The light-harvesting complexes in photosynthesis

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Photosynthesis is a complex biological process whereby plants, algae and other photosynthetic organisms use solar photons to produce organic compounds. The process is divided into two types: oxygenic photosynthesis in which water is required and oxygen is released, and anoxy- genic photosynthesis where water is not required and no oxygen is produced. Green plants,algae and cyanobacteria perform oxygenic photosynthesis and the overall process can be de-scribed by the following chemical equation where the terms on the left side of the equation represent the two reactants carbon dioxide (CO2)and water (H2O). The water on the reactants side is used as an electron donor for redox reactionsinvolved in the primary light energy stabilization. In the presence of light energy, the products of this reaction are glucose (C6H12O6), water (H2O) and oxygen (O2). This resultant oxygen originates from water and not from the carbon dioxide (CO2). Photosynthesis has been di-vided into two phases: the light dependent reactions, occurring in the thylakoid membrane; and light independent reactions such as the Calvin cycle that occurs in the chloroplast stroma [1].The light dependent reactions for the oxygenic photosynthesis are carried out by four differ-ent multi-protein complexes known as photosystem I (PSI), photosystem II (PSII), cytochrome b6f (Cyt b6f), and the adenosine triphosphate (ATP) synthase enzyme. In plants and green al-gae, all of these protein complexes are situated in the thylakoid membrane (the membrane that surrounds the thylakoid). The thylakoids in turn are found as stacked or elongated unstacked membranous sacks in an organelle called the chloroplast [2]. The shape of the chloroplast is similar to the shape of a convex lens and has a diameter of a few micrometers, with about ten chloroplasts inside each cell of the photosynthetic organisms [1,3].

The light-harvesting complexes in photosynthesis

The light absorption process is the first step in photosynthesis. This process is performed by the light-harvesting pigment-protein complexes of photosynthetic organisms, also known as the antenna complexes. These complexes contain a number of pigment molecules, mainly chlorophyll and carotenoid, which are described in sections 1.2.1 and 1.2.2, respectively. These pigments are responsible for absorbing light, and funnelling the excitation energy with high efficiency to the pigments (special chlorophylls (P680)) in the RC of PSI and PSII [6, 7], on a timescale of a few hundreds of picoseconds (10 12s) [8]. In the reaction center the absorbed excitation energy induces a charge-separation, which is then stabilized for few milliseconds in order to allow electron migration to Fd and FNR enzymes for the reduction of NADP to NADPH. Antenna pigments’ type, organization, arrangement and concentration vary between different photosynthetic organisms and different types of LHCs of the same organism. In this study, the focus is on light-harvesting complex II (LHCII) in PSII of higher plants [6, 9–13], and the fucoxanthin-chlorophyll protein (FCPb), one of the two main LHCs of diatoms [14,15].These complexes are described in sections 1.2.3 and 1.2.4, respectively.

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Fucoxanthin-chlorophyll protein, the major light-harvesting com-

Diatoms are unicellular marine organisms capable of oxygenic photosynthesis, and form a major group of algae that are characterised by their decorative silica shell [33]. They are the major players in the biochemical cycle of silicon, carbon, nitrogen, and phosphorus which have a significant effect on the global climate in ocean and fresh water environments [34]. Diatoms existin two main groups known as pennate and centric diatoms. The pennate diatoms are needle-like in shape and have two plastids (chloroplasts) per cell, whereas the centric diatoms have a rotational symmetry and they contain more than two plastids per cell [33]. The membrane-intrinsic light-harvesting protein complexes of diatoms fall in the same family as LHCII of higher plants and green algae. However, there are differences in the membrane topology and pigment com positions [33, 35]. To date, the protein structure of the fucoxanthin-chlorophyll protein (FCP) complex is not available.

Exciton concept

The exciton concept is a quantum model that is used to describe the excitation energy dynamics
(relaxation) of strongly coupled molecules such as the pigments of photosynthetic systems. The idea is that when a sample containing strongly coupled molecules is excited, the excited state dynamics cannot be explained by the excitation of a single molecule, because the excitation energy is spread among several molecules (delocalized). In this case, the excitation energy relaxation is assumed to be a coherent process due to the strong interaction between molecules of the system.

1 Introduction
1.1 Photosynthesis
1.2 The light-harvesting complexes in photosynthesis
1.3 Excitation energy transfer
1.4 Exciton concept
1.5 Excitation annihilation in photosynthetic systems
1.6 Non-photochemical quenching
1.7 Aim of this work
1.8 Thesis outline
2 Techniques and Methods
2.1 Ultrashort laser pulse generation and manipulation
2.2 Ultrafast laser spectroscopy and control
2.3 Transient absorption spectroscopy
2.4 Ultrafast laser control techniques
3 Experimental setup
3.1 Transient absorption spectroscopy setup
3.2 Experimental setup for coherent control
3.3 Characterisation of the 4F setup
3.4 Experimental setup of the FROG
3.5 Genetic Algorithm
3.6 Visualization of the GA individuals in a joint time-frequency basis
3.7 Pump-probe setups of LaserLaB Amsterdam
3.8 Appendix: Supplementary information
4 Laser coherent control of excitation energy flow in the LHCII complex
4.1 Abstract
4.2 Introduction
4.3 Materials and spectroscopic methods
4.4 Results
4.5 Discussion
4.6 Conclusion
4.7 Future recommendations
5 Energy dissipation mechanisms in the FCPb light-harvesting complex of the di-atom Cyclotella meneghiniana
5.1 Introduction
5.2 Materials and methods
5.3 Results
5.4 Discussion
5.5 Conclusions
5.6 Appendix: Supplementary information
6 Summary

Spectroscopy and control of ultrafast energy dynamics in natural light–harvesting complexes

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