Stability in Quantum Games Azhar Iqbal and Taksu Cheon -- 13.1. Evolutionary Game Theory and Evolutionary Stability.

13.1.1. Population setting of evolutionary game theory -- 13.2. Quantum Games -- 13.3. Evolutionary Stability in Quantum Games -- 13.3.1. Evolutionary stability in EWL scheme -- 13.3.2. Evolutionary stability in MW quantization scheme -- 13.4. Concluding Remarks -- References -- 14. Quantum Transmemetic Intelligence Edward W. Piotrowski and Jan S ladkowski -- 14.1. Introduction -- 14.2. A QuantumModel of FreeWill -- 14.3. Quantum Acquisition of Knowledge -- 14.4. Thinking as a Quantum Algorithm -- 14.5. Counterfactual Measurement as a Model of Intuition -- 14.6. Quantum Modi.cation of Freud's Model of Consciousness -- 14.7. Conclusion -- Acknowledgements -- References -- Part 5: The Debate -- 15. Dreams versus Reality: Plenary Debate Session on Quantum Computing -- 16. Plenary Debate: Quantum E.ects in Biology: Trivial or Not? -- 17. Nontrivial Quantum Effects in Biology: A Skeptical Physicists' View Howard Wiseman and Jens Eisert -- 17.1. Introduction -- 17.2. A Quantum Life Principle -- 17.2.1. A quantum chemistry principle? -- 17.2.2. The anthropic principle -- 17.3. Quantum Computing in the Brain -- 17.3.1. Nature did everything first? -- 17.3.2. Decoherence as the make or break issue -- 17.3.3. Quantum error correction -- 17.3.4. Uselessness of quantum algorithms for organisms -- 17.4. Quantum Computing in Genetics -- 17.4.1. Quantum search -- 17.4.2. Teleological aspects and the fast-track to life -- 17.5. Quantum Consciousness -- 17.5.1. Computability and free will -- 17.5.2. Time scales -- 17.6. QuantumFreeWill . -- 17.6.1. Predictability and free will -- 17.6.2. Determinism and free will -- Acknowledgements -- References -- 18. That's Life!-The Geometry of π Electron Clouds Stuart Hamero. -- 18.1. What is Life? -- 18.2. Protoplasm: Water, Gels and Solid Non-polar Regions -- 18.3. Van der Waals Forces.

18.4. Kekule's Dream and π Electron Resonance -- 18.5. Proteins-The Engines of Life -- 18.6. Anesthesia and Consciousness -- 18.7. Cytoskeletal Geometry: Microtubules, Cilia and Flagella -- 18.8. Decoherence -- 18.9. Conclusion -- Acknowledgements -- References -- Appendix 1. Quantum Computing in DNA π Electron Stacks -- Appendix 2. Penrose-Hameroff OrchORModel -- Index.

This book presents the hotly debated question of whether quantum mechanics plays a non-trivial role in biology. In a timely way, it sets out a distinct quantum biology agenda. The burgeoning fields of nanotechnology, biotechnology, quantum technology, and quantum information processing are now strongly converging. The acronym BINS, for Bio-Info-Nano-Systems, has been coined to describe the synergetic interface of these several disciplines. The living cell is an information replicating and processing system that is replete with naturally-evolved nanomachines, which at some level require a quantum mechanical description. As quantum engineering and nanotechnology meet, increasing use will be made of biological structures, or hybrids of biological and fabricated systems, for producing novel devices for information storage and processing and other tasks. An understanding of these systems at a quantum mechanical level will be indispensable.

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