This book introduces basic principles of light-matter interaction, photophysics, and photosynthesis in a brief manner in order to elucidate principles of complex signaling networks that enable spatiotemporally directed macroscopic processes. We will start with random walk processes typically used to describe excitation energy transfer in plant lightharvesting complexes and later focus on coupled systems such as the communication network of reactive oxygen species (ROS) which are embedded into the plant metabolism and enable an information transfer from molecules to the overall organism as a bottom up process. In addition the microscale dynamics always accepts signals on the bottom level that can be understood as a top down communication. One example is the activation of genes by ROS caused by macroscopic events like strong sunlight or atmospheric variations that activate a change in composition of the microscopic environment by producing new proteins.

Typical bottom up processes are cascades that start with gene activation and protein translation regulating plant growth and morphology. Top down messengers triggered by macroscopic actuators like sunlight, gravity, environment or any forms of stress, on the other hand, activate gene regulation on the molecular level and therefore concern the dynamics of single molecules under the constraints of macroscopic factors. In this book the generation and monitoring as well as the role of ROS in photosynthetic organisms as typical messengers in complex networks are primarily treated in a scientific manner. All findings are supported by our own research results and recent publications. Additionally, the principles of top down and bottom up messaging are presented in the form of a philosophical discussion.

The first chapter focuses on a theoretical approach according to the Principle of Synergetics (Haken, 1990) to understand coupling, networks, and emergence of unpredictable phenomena. The approach is used to model light absorption, electron transfer and membrane dynamics in plants. Special focus will be placed on nonlinear processes that form the basic principle for the accumulation of energy reservoirs and on the formation of forces that are able to control the dynamics of macroscopic devices.

The formalism of rate equations is presented as a general scheme to formulate dynamical equations for arbitrarily complex systems. Key is the definition of “states” as an intensity level or a pattern that carries a certain amount of information, and their dynamics which are assessed by evaluating the probability of transfer from one state to another. In fact, rate equations are not only used to describe energy transfer processes in photosynthesis but in many systems, for instance, optical transitions, particle reactions, complex chemical reactions and more general information processing in complex networks. Rate equations are also used to describe complex systems such as sociological networks.

The second chapter describes the basic principles of the light reaction in photosynthesis from absorption to the storage of free Gibbs energy in the form of energy rich chemical compounds. The roles of different processes that support light energy transduction, on the one hand, and nonphotochemical quenching, on the other hand, are elucidated with special focus on the context of a highly adapted system that has developed as an advanced structure for energy conversion during evolution in its local environment.

In the third chapter the formation, decay, monitoring, and the functional role of ROS - mainly H2O2, Ю2, Oy are described and the fourth chapter especially focuses on the messenger role of ROS. The ambivalent picture of oxidative degradation and signal transduction during exposure of oxygen-evolving, photosynthetic organisms to oxidative stress isteluci- dated. Both degradation and activation are important mechanisms of ROS signaling. Reaction schemes are presented for the formation and monitoring of ROS and their participation in stress signal transduction pathways both within prokaryotic cyanobacteria as well as from chloroplasts to the nuclear genome in plants. It is suggested that redoxregulated systems, mitogen-activated protein kinase cascades and transcription factor networks play a key role in the ROS-dependent signaling systems in plant cells and for their spatiotemporal morphology and lifespan.

Chapter five focuses on evolution. It is emphasized that mainly the local environment of evolving organisms enforces directed evolution resulting in quick changes of the phenotype if the genetic diversity of the organisms is large enough. In that sense leaps in evolution necessarily follow volatile changes of the environment. It might be possible that ROS are the most important driving forces in evolution.

The last chapter finally offers a glance at how the described concepts can be used to describe other biological principles and multiscale hierarchical systems in society, politics and economics. The book is intended for a broad range of researchers and students, and everyone who is interested in learning about the most important global process on our planet - the process of photosynthesis. We would like to believe that this book will stimulate future researchers of photosynthesis and lead to progress in our understanding of the mechanisms of photosynthesis and their practical use in biotechnology and in human life.

We express our sincere gratitude to the two referees: the Academician of the Russian Academy ofSciences (RAS) Prof. V.A. Shuvalov and Prof. T. Tomo of Tokyo University of Science, Tokyo, Japan. We are extremely grateful to Corresponding Member of RAS Vl.V. Kuznetsov, Corresponding Member of RAS A.B. Rubin, and Professors D.A. Los, A.M. Nosov, V.Z. Paschenko, A.N. Tikhonov, G.V. Maksimov, V.V. Klimov, A.A. Tsygankov, and Drs. V.D. Kreslavski, S.K. Zharmukhamedov, I.R. Fomina, J. Karakeyan for their permanent help and fruitful advice. We are also indebted to Professors T. Friedrich, N. Budisa, P. Hildebrandt, L. Kroh, H.J. Eichler, Drs. M. Vitali, V. Tejwani, C. Junghans, N. Tavraz, J. Laufer, and J. Mark from TU Berlin and Drs. E.G. Maksimov and N. Belyaeva from Moscow State University, Prof. J. Pieper from University of Tartu, Prof. H. Paulsen from Johannes Gutenberg-Universitat Mainz, Prof. F. Zappa and Dr. D. Bronzi from Politecnico di Milano, and Prof. R. Rigler, Drs. J. Jarvet, and V. Vukojevic from the Karolinska Institute in Stockholm.

We express our deepest gratitude to Russian Science Foundation (№ 14-04-00039) and the German Research Foundation DFG (cluster of excellence “Unifying Concepts in Catalysis”) and the Federal Ministry of Education and Research for funding bilateral cooperation between Germany and Russia (RUS 10/026 and 11/014). We acknowledge COST for financial support in the framework of COST action MP1205. We thank F. Schmitt for preparing Figs. 4, 5, 7, 10, 11, 18, 27A, 50, 51, 71, 75, 79 and 80. Further gratitude belongs to M. Nabugodi and J.M. Zinn for proofreading of the manuscript. F.-J. Schmitt especially thanks Joachim Herz

Stiftung and Stifterverband fur die Deutsche Wissenschaft for the fellowship IGT-educationTUB.

We are grateful to Scrivener Publishing, Wiley and Izhevsk Institute of Computer Sciences for their cooperation in producing this book.

Franz-Josef Schmitt

Institute of Physical Chemistry, Max-Volmer-Laboratory for Biophysical Chemistry, Technische Universitat Berlin (e-mail: This email address is being protected from spam bots, you need Javascript enabled to view it )

Suleyman I. Allakhverdiev

Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, Russian Academy of Sciences, Moscow;

Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region; Department of Plant Physiology, Faculty of Biology,

M.V. Lomonosov Moscow State University; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University),

Moscow, Russia;

Bionanotechnology Laboratory, Institute of Molecular Biology and Biotechnology, Azerbaijan National Academy of Sciences,

Baku, Azerbaijan;

Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, Republic of Korea (e-mail: This email address is being protected from spam bots, you need Javascript enabled to view it )

Franz-Josef Schmitt is a research assistant at the Institute of Physical Chemistry, Technische Universitat Berlin (TU Berlin). He finished his doctoral thesis with “summa cum laude” in physics in 2011 in Prof. Hans-Joachim Eichler’s working group on Laser Physics under the supervision of Prof. Gernot Renger. The thesis is entitled “Picobiophotonics for the investigation of Pigment-Pigment and Pigment-Protein interactions in Photosynthetic Complexes”.

Dr. Schmitt holds a series of scientific awards including the Chorafas award for extraordinary scientific results (2009) and the Stifterverb and Fellowship for excellence in teaching (2014) awarded by Joachim Herz Stiftung for his teaching project IGT-education TUB. He was recently awarded twice with a young talents award (2013) and received best poster awards (2014) for his invited presentations at the conference on Photosynthesis research for Sustainability in Baku, Azerbaijan and Moscow, Russia, respectively. More than 80 research papers, two patents, one book chapter and 200 partially invited talks on international conferences summarize his research in Photosynthesis, Nanobiophotonics, Environmental Spectroscopy and didactics. Dr. Schmitt was group leader of the reform project “educationZEN” that developed new teaching formats for Mathematics education and internships in the Nature Sciences and Engineering. His research fields comprise protein dynamics and protein-cofactor interaction, energy transfer and conversion in organic systems, information processing in complex networks and general biophysics and biotechnology. Dr. Schmitt is coordinating editor of the topical issue on “Optofluidics and Biological Materials” of the open access journal “Optofluidics, Microfluidics and Nanofluidics” (de Gruyter open) and guest editor of the open access journal SOAJ NanoPhotoBioSciences. He was substitutional Management Committee member of COST action MP 1205 and member of the Faculty Council of the Department of Mathematics and Nature Sciences (2007-2017). He is a member of the Academic Senate (since 2010), and Chairman of the Extended Academic Senate of TU Berlin (since 2015).

Suleyman I. Allakhverdiev is the Head of the Controlled Photobiosynthesis Laboratory at the Institute of Plant Physiology of the Russian Academy of Sciences (RAS), Moscow; Chief Research Scientist at the Institute of Basic Biological Problems RAS, Pushchino, Moscow Region; Professor at M.V. Lomonosov Moscow State University, Moscow; Professor at Moscow Institute of Physics and Technology (State University), Moscow, Russia; Head of Bionanotechnology Laboratory at the Institute of Molecular Biology and Biotechnology of the Azerbaijan National Academy of Sciences, Baku, Azerbaijan, and Invited-Adjunct Professor at the Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, Republic of Korea. He is originally from Chaykend (Karagoyunly/Dilichanderesi), Armenia, and he obtained both his B.S. and M.S. in Physics from the Department of Physics, Azerbaijan State University, Baku. He obtained his Dr.Sci. degree (highest/top degree in science) in Plant Physiology and Photobiochemistry from the Institute of Plant Physiology, RAS (2002, Moscow), and Ph.D. in Physics and Mathematics (Biophysics), from the Institute of Biophysics, USSR (1984, Pushchino). His Ph.D. advisors were Academician Alexander A. Krasnovsky and Dr. Sci. Vyacheslav V. Klimov. He worked for many years (1990-2007) as visiting scientist at the National Institute for Basic Biology (with Prof. Norio Murata), Okazaki, Japan, and in the Department de Chimie-Biologie, Universite du Quebec at Trois Rivieres (with Prof. Robert Carpentier), Quebec, Canada (1988-1990). He has been a guest editor of more than thirty special issues in international peer-reviewed journals. At present, he is a member of the Editorial Board of more than fifteen international journals. Besides being editor-in-chief of SOAJ NanoPhotoBioSciences, associate editor of the International Journal of Hydrogen Energy, section editor of the BBA Bioenergetics, associate editor of the Photosynthesis Research, associate editor of the Functional Plant Biology, and associate editor of the Photosynthetica, he also acts as a referee for major international journals and grant proposals. He has authored (or co-authored) more than 400 research papers, six patents and eight books. He has organized more than ten international conferences on photosynthesis. His research interests include the structure and function of photosystem II, water-oxidizing complex, artificial photosynthesis, hydrogen photoproduction, catalytic conversion of solar energy, plants under environmental stress, and photoreceptor signaling.

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