1,720,966 research outputs found
Pseudoknots in a homopolymer
No full textAfter a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the pseudoknot number (N(pk)) at different temperature regimes in two and three dimensions. We find that, although the total number of pseudoknots is extensive at all temperatures, the number of those forming between the two halves of the chain diverges logarithmically at (both dimensions) and below (two dimensions only) the theta temperature. We later introduce a simple model that emphasizes the role of pseudoknot formation during collapse. The resulting phase diagram involves swollen, branched, and collapsed homopolymer phases with transitions between each pair
Supercoil formation in DNA denaturation
No full textWe generalize the Poland-Scheraga model to the case of a circular DNA,
taking into account the twisting of the two strains around each other.
Guided by recent single-molecule experiments on DNA strands, we assume
that the torsional stress induced by denaturation enforces the formation
of supercoils whose writhe absorbs the linking number expelled by the
loops. Our model predicts that when the entropy parameter of a loop
satisfies c <= 2, denaturation transition does not take place. On the
other hand, for c>2, a first-order denaturation transition is consistent
with our model and may take place in the actual system, as in the case
with no supercoils. These results are in contrast with other treatments
of circular DNA melting where denaturation is assumed to be accompanied
by an increase in twist rather than writhe on the bound segments
New results on the melting thermodynamics of a circular DNA chain
No full textWe investigate the impact of supercoil period and nonzero supercoil
formation energy on the thermal denaturation of a circular DNA. Our
analysis is based on a recently proposed generalization of the Poland
Scheraga model that allows the DNA melting to be studied for plasmids
with circular topology, where denaturation is accompanied by formation
of supercoils. We find that the previously obtained first-order melting
transition persists under the generalization discussed. The dependence
of the size of the order-parameter jump at the transition point and the
associated melting temperature are obtained analytically
Percolation transition in a dynamically clustered network
No full textWe consider a percolationlike phenomenon on a generalization of the Barabasi-Albert model, where a modification of the growth dynamics directly allows formation of disconnected clusters. The transition is located with high precision by an original numerical technique based on the comparison of the largest and second largest clusters. A careful investigation focusing on finite size scaling allows us to highlight properties which would hardly be accessible by an analytical solution of cluster growth equations in the stationary limit. Our analysis shows that some critical features of the percolation transition are different from those observed in the case of dilution in fully grown networks. At variance with other models of percolation on growing networks we also find evidence that the order parameter approaches zero as a power of the field p-p(c) driving the transition, rather than as a stretched exponential.This behavior does not agree with the Berezinskii-Kosterlitz-Thouless scenario found in other similar models. For describing the phase in which a giant cluster develops, a key role is played by the crossover number of nodes N-x similar to(p-p(c))(-zeta) with zeta similar or equal to 4. This power law behavior and that of other quantities are conjectured on the basis of scaling arguments and numerical evidence
Percolation transition in a dynamically clustered network
No full textWe consider a percolationlike phenomenon on a generalization of the Barabási-Albert model, where a modification of the growth dynamics directly allows formation of disconnected clusters. The transition is located with high precision by an original numerical technique based on the comparison of the largest and second largest clusters. A careful investigation focusing on finite size scaling allows us to highlight properties which would hardly be accessible by an analytical solution of cluster growth equations in the stationary limit. Our analysis shows that some critical features of the percolation transition are different from those observed in the case of dilution in fully grown networks. At variance with other models of percolation on growing networks we also find evidence that the order parameter approaches zero as a power of the field p- pc driving the transition, rather than as a stretched exponential. This behavior does not agree with the Berezinskii-Kosterlitz- Thouless scenario found in other similar models. For describing the phase in which a giant cluster develops, a key role is played by the crossover number of nodes Nx ∼ (p- pc) -ζ with ζ 4. This power law behavior and that of other quantities are conjectured on the basis of scaling arguments and numerical evidence. © 2007 The American Physical Society
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
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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