1,721,147 research outputs found
Computational characterization of dimerization and ligand binding in biological systems
Full text linkThe self-association of proteins to form dimers or higher-order oligomers is a very common phenomenon in biology. Protein dimerization or oligomerization acts as a control tool for the execution of functions in many biological systems. Three systems were studied by computational methods in this thesis. Cyclic diguanylic acid (CDG) is a ubiquitous messenger involved in bacterial signaling networks. CDG can form an intercalated dimer and bind at the inhibition site of PleD. MD simulations were carried out for the CDG dimer as well as the analogue of CDG (endo-S-CDG) in solution and binding to the PleD protein. It was demonstrated, that dimeric CDG is only marginally stabilized even in high concentration. The results help the fundamental understanding of c-di-GMP and preventing biofilm formation. Insulin is a small protein that plays an eminent role in controlling glucose uptake in cells. Insulin can associate as a dimer which leads to diabetes. The key role of the B24 residue for insulin dimerization was identified. Our work provided an insight for designing analogues of human insulin and thus a therapy for diabetes
Atomistic simulations of transition metal catalyzed reactions using specialized force fields and quantum mechanical methods
Full text linkIn this thesis, we utilized current computational methods for exploring molecular architectures and dynamical properties of metal-catalyzed reactions. The importance of transition metals (TM) in catalysis was our motivation to work on the development of new empirical force fields and their applications.
TM specialized force fields provide the possibility to characterize complex geometries and relate them to their reactivity. Therefore, we parametrized the VALBOND TRANS force field by refining non-bonded parameters for a large test set of octahedral iridium(III) compounds. The optimized force field allowed a successful ranking of lowest-energy diastereomers and the performance of subsequent molecular dynamic (MD) simulations. Inspired by the natural process of the photosynthesis, Ir-catalysts are also relevant for the light-induced artifical oxidation of water leading to the synthesis of dioxygen. Using parameterized force fields, we studied the role of half-sandwich iridium complexes in different proposed reaction mechanisms. The applied force fields could help to understand catalytic cycles and to establish a basis to guide experimental screenings of new effective catalysts. TM complexes are also key components in harvesting solar energy which encouraged us to investigate the function of relevant compounds such as ruthenium-tris-(2,2'-bipyridine). Its electronic excitation led to a non-equilibrium system in which excess energy was redistributed to the surrounding solvent. The determined energy transfer to the solvent and the vibrational signatures of the surrounding water supplied an explanation for experimental findings
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
Atomistic simulations of reactive processes from gas to condensed phase
Full text linkIn this thesis, we use advance computational methods to explore molecular reaction dynamics
in gas and condensed phase. The molecular reactions that we describe in here have been
studied for the last 25 years, using computational methods, from stratospheric chemistry
to biochemistry.
We will first describe the vibrationally induced dissociation of H2SO4 to H2O and SO3 in
stratospheric conditions, which is one of the important reactive steps in the Earth's
atmosphere. Although this reaction has great significance in atmospheric chemistry, the
exact mechanism whereby the reaction happens is still unknown. It has been postulated that
the photodissociation of H2SO4 to form sulfur trioxide and water, can explain the anomalous
enhancement of the polar stratospheric sulfate aerosol layer in the springtime. This
photodissociation process was previously assumed to take place via absorption ultraviolet
(UV) radiation, to produce a dissociative electronically excited state. However, the
electronic absorption spectrum of H2SO4 up to 140 nm could not be found experimentally.
Alternative mechanisms, including vibrationally induced dissociation, were proposed. Using
adiabatic reactive molecular dynamics (ARMD) simulations with validated force fields for
the product and reactant channels, it is shown through explicit atomistic simulation that
by exciting the v9 OH-stretching mode, photodissociation can occur on the picosecond time
scale. With the potential energy surfaces used in the present work, v9 = 4 is sufficient
for this process. Because ARMD simulations allow multiple and long-time simulations, both
nonstatistical, impulsive H-transfer and statistical, intramolecular vibration energy
redistribution (IVR) regimes of the decomposition were found.
Another exciting reaction that we studied, this time in the condense phase, is the
[3,3]-sigmatropic rearrangement of allyl vinyl ethers. This is an important reaction due to
its special synthetic relevance, which allows the preparation of gamma, delta-unsaturated
carbonyl compounds. The intramolecular cyclic character (six-membered ring) of the
rearrangement is generally accepted. However, an understanding of the precise nature and
geometry of the transition state and the exact mechanism is still controversial. It is
generally accepted, evidenced by ab initio calculations using implicit solvent, that the
reaction proceed through chair-like intermediates. In this investigation, using high level
ab initio calculations, and ab initio Molecular Dynamics, we found that the reaction
proceeds via boat-like transition state. This finding allows to initiate new studies about
the real characterization of the transition state and hence its reaction mechanism.
Finally, we will describe the initial mechanism whereby the activation of the diguanylate
cyclase the PleD protein in Caulobacter crescentus is taking place. PleD is widely studied
since it participate in the formation of the ubiquitous second messenger, cyclic-di-GMP,
involved in bacterial biofilm formation and persistence.
PleD protein has an import role during the cell cycle of "C. cresentus". The active form of
diguanylate cyclase PleD localizes to the stalked pole of differentiating C. crescentus
cells. Pled is responsible for turning off flagellum rotations and inhibiting motility
before genome replication begins and also for regenerating motility after differentiation
has completed. Here we describe the coupling between the Phe102 and Thr83, in the active
form of the protein. This coupling is highly influenced by phosphorylation, and the
mechanisms seem to be key to form active dimers
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
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
- …
