Franz-Josef Schmitt, PhD, is a researcher and group leader at Technische Universität Berlin (TU Berlin). Dr. Schmitt holds a series of scientific awards and has authored more than 80 research papers, two patents, one book chapter and 200 presentations that draw upon his research in photosynthesis, nanobiophotonics, environmental spectroscopy and didactics. He is a Coordinating Editor for the journal, Optofluidics, Microfluidics and Nanofluidics, Guest Editor for the journal, NanoPhotoBioSciences, and he is has been heavily involved in academic affairs at TU Berlin in multiple departments and committees.Suleyman I. Allakhverdiev, PhD, is the Head of the Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, in the Russian Academy of Sciences (RAS), Moscow. He is also the Chief Research Scientist at the Institute of Basic Biological Problems within RAS, a professor at Moscow State University, a professor at the Moscow Institute of Physics and Technology (State University), Head of Bionanotechnology Laboratory at the Institute of Molecular Biology and Biotechnologies, Azerbaijan National Academy of Sciences, and an Invited-Adjunct Professor in the Department of New Biology at the Daegu Gyeongbuk Institute of Science& Technology (DGIST), Daegu, Republic of Korea. He is Associate Editor of the International Journal of Hydrogen Energy, Associate Editor of the journal, Photosynthesis Research, Section Editor of BBA Bioenergetics, Associate Editor of Functional Plant Biology, Associate Editor of Photosynthetica, and a member of the editorial boards of 15 other international journals. He has been the Guest Editor of more than 30 special issues in peer-reviewed journals, and he has authored or co-authored over 400 papers in various scholarly journals. He has also written eight books and holds six patents. He has been working as a visiting professor in over 30 countries and has presented oral presentations at more than 80 international and national conferences. He has also organized ten international conferences on photosynthesis. and about 40 technical presentations.

• Abstract ixForeward 1 xiForeward 2 xiiiPreface xv1 Multiscale Hierarchical Processes 11.1 Coupled Systems, Hierarchy and Emergence 21.2 Principles of Synergetics 121.3 Axiomatic Motivation of Rate Equations 151.4 Rate Equations in Photosynthesis 191.5 Top down and Bottom up Signaling 232 Photophysics, Photobiology and Photosynthesis 272.1 Light Induced State Dynamics 272.2 Rate Equations and Excited State Dynamics in Coupled Systems 412.3 Light-Harvesting, Energy and Charge Transfer and Primary Processes of Photosynthesis 642.4 Antenna Complexes in Photosynthetic Systems 702.5 Fluorescence Emission as a Tool for Monitoring PS II Function 912.6 Excitation Energy Transfer and Electron Transfer Steps in Cyanobacteria Modeled with Rate Equations 932.7 Excitation Energy and Electron Transfer in Higher Plants Modeled with Rate Equations 1052.8 Nonphotochemical Quenching in Plants and Cyanobacteria 1142.9 Hierarchical Architecture of Plants 1183 Formation and Functional Role of Reactive Oxygen Species (ROS) 1233.1 Generation, Decay and Deleterious Action of ROS 1253.2 Monitoring of ROS 1373.3 Signaling Role of ROS 1514 ROS Signaling in Coupled Nonlinear Systems 1574.1 Signaling by Superoxide and Hydrogen Peroxide in Cyanobacteria 1584.2 Signaling by Singlet Oxygen and Hydrogen Peroxide in Eukaryotic Cells and Plants 1634.3 ROS and Cell Redox Control and Interaction with the Nuclear Gene Expression 1674.4 ROS as Top down and Bottom up Messengers 1744.5 Second Messengers and Signaling Molecules in H2O2 Signaling Chains and (Nonlinear) Networking 1914.6 ROS-Waves and Prey-Predator Models 1924.7 Open Questions on ROS Coupling in Nonlinear Systems 1965 Th e Role of ROS in Evolution 1995.1 Th e Big Bang of the Ecosphere 2005.2 Complicated Patterns Result from Simple Rules but Only the Useful Patterns are Stable 2015.3 Genetic Diversity and Selection Pressure as Driving Forces for Evolution 2056 Outlook: Control and Feedback in Hierarchical Systems in Society, Politics and Economics 209Bibliography 213Appendix 249Index 259

Franz-Josef Schmitt, PhD, is a researcher and group leader at Technische Universität Berlin (TU Berlin). Dr. Schmitt holds a series of scientific awards and has authored more than 80 research papers, two patents, one book chapter and 200 presentations that draw upon his research in photosynthesis, nanobiophotonics, environmental spectroscopy and didactics. He is a Coordinating Editor for the journal, Optofluidics, Microfluidics and Nanofluidics, Guest Editor for the journal, NanoPhotoBioSciences, and he is has been heavily involved in academic affairs at TU Berlin in multiple departments and committees.Suleyman I. Allakhverdiev, PhD, is the Head of the Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, in the Russian Academy of Sciences (RAS), Moscow. He is also the Chief Research Scientist at the Institute of Basic Biological Problems within RAS, a professor at Moscow State University, a professor at the Moscow Institute of Physics and Technology (State University), Head of Bionanotechnology Laboratory at the Institute of Molecular Biology and Biotechnologies, Azerbaijan National Academy of Sciences, and an Invited-Adjunct Professor in the Department of New Biology at the Daegu Gyeongbuk Institute of Science& Technology (DGIST), Daegu, Republic of Korea. He is Associate Editor of the International Journal of Hydrogen Energy, Associate Editor of the journal, Photosynthesis Research, Section Editor of BBA Bioenergetics, Associate Editor of Functional Plant Biology, Associate Editor of Photosynthetica, and a member of the editorial boards of 15 other international journals. He has been the Guest Editor of more than 30 special issues in peer-reviewed journals, and he has authored or co-authored over 400 papers in various scholarly journals. He has also written eight books and holds six patents. He has been working as a visiting professor in over 30 countries and has presented oral presentations at more than 80 international and national conferences. He has also organized ten international conferences on photosynthesis. and about 40 technical presentations.

• Abstract ixForeward 1 xiForeward 2 xiiiPreface xv1 Multiscale Hierarchical Processes 11.1 Coupled Systems, Hierarchy and Emergence 21.2 Principles of Synergetics 121.3 Axiomatic Motivation of Rate Equations 151.4 Rate Equations in Photosynthesis 191.5 Top down and Bottom up Signaling 232 Photophysics, Photobiology and Photosynthesis 272.1 Light Induced State Dynamics 272.2 Rate Equations and Excited State Dynamics in Coupled Systems 412.3 Light-Harvesting, Energy and Charge Transfer and Primary Processes of Photosynthesis 642.4 Antenna Complexes in Photosynthetic Systems 702.5 Fluorescence Emission as a Tool for Monitoring PS II Function 912.6 Excitation Energy Transfer and Electron Transfer Steps in Cyanobacteria Modeled with Rate Equations 932.7 Excitation Energy and Electron Transfer in Higher Plants Modeled with Rate Equations 1052.8 Nonphotochemical Quenching in Plants and Cyanobacteria 1142.9 Hierarchical Architecture of Plants 1183 Formation and Functional Role of Reactive Oxygen Species (ROS) 1233.1 Generation, Decay and Deleterious Action of ROS 1253.2 Monitoring of ROS 1373.3 Signaling Role of ROS 1514 ROS Signaling in Coupled Nonlinear Systems 1574.1 Signaling by Superoxide and Hydrogen Peroxide in Cyanobacteria 1584.2 Signaling by Singlet Oxygen and Hydrogen Peroxide in Eukaryotic Cells and Plants 1634.3 ROS and Cell Redox Control and Interaction with the Nuclear Gene Expression 1674.4 ROS as Top down and Bottom up Messengers 1744.5 Second Messengers and Signaling Molecules in H2O2 Signaling Chains and (Nonlinear) Networking 1914.6 ROS-Waves and Prey-Predator Models 1924.7 Open Questions on ROS Coupling in Nonlinear Systems 1965 Th e Role of ROS in Evolution 1995.1 Th e Big Bang of the Ecosphere 2005.2 Complicated Patterns Result from Simple Rules but Only the Useful Patterns are Stable 2015.3 Genetic Diversity and Selection Pressure as Driving Forces for Evolution 2056 Outlook: Control and Feedback in Hierarchical Systems in Society, Politics and Economics 209Bibliography 213Appendix 249Index 259

Franz-Josef Schmitt, PhD, is a researcher and group leader at Technische Universität Berlin (TU Berlin). Dr. Schmitt holds a series of scientific awards and has authored more than 80 research papers, two patents, one book chapter and 200 presentations that draw upon his research in photosynthesis, nanobiophotonics, environmental spectroscopy and didactics. He is a Coordinating Editor for the journal, Optofluidics, Microfluidics and Nanofluidics, Guest Editor for the journal, NanoPhotoBioSciences, and he is has been heavily involved in academic affairs at TU Berlin in multiple departments and committees.Suleyman I. Allakhverdiev, PhD, is the Head of the Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, in the Russian Academy of Sciences (RAS), Moscow. He is also the Chief Research Scientist at the Institute of Basic Biological Problems within RAS, a professor at Moscow State University, a professor at the Moscow Institute of Physics and Technology (State University), Head of Bionanotechnology Laboratory at the Institute of Molecular Biology and Biotechnologies, Azerbaijan National Academy of Sciences, and an Invited-Adjunct Professor in the Department of New Biology at the Daegu Gyeongbuk Institute of Science& Technology (DGIST), Daegu, Republic of Korea. He is Associate Editor of the International Journal of Hydrogen Energy, Associate Editor of the journal, Photosynthesis Research, Section Editor of BBA Bioenergetics, Associate Editor of Functional Plant Biology, Associate Editor of Photosynthetica, and a member of the editorial boards of 15 other international journals. He has been the Guest Editor of more than 30 special issues in peer-reviewed journals, and he has authored or co-authored over 400 papers in various scholarly journals. He has also written eight books and holds six patents. He has been working as a visiting professor in over 30 countries and has presented oral presentations at more than 80 international and national conferences. He has also organized ten international conferences on photosynthesis. and about 40 technical presentations.

• Abstract ixForeward 1 xiForeward 2 xiiiPreface xv1 Multiscale Hierarchical Processes 11.1 Coupled Systems, Hierarchy and Emergence 21.2 Principles of Synergetics 121.3 Axiomatic Motivation of Rate Equations 151.4 Rate Equations in Photosynthesis 191.5 Top down and Bottom up Signaling 232 Photophysics, Photobiology and Photosynthesis 272.1 Light Induced State Dynamics 272.2 Rate Equations and Excited State Dynamics in Coupled Systems 412.3 Light-Harvesting, Energy and Charge Transfer and Primary Processes of Photosynthesis 642.4 Antenna Complexes in Photosynthetic Systems 702.5 Fluorescence Emission as a Tool for Monitoring PS II Function 912.6 Excitation Energy Transfer and Electron Transfer Steps in Cyanobacteria Modeled with Rate Equations 932.7 Excitation Energy and Electron Transfer in Higher Plants Modeled with Rate Equations 1052.8 Nonphotochemical Quenching in Plants and Cyanobacteria 1142.9 Hierarchical Architecture of Plants 1183 Formation and Functional Role of Reactive Oxygen Species (ROS) 1233.1 Generation, Decay and Deleterious Action of ROS 1253.2 Monitoring of ROS 1373.3 Signaling Role of ROS 1514 ROS Signaling in Coupled Nonlinear Systems 1574.1 Signaling by Superoxide and Hydrogen Peroxide in Cyanobacteria 1584.2 Signaling by Singlet Oxygen and Hydrogen Peroxide in Eukaryotic Cells and Plants 1634.3 ROS and Cell Redox Control and Interaction with the Nuclear Gene Expression 1674.4 ROS as Top down and Bottom up Messengers 1744.5 Second Messengers and Signaling Molecules in H2O2 Signaling Chains and (Nonlinear) Networking 1914.6 ROS-Waves and Prey-Predator Models 1924.7 Open Questions on ROS Coupling in Nonlinear Systems 1965 Th e Role of ROS in Evolution 1995.1 Th e Big Bang of the Ecosphere 2005.2 Complicated Patterns Result from Simple Rules but Only the Useful Patterns are Stable 2015.3 Genetic Diversity and Selection Pressure as Driving Forces for Evolution 2056 Outlook: Control and Feedback in Hierarchical Systems in Society, Politics and Economics 209Bibliography 213Appendix 249Index 259