| Preface |
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iii | |
| Introduction |
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xi | |
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xi | |
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Biological and thermodynamic evolution |
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xii | |
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Bioenergetics as a challenge to physics |
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xiv | |
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Catalytic efficiency increases together with entropy production |
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xv | |
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Brain bioenergetics has no competition in its intensity |
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xvii | |
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Life accelerates the thermodynamic evolution |
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xvii | |
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Bioenergetics, ecology and global climate changes |
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xviii | |
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The overview of presented topics |
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xix | |
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Definitions and explanations from Introduction |
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xix | |
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xxi | |
| 1 Mitchell's Chemiosmotic Theory: The Background |
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1 | (11) |
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1.1 The background and early developments |
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1 | (2) |
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1.2 Living cells are equally brilliant chemists and physicists |
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3 | (1) |
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1.3 The chemiosmotic hypothesis |
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3 | (1) |
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1.4 The impact after the Nobel Prize award to Peter Mitchell |
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4 | (1) |
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1.5 Glynn Research Institute: An eccentric experiment |
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5 | (1) |
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1.6 Chemiosmotic hypothesis maturation into the chemiosmotic theory |
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5 | (2) |
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1.7 Mitchell's last publication in 1991 |
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7 | (1) |
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Definitions and explanations |
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8 | (1) |
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9 | (3) |
| 2 Membrane Bioenergetics in a Nutshell |
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12 | (4) |
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2.1 The importance of membranes and membrane proteins |
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12 | (1) |
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2.2 Membrane proton pumps |
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13 | (1) |
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2.3 Energy transducing membranes |
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13 | (1) |
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2.4 Primary and secondary proton pumps |
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14 | (1) |
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2.5 A bridge to the universe must not be blocked |
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14 | (1) |
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Definitions and explanations |
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15 | (1) |
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15 | (1) |
| 3 Irreversible Thermodynamics and Coupled Biochemical Reactions |
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16 | (11) |
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3.1 Entropy concepts and Onsager-Prigogine's description of driving and driven force-flux couple |
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16 | (5) |
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3.2 Far from equilibrium static head state analogy, slip coefficients and an effective degree of coupling |
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21 | (2) |
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3.3 Is power production equivalent to partial entropy production responsible for the emergence of the output work and force? |
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23 | (1) |
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Definitions and explanations |
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24 | (1) |
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25 | (2) |
| 4 What is Life? |
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27 | (5) |
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4.1 A physicist in love with life |
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27 | (2) |
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4.2 Schrodinger's passion for understanding the secrets of life initiated molecular biology |
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29 | (2) |
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Definitions and explanations |
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31 | (1) |
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31 | (1) |
| 5 Some Answers to Schrodinger's Questions |
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32 | (17) |
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5.1 The stability paradox |
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32 | (2) |
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5.2 Photons as "food" for life |
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34 | (1) |
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5.3 Prigogine and Ziman dispute about minimum or maximum entropy production |
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34 | (1) |
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5.4 Andriesse and Juretie dispute about minimal entropy production in photosynthesis |
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35 | (2) |
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5.5 Jennings' dispute with Lavergne, Kox, and Parson about negative entropy production in photosynthesis |
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37 | (1) |
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5.6 Prigogine's theorem is not the physical principle, but it is mixed up with his concept of dissipative structures |
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38 | (2) |
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5.7 Prigogine's authority promoted skepticism toward the study of increased entropy production response after external forcing |
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40 | (1) |
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5.8 Where we stand with defining life? |
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41 | (1) |
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5.9 Dissipative adaptation concept |
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41 | (1) |
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5.10 Self-emergence models |
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42 | (1) |
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5.11 Life as self-organized dynamical order |
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43 | (2) |
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Definitions and explanations |
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45 | (1) |
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45 | (4) |
| 6 Protonmotive Force |
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49 | (3) |
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51 | (1) |
| 7 Membrane Proteins |
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52 | (47) |
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7.1 Introduction to membrane proteins |
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52 | (2) |
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7.2 Classification of membrane proteins |
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54 | (1) |
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7.3 The reentrant topology of monotopic membrane protein |
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55 | (1) |
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7.4 Helix-break-helix structure of membrane-associated antimicrobial peptides |
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56 | (1) |
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7.5 Membrane-associated amphipathic helices |
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57 | (1) |
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7.6 Pore loop domains from ion channels |
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57 | (1) |
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7.7 Monotopic lipid-anchored protein caveolin |
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58 | (9) |
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7.7.1 How dynamic beauty of eukaryotic plasma membrane decorations emerged during evolution? |
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58 | (1) |
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7.7.2 Mechanoprotection by flattening the caveolae |
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59 | (1) |
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7.7.3 Caveolin: 1 multitasking roles are implicated in about 300 biological processes |
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60 | (1) |
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7.7.4 Surprisingly sparse knowledge and abundance of wrong predictions about the caveolin-1 structure |
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61 | (2) |
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7.7.5 Caveol in signatures |
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63 | (1) |
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7.7.6 The minimal scaffolding domain named surrogate peptide |
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63 | (1) |
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7.7.7 The importance of posttranslational modifications |
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64 | (1) |
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7.7.8 Disease-causing mutations in COV1 gene reveal molecular details about caveolin-1 structure-function connection |
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65 | (1) |
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7.7.9 Gain-of-function mutations in caveolin-3 can cause various skeletal muscle diseases and congenital heart syndrome |
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66 | (1) |
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7.8 Syndecans: Bitopic membrane proteins |
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67 | (6) |
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7.8.1 Communication mediated by exosomes and syndecans |
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67 | (1) |
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7.8.2 Simple bioinformatic tools can locate islands of order in syndecan sequences |
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68 | (1) |
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7.8.3 Syndecans are both hubs and molecular switches in the protein-interaction network responsible for normal development or cancer progression |
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68 | (1) |
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7.8.4 Structure-function connection for syndecan interactome |
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69 | (1) |
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7.8.5 The application of syndecan-4 in neovascularization |
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70 | (1) |
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7.8.6 Syndecans role in brain maturation and neurogenesis |
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71 | (1) |
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7.8.7 Are syndecans involved in establishing protein gradients during organogenesis? |
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72 | (1) |
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7.8.8 Homodimeric and heterodimeric interactions among syndecans |
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72 | (1) |
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73 | (4) |
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7.9.1 Presenilin and amyloid cascade hypothesis |
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73 | (1) |
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7.9.2 Transmembrane topology and 3D structure |
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74 | (1) |
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7.9.3 Mutations associated with Alzheimer's disefise |
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75 | (1) |
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7.9.4 Elusive operation of the hatchet enzyme |
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75 | (2) |
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77 | (4) |
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7.10.1 The remarkable sensitivity of rhodopsin's quantum detector function |
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77 | (1) |
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7.10.2 Rhodopsin's structure |
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78 | (2) |
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7.10.3 Why phototransduction cascade is tightly coupled to high entropy production? |
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80 | (1) |
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7.11 Cytochrome c oxidase |
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81 | (7) |
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7.11.1 Oxygen-mediated water synthesis coupled to proton pumping |
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81 | (1) |
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7.11.2 Cytochrome c oxidase structure |
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82 | (1) |
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7.11.3 The illogical manner in which nature puts together the cytochrome c oxidase polypeptides |
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83 | (1) |
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7.11.4 The proton pumping cycle requires the participation of metal atoms |
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84 | (1) |
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7.11.5 Is the active site "breathing" in the cytochrome c oxidase? |
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85 | (1) |
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7.11.6 How enzyme controls the strength and direction of the colossal electric field in critical proton-gating situations? |
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86 | (1) |
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7.11.7 The thermodynamic efficiency of cytochrome c oxidase |
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87 | (1) |
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Definitions and explanations |
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88 | (2) |
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90 | (9) |
| 8 The Maximum Entropy Production: Applications in the Bioenergetics of Bacterial Photosynthesis |
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99 | (19) |
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8.1 Brief personal introduction |
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99 | (2) |
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8.2 Entropy production calculations for the simplified models of photosynthesis |
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101 | (3) |
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8.3 The Maximal Transitional Entropy Production (MTEP) theorem and its applications |
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104 | (1) |
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8.4 The backpressure effect, optimal and maximal thermodynamic efficiency |
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105 | (2) |
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8.5 Benefits of increased dissipation for the thermodynamics of photosynthesis |
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107 | (2) |
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8.6 Biotechnological applications |
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109 | (1) |
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8.7 Feedback from research papers citing our 2003 contribution to the thermodynamics of photosynthesis |
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110 | (3) |
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Definitions and explanations |
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113 | (1) |
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113 | (5) |
| 9 Coupling Thermodynamics with Biological Evolution through Bioenergetics |
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118 | (17) |
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9.1 Fundamental principles |
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118 | (3) |
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9.2 Efficiency of biological processes |
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121 | (1) |
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9.3 Power transfer in the nonlinear domain |
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122 | (3) |
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9.4 Evolution-coupling hypothesis |
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125 | (3) |
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9.5 Self-ordering and self-organization as a natural system response to increased dissipation |
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128 | (2) |
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9.6 Game of life as a side reaction |
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130 | (1) |
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Definitions and explanations |
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130 | (1) |
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131 | (4) |
| 10 Perfect Enzymes, According to Biochemists |
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135 | (11) |
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10.1 Enhancing the reaction rates |
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135 | (1) |
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10.2 Coupling enzyme kinetics to dissipation |
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136 | (1) |
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10.3 The MTEP theorem tool for the identification of rate-limiting transitions |
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137 | (2) |
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10.4 Entropy production and evolutionary distances |
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139 | (2) |
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10.5 Iterative entropy production maximizations for both proton transfer steps |
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141 | (1) |
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10.6 Life had enough time to explore how order can develop by increasing disorder |
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142 | (2) |
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Definitions and explanations |
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144 | (1) |
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144 | (2) |
| 11 ATP Synthase Molecular Motor |
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146 | (20) |
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11.1 What is unique about ATP synthase and ATP turnover? |
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146 | (1) |
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11.2 Being praised for errors |
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147 | (1) |
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11.3 Questions about ATP synthase mechanism of action shaped the bioenergetics |
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148 | (1) |
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11.4 The Martian scientists |
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149 | (1) |
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11.5 The learning curve includes recovering from errors end adding educated insight |
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150 | (1) |
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11.6 The caloric catastrophe question and Nobel Prizes |
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151 | (1) |
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11.7 First breakthrough in solving the mechanism of proton-driven ATP synthesis |
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151 | (1) |
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11.8 Rotary catalysis: The second breakthrough concept by Paul Boyer |
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152 | (1) |
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11.9 Direct experimental evidence for rotary catalysis by other research groups |
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153 | (1) |
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11.10 Optimization of the transitions' state parameters |
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153 | (3) |
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11.11 MTEP theorem application and rate-determining catalytic steps |
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156 | (1) |
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11.12 Tangled impact after the publication of thermodynamic optimization for ATP synthase |
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157 | (4) |
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11.13 Our conjecture and concluding thoughts |
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161 | (1) |
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Definitions and explanations |
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162 | (1) |
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162 | (4) |
| 12 Bacteriorhodopsin: Light-harvesting Movie Star |
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166 | (15) |
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12.1 Bacteriorhodopsin light cycle and its optimization |
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166 | (5) |
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12.2 How perfect is photon free-energy conversion by bacteriorhodopsin? |
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171 | (3) |
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12.3 Spin-off projects including bacteriorhodopsin and other bR-like proteins |
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174 | (4) |
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Definitions and explanations |
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178 | (1) |
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178 | (3) |
| 13 The Protonmotive Force in Geochemistry and the Origin Question: Is the Origin of Bioenergetics Connected with the Origin of Life? |
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181 | (10) |
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13.1 Is bioenergetics more ancient than genetic code? |
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181 | (3) |
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13.2 Closing the gap between geochemistry and biochemistry |
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184 | (2) |
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13.3 The "dissipation-first" hypothesis for the origin of life |
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186 | (1) |
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Definitions and explanations |
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187 | (1) |
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188 | (3) |
| 14 Integrating Glycolysis with Oxidative Phosphorylation by Hexokinases |
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191 | (10) |
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14.1 Hexokinases are ancient housekeeping enzymes |
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191 | (2) |
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14.2 Conformational changes associated with water ejection and entropy production |
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193 | (1) |
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14.3 Is hexokinase-2 the gatekeeper for life and death? |
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194 | (3) |
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Definitions and explanations |
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197 | (1) |
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198 | (3) |
| 15 Bioenergetics of the Brain, Aging, and Cancer Cells as Bridged by a-synuclein |
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201 | (18) |
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15.1 Hallmarks of aging and cancer |
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201 | (2) |
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15.2 Alpha-synuclein connection to neurodegenerative diseases |
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203 | (1) |
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15.3 Low concentration of regulation signal ions and molecules |
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204 | (1) |
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15.4 Alpha-synuclein oligomers can dissipate the mitochondria) membrane potential |
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205 | (1) |
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15.5 Structure-function dissection of a-synuclein domains |
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205 | (3) |
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15.6 Misfolding, mobility, promiscuous interactions, and prion diseases |
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208 | (1) |
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15.7 Abnormal protein-protein interactions can lead to a bioenergetic collapse |
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209 | (2) |
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15.8 The paradoxical nature of brain cell bioenergetics |
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211 | (1) |
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15.9 Regulatory hotspots control the entropy production rate |
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212 | (1) |
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Definitions and explanations |
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213 | (1) |
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213 | (6) |
| 16 Retrospections, Contrasting Viewpoints, Incentives, Challenges, Prospects, and Conclusions |
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219 | (36) |
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16.1 Life is the evolution and multiplication of dissipation-steering systems |
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219 | (1) |
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16.2 Love and hate for irreversible entropy increase |
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220 | (1) |
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16.3 The predictive power of causal entropic principle |
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221 | (1) |
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16.4 Earth's-specific geosphere-biosphere connection does not exist anywhere else in the universe |
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222 | (1) |
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16.5 The "birth canal" of biology |
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222 | (1) |
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16.6 Dissecting entropy production is not an exercise in futility |
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223 | (1) |
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16.7 Is the output power maximized? |
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224 | (3) |
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16.8 Is the entropy generation minimized? |
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227 | (2) |
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16.9 Fine regulation of brain's bioenergetics and heat production |
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229 | (1) |
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16.10 The lower limit for bioenergetics of dormant cells |
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230 | (1) |
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16.11 The upper limit for the bioenergetics' entropy production |
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231 | (1) |
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16.12 Allocating dissipation |
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231 | (1) |
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16.13 Quantum thermodynamics on the horizon? |
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232 | (1) |
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16.14 Bioenergetics of photosynthesis and respiration from the entropy production viewpoint |
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233 | (1) |
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16.15 What should be maximized, partial, or total entropy production to get an insight into the self-organized establishment of order? |
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234 | (5) |
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16.16 The turbulence and active matter challenge |
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239 | (2) |
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16.17 What is the appropriate statistical entropy definition for complex systems? |
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241 | (3) |
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16.18 The relevance of the least action principle in bioenergetics |
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244 | (1) |
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16.19 How bioenergetics bridges life to the universe? |
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244 | (2) |
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Definitions and explanations |
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246 | (1) |
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247 | (8) |
| Index |
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255 | |
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