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

Visualization Graphs and Results of Technical Analysis for Cryptocurrency Markets

Tato diplomová práce se zabývá vizualizací grafů pro technickou analýzu obchodování s kryptoměnami na vybraných burzách, především Binance. Cílem je vytvořit nástroj, který umožní názorně a v intuitivní formě interpretovat výsledky analýz, usnadnit rozhodování o nákupu či prodeji kryptoměn a minimalizovat ztráty způsobené vysokou volatilitou kurzů. Teoretická část práce zahrnuje krátký úvod do světa kryptoměn a popis vybraných kryptoměnových burz. Dále se pak v teoretické části objevuje analýza dostupných nástrojů pro vizualizaci historických obchodů a technické analýzy, a popis obchodovacích botů používaných na Binance. Praktická část práce je zaměřena na implementaci webové aplikace, napojené na platformu TradingView, a vytvoření vizualizační komponenty pro technickou analýzu. V neposlední řadě je součástí také testování výsledného řešení.This thesis deals with the visualization of charts for technical analysis of cryptocurrency trading on selected exchanges, mainly Binance. The aim is to create a tool that allows to visually and intuitively interpret the results of the analysis, to facilitate the decision to buy or sell cryptocurrencies and to minimize losses caused by high volatility of the exchange rates. The theoretical part of the thesis includes a short introduction to the world of cryptocurrencies and a description of selected cryptocurrency exchanges. Then, the theoretical part includes an analysis of available tools for visualizing historical trades and technical analysis, and a description of trading bots used on Binance. The practical part of the thesis focuses on the implementation of a web application, connected to the TradingView platform, and the creation of a visualization component for technical analysis. Last but not least, testing of the resulting solution is also included.460 - Katedra informatikyvýborn

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