In situ mapping of the energy flow through the entire photosynthetic apparatus

Absorption of sunlight is the first step in photosynthesis, which provides energy for the vast majority of organisms on Earth. The primary processes of photosynthesis have been studied extensively in isolated light-harvesting complexes and reaction centres, however, to understand fully the way in which organisms capture light it is crucial to also reveal the functional relationships between the individual complexes. Here we report the use of two-dimensional electronic spectroscopy to track directly the excitation-energy flow through the entire photosynthetic system of green sulfur bacteria. We unravel the functional organization of individual complexes in the photosynthetic unit and show that, whereas energy is transferred within subunits on a timescale of subpicoseconds to a few picoseconds, across the complexes the energy flows at a timescale of tens of picoseconds. Thus, we demonstrate that the bottleneck of energy transfer is between the constituents

Monkey C Language Support in VS Code

V této bakalářské práci se budu zabývat vývojem rozšíření pro Visual Studio Code, jenž bude poskytovat podporu pro jazyk Monkey C. V teoretické části dojde k představení prostředí Visual Studio Code a nahlédnutí do problematiky vývoje rozšíření v tomto prostředí. Dále bude představen také jazyk Monkey C. V praktické části práce bude popsán nástroj ANTLR, který je schopen generovat vlastní překladač jazyka pomocí bezkontextové gramatiky, parsováním kódu a jeho syntaktickou analýzou. Dále bude v praktické části rozebrán návrh a implementace rozšíření, společně s popisem jednotlivých jeho částí. Závěrem bude výsledné rozšíření testováno a výsledky zhodnoceny.In this bachelor thesis I will deal with the development of extension for Visual Sstudio Code, which will provide full support for Monkey C language. In thoretical part will be introduced Visual Studio Code environment and insight into the development of extensions in this environment.The practical part of the thesis will describe the ANTLR tool, which is able to generate its own language compiler using context-free grammar, code parsing and its syntactic analysis. Furthermore, the practical part will discuss the design and implementation of the extension, along with a description of its individual parts. Finally, the resulting extension will be tested and the results evaluated.460 - Katedra informatikyvelmi dobř

Transfer of Vibrational Coherence Through Incoherent Energy Transfer Process in F\"{o}rster Limi

We study transfer of coherent nuclear oscillations between an excitation energy donor and an acceptor in a simple dimeric electronic system coupled to an unstructured thermodynamic bath and some pronounced vibrational intramolecular mode. Our focus is on the non-linear optical response of such a system, i.e. we study both excited state energy transfer and the compensation of the so-called ground state bleach signal. The response function formalism enables us to investigate a heterodimer with monomers coupled strongly to the bath and by a weak resonance coupling to each other (F\"{o}rster rate limit). Our work is motivated by recent observation of various vibrational signatures in 2D coherent spectra of energy transferring systems including large structures with a fast energy diffusion. We find that the vibrational coherence can be transferred from donor to acceptor molecules provided the transfer rate is sufficiently fast. The ground state bleach signal of the acceptor molecules does not show any oscillatory signatures, and oscillations in ground state bleaching signal of the donor prevail with the amplitude which is not decreasing with the relaxation rate.Comment: 11 pages, 9 figure

Unraveling the nature of coherent beatings in chlorosomes.

Coherent two-dimensional (2D) spectroscopy at 80 K was used to study chlorosomes isolated from green sulfur bacterium Chlorobaculum tepidum. Two distinct processes in the evolution of the 2D spectrum are observed. The first being exciton diffusion, seen in the change of the spectral shape occurring on a 100-fs timescale, and the second being vibrational coherences, realized through coherent beatings with frequencies of 91 and 145 cm(-1) that are dephased during the first 1.2 ps. The distribution of the oscillation amplitude in the 2D spectra is independent of the evolution of the 2D spectral shape. This implies that the diffusion energy transfer process does not transfer coherences within the chlorosome. Remarkably, the oscillatory pattern observed in the negative regions of the 2D spectrum (dominated by the excited state absorption) is a mirror image of the oscillations found in the positive part (originating from the stimulated emission and ground state bleach). This observation is surprising since it is expected that coherences in the electronic ground and excited states are generated with the same probability and the latter dephase faster in the presence of fast diffusion. Moreover, the relative amplitude of coherent beatings is rather high compared to non-oscillatory signal despite the reported low values of the Huang-Rhys factors. The origin of these effects is discussed in terms of the vibronic and Herzberg-Teller couplings

Two-Dimensional Electronic Spectroscopy Reveals Ultrafast Energy Diffusion in Chlorosomes.

Chlorosomes are light-harvesting antennae that enable exceptionally efficient light energy capture and excitation transfer. They are found in certain photosynthetic bacteria, some of which live in extremely low-light environments. In this work, chlorosomes from the green sulfur bacterium Chlorobaculum tepidum were studied by coherent electronic two-dimensional (2D) spectroscopy. Previously uncharacterized ultrafast energy transfer dynamics were followed, appearing as evolution of the 2D spectral line-shape during the first 200 fs after excitation. Observed initial energy flow through the chlorosome is well explained by effective exciton diffusion on a sub-100 fs time scale, which assures efficiency and robustness of the process. The ultrafast incoherent diffusion-like behavior of the excitons points to a disordered energy landscape in the chlorosome, which leads to a rapid loss of excitonic coherences between its structural subunits. This disorder prevents observation of excitonic coherences in the experimental data and implies that the chlorosome as a whole does not function as a coherent light-harvester

Superradiance of bacteriochlorophyll c aggregates in chlorosomes of green photosynthetic bacteria

Chlorosomes are the main light-harvesting complexes of green photosynthetic bacteria that are adapted to a phototrophic life at low-light conditions. They contain a large number of bacteriochlorophyll c, d, or e molecules organized in self-assembling aggregates. Tight packing of the pigments results in strong excitonic interactions between the monomers, which leads to a redshift of the absorption spectra and excitation delocalization. Due to the large amount of disorder present in chlorosomes, the extent of delocalization is limited and further decreases in time after excitation. In this work we address the question whether the excitonic interactions between the bacteriochlorophyll c molecules are strong enough to maintain some extent of delocalization even after exciton relaxation. That would manifest itself by collective spontaneous emission, so-called superradiance. We show that despite a very low fluorescence quantum yield and short excited state lifetime, both caused by the aggregation, chlorosomes indeed exhibit superradiance. The emission occurs from states delocalized over at least two molecules. In other words, the dipole strength of the emissive states is larger than for a bacteriochlorophyll c monomer. This represents an important functional mechanism increasing the probability of excitation energy transfer that is vital at low-light conditions. Similar behaviour was observed also in one type of artificial aggregates, and this may be beneficial for their potential use in artificial photosynthesis.</p

Efficiency of excitation energy trapping in the green photosynthetic bacterium Chlorobaculum tepidum

During the millions of years of evolution, photosynthetic organisms have adapted to almost all terrestrial and aquatic habitats, although some environments are obviously more suitable for photosynthesis than others. Photosynthetic organisms living in low-light conditions require on the one hand a large light-harvesting apparatus to absorb as many photons as possible. On the other hand, the excitation trapping time scales with the size of the light-harvesting system, and the longer the distance over which the formed excitations have to be transferred, the larger the probability to lose excitations. Therefore a compromise between photon capture efficiency and excitation trapping efficiency needs to be found. Here we report results on the whole cells of the green sulfur bacterium Chlorobaculum tepidum. Its efficiency of excitation energy transfer and charge separation enables the organism to live in environments with very low illumination. Using fluorescence measurements with picosecond resolution, we estimate that despite a rather large size and complex composition of its light-harvesting apparatus, the quantum efficiency of its photochemistry is around ~87% at 20 °C, ~83% at 45 °C, and about ~81% at 77 K when part of the excitation energy is trapped by low-energy bacteriochlorophyll a molecules. The data are evaluated using target analysis, which provides further insight into the functional organization of the low-light adapted photosynthetic apparatus.</p

The structural and functional role of carotenoids in chlorosomes

Chlorosomes are large light-harvesting complexes found in three phyla of anoxygenic photosynthetic bacteria. Chlorosomes are primarily composed of self-assembling pigment aggregates. In addition to the main pigment, bacteriochlorophyll c, d, or e, chlorosomes also contain variable amounts of carotenoids. Here, we use X-ray scattering and electron cryomicroscopy, complemented with absorption spectroscopy and pigment analysis, to compare the morphologies, structures, and pigment compositions of chlorosomes from Chloroflexus aurantiacus grown under two different light conditions and Chlorobaculum tepidum. High-purity chlorosomes from C. aurantiacus contain about 20% more carotenoid per bacteriochlorophyll c molecule when grown under low light than when grown under high light. This accentuates the light-harvesting function of carotenoids, in addition to their photoprotective role. The low-light chlorosomes are thicker due to the overall greater content of pigments and contain domains of lamellar aggregates. Experiments where carotenoids were selectively extracted from intact chlorosomes using hexane proved that they are located in the interlamellar space, as observed previously for species belonging to the phylum Chlorobi. A fraction of the carotenoids are localized in the baseplate, where they are bound differently and cannot be removed by hexane. In C. tepidum, carotenoids cannot be extracted by hexane even from the chlorosome interior. The chemical structure of the pigments in C. tepidum may lead to π-π interactions between carotenoids and bacteriochlorophylls, preventing carotenoid extraction. The results provide information about the nature of interactions between bacteriochlorophylls and carotenoids in the protein-free environment of the chlorosome interior.This study was supported by grants from the Academy of Finland (1213467 and 1129684 Centre of Excellence in Virus Research 2006-2011 to S.J.B. and R.T.; 1118462 to R.T), Biocentrum Helsinki (S.J.B.), and the Czech Science Foundation (project P501/12/G055 to J.P.). C. aurantiacus cell growth and sample preparation was carried out by A.M.C. as part of the Photosynthetic Antenna Research Center (PARC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under award number DE-SC 0001035.Peer reviewe