1,721,042 research outputs found
Ordered and stochastic behavior in a two-dimensional Lennard-Jones system
No full textWe study by computer simulation the behavior at low energy of a two-dimensional Lennard-Jones system. The dynamics of the system are analyzed by computing the mean value of the energies of the normal modes, their autocorrelation and cross-correlation functions, and their Fourier spectra. When the energy is lowered the system undergoes a stochastic transition, made evident by qualitative changes occurring in the dynamics. The autocorrelation functions exhibit a twofold behavior: a rapid exponential-like decay which dominates at high energy and a slow decay which dominates at low energy. The Fourier spectrum appears to be continuous at high energy and becomes discrete at low energy. At the lowest energy considered by us, normal modes no longer exhibit a trend toward energy equipartition, at least within the times of our simulation; this fact is due to the onset of selection rules for the energy exchanges among modes. These phenomena occur in a physically significant energy range. For the sake of comparison we have performed a similar analysis on the Hénon-Heiles model, obtaining a relevant concordance
Molecular dynamics simulation of intrinsically disordered proteins
No full textIntrinsically disordered proteins are biomolecules that do not have a definite 3D structure; therefore, their dynamical simulation cannot start from a known list of atomistic positions, such as a Protein Data Bank file. We describe a method to start a computer simulation of these proteins. The first step of the procedure is the creation of a multi-rod configuration of the molecule, derived from its primary sequence. This structure is dynamically evolved in vacuo until its gyration radius reaches the experimental average value; at this point solvent molecules, in explicit or implicit implementation, are added to the protein and a regular molecular dynamics simulation follows. We have applied this procedure to the simulation of tau, one of the largest totally disordered proteins
Transient tertiary structures in tau, an intrinsically disordered protein
No full textAn intrinsically disordered protein (IDP) does not have a definite 3D structure, and because of its highly flexible nature it evolves dynamically in very large and diverse regions of the phase space. A standard molecular dynamics run can sample only a limited region of the latter; even though this kind of simulation may be effective in sampling local temporary secondary structures, it is not sufficient to highlight properties that require a larger sampling of the phase space to be detected, like transient tertiary structures. But if the structure of an IDP is dynamically evolved using metadynamics (an algorithm that keeps track of the regions of the phase space already sampled), the system can be forced to wander in a much larger region of the phase space. We have applied this procedure to the simulation of tau, one of the largest totally disordered proteins. Combining the results of the simulation with small-angle X-ray scattering yields a significant improvement in the sampling of the phase space in comparison with standard molecular dynamics, and provides evidence of extended hairpin- and paperclip-like transient tertiary structures of the molecule. The more persistent tertiary pattern is a hairpin folding encompassing part of the N-terminal, the proline-rich domain, the former repeat and a functionally relevant part of the second repeat
Transient secondary structures in tau, an intrinsically disordered protein
No full textThe tau protein belongs to the category of Intrinsically Disordered Proteins (IDPs), which in their native state do not have an average stable structure and fluctuate between many conformations. In its physiological state, tau helps nucleating and stabilizing the microtubules in the axons of the neurons. On the other hand, the same tau is involved in the development of the Alzheimer disease, when it aggregates in paired helical filaments (PHFs) forming fibrils, which form insoluble tangles. The beginning of the pathological aggregation of tau has been attributed to a local transition of protein portions from random coil to a beta-sheet. These structures would very likely be transient; therefore, we performed a Molecular Dynamics simulation of tau to gather information on the existence of segments of tau endowed with a secondary structure. We combined the results of our simulation with small-angle X-ray scattering experimental data to extract from the dynamics a set of most probable conformations of tau. The analysis of these conformations highlights the presence of transient secondary structures like turns, beta-bridges, beta-sheets, and alpha-helices. It also shows that a large segment of the N-terminal region is found near the repeats domain, in a globular-like shape
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
Stochastic transition in two-dimensional Lennard-Jones systems
No full textWe study by computer simulation the behavior at low energy of two-dimensional Lennard-Jones systems, with square or triangular cells and a number of degrees of freedom N up to 128. These systems exhibit a transition from ordered to stochastic motions, passing through a region of intermediate behavior. We thus find two stochasticity borders, which separate in the phase space the ordered, intermediate, and stochastic regions. The corresponding energy thresholds have been determined as functions of the frequency ω of the initially excited normal modes; they generally increase with ω and appear to be independent of N. Their values agree with those found by other authors for one-dimensional LJ systems. We computed also the maximal Lyapunov characteristic exponent χ* of our systems, which is a typical measure of stochasticity; this analysis shows that even in the ordered region certain stochastic features may persist. At higher energies, χ* increases linearly with the energy per degree of freedom e. The law χ*(e) has been determined in the thermodynamic limit by extrapolation. The values found for the stochasticity thresholds fall in a physically significant energy range. The behavior of the thresholds as a function of ω and N is compatible with the hypothesis on the existence of a classical zero-point energy, advanced by Cercignani, Galgani, and Scotti
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
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
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