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Electronic structure and properties of materials for artificial photosynthesis
Full text linkThe oxygen evolution reaction during the photosynthesis process performed in plants,
algae and cyanobacteria is possibly one of the most important reactions on the planet
that sustain most life on our planet. Understanding the structure and function of the
"engine of life", the oxygen-evolving complex (OEC) in the active site of Photosystem
II (PSII), has been one of the great and persistent challenges of modern science. Over
the past decades, immense progress has been achieved in understanding the structure
and mechanism of photosynthetic reactions. This progress is in large part due to
the refinement of preparative protocols, X-Ray Diffractometry (XRD), site-directed
mutagenesis, Electron Paramagnetic Resonance (EPR) spectroscopy, the coming
of age of X-ray Free Electron Laser (XFEL) diffractometry and computational
approaches in the investigation of PS II. Nevertheless, key mechanistic and electronic
details of water oxidation still remain highly contentious. Elucidation of these
details is complicated by the fact that the active site of PSII exists in four natural
metastable oxidation states, as well as putative unnatural forms that are plausibly
induced during experimental investigation.
The leading motivation of the scientific community studying PSII is ultimately the
development of new catalysts and even bio-inspired solar cells, that will produce clean
and sustainable energy for the world. Over the last hundred years, approximately
80% of worldwide energy consumption has been based on fossil fuels, including coal,
oil, and natural gas. However, humankind now has to face the consequences arising
from this dependence on fossil fuels. Worldwide energy consumption is expected
to increase by over 50% by the mid-2000s (see Fig. 0.1). Because fossil fuels are
finite and regional around the world, it is greatly challenging to ensure that this
demand can be met, in the face of possible political tensions and other potential
problems with energy supplies. Due to the usage of fossil fuels, large quantities
of emissions, e.g., CO2, SO2, and oxide particles, are the predominant reasons for
global warming and severe pollution. Recent reports from the Intergovernmental
Panel on Climate Change emphasized the necessity of decreasing CO2 emissions
on a global scale to the zero level before the next century. These arguments make
the development of sustainable and carbon-neutral energy technologies one of the
most urgent challenges facing humankind all over the world. Wind, ocean currents,
tides, and waves are all potential sources of energy, but by far the most abundant
renewable energy source on the planet is solar energy: solar illumination on Earth
every hour is greater than the worldwide energy consumption for a whole year [35].
Therefore, the conversion and utilization of solar energy is a promising solution
for energy problems. An intriguing potential solution to the expected shortfall in
energy supplies is artificial photosynthesis [108], whereby light energy can be stored in chemical bonds and, hence, be made available as fuels [18, 200, 19, 364].
Synthetic molecular and heterogeneous manganese analogues still struggle to
mimic the function and performance of the OEC. This is partly because these
distinctive features are not intrinsic to the Mn4CaO5 core of the OEC but depend
on its environment and result from elaborate gating and regulation mechanisms
for coordinating the coupling of proton-electron transfer and the access, delivery,
binding, positioning, activation, and coupling of substrate waters to form dioxygen.
The high level of geometric and electronic control, both spatial and temporal, extends
along the whole catalytic cycle and involves simultaneously the Mn4CaO5 cluster, its
first coordination sphere, and the protein matrix that controls the flow of electrons,
protons, substrates, and products.
From the side of theoretical methods great progresses have been made in recent
years. Due to the success of the density functional theory (DFT), not only in
the field of solid state physics, but also on liquids and molecular compounds, it is
possible to obtain the electronic structure of few hundreds atoms with an acceptable
computational effort. Using the information provided by the experiments as starting
point, it is possible to employ DFT to refine the geometries in relationship with
the electron ground-state or different electronic states, to calculate the electron
and spin density for a given system and to estimate spectroscopic properties. The
coupling of DFT with molecular dynamics also allows us to perform ab-initio molecular dynamics of large systems at finite temperature to fully consider entropic
contributions and low-energy conformational changes. Computational techniques can
also provide considerable support in the analysis and interpretation of the complex
IR spectra of such biological systems. In this thesis, the molecular and electronic
structures of the multinuclear manganese containing bioinorganic system together
with oxygen-evolving complex of PS II are investigated using DFT-based methods
for the theoretical modeling of vibrational spectra in the gas phase by normal mode
analysis and molecular dynamics simulations.
Research on biological water oxidation traverses scientific fields and concentrates
the efforts of a multitude of experimental and theoretical approaches. Different
methods of investigation naturally lead to distinct views on the OEC. These are
often complementary but at times are contradictory, and it is not always obvious
whether the contradictions already exist in the data or arise from their suggested
interpretations. Nevertheless, the overarching goals are common to all experimental
and theoretical studies. These are not limited to the geometric and electronic
structure of the cluster in each state of the cycle but encompass the role of the
protein matrix, the channels, and secondary components of the second sphere of the
cluster, such as the chloride ions.
Chapter I of the thesis considers in detail the progress that have been done so
far in structural and spectroscopic studies of OEC and its synthetic mimics given
together with the general introduction on photosynthetic reactions occurring in the
leaf. Theoretical background of the computational methods used in present work is
given in detail in Chapter II.
In this thesis, we explored the potentialities and the reliability of different
state-of-the-art computational techniques for the investigation of the structural and
vibrational properties of complex macromolecular materials of biochemical importance.
The use of FTIR spectroscopy to probe the structure and function of the OEC
complex in PS II has a long history. The synthesis of a very close structural mimic of
the catalytic center has opened up the opportunity to perform a comprehensive and
parallel study of both the natural and artificial compounds and of their vibrational
modes. Chapter III is dedicated to the detailed assignment of the bands in the midand
low-frequencies region by static and dynamic vibrational spectra calculations of
the unique biomimetic complex. The detailed parallel analysis between the Natural
and Synthetic complexes also provided a comprehensive characterization of the
vibrational fingerprints in such class of cubane-like Mn-based compounds and is
reported in Chapter IV. In Chapter V of the thesis we discussed the electronic and
structural properties of the novel Mn4O4 synthetic compound mimicking the EPR
spectroscopic nature of OEC in S2 state
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Hemodynamic modification induced by left bundle branch block
No full textHemodynamic modification induced by left bundle branch bloc
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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