1,720,958 research outputs found
Linear Catenanes in Channel Confinement
Full text linkWe use Langevin dynamics simulations to investigate the behavior of linear catenanes under channel confinement. We consider model poly[n]catenanes of n = 100 rings, each of m = 40 beads, and present a comprehensive analysis of their statics and dynamics in cylindrical channels of various diameters. To highlight the impact of mechanical bonding, we compare the catenane behavior to an equivalent chain of beads under the same conditions. We show that linear catenanes exhibit various confinement regimes, including a de Gennes one for intermediate channel widths and an overstretching response for strong confinement, which is unique to catenanes. The catenane's relaxation dynamics also diverge from conventional polymers at strong confinement, presenting much slower modes. Through systematic analysis of the size, shape, and orientation of the concatenated rings and their mechanical bonds, we shed light on the underlying mechanisms driving the catenane's static and dynamic responses to confinement
Effect of Ring Rigidity on the Statics and Dynamics of Linear Catenanes
Full text linkWe used molecular dynamics simulations to investigate the statics and dynamics of poly[n]catenanes for different bending rigidities of the constituent rings. We show that stiffer rings yield catenanes with more extended and, at the same time, more flexible backbones. The softening of the backbone reflects the decreasing steric interactions of catenated rings as their shape becomes more oblate due to increased rigidity. The internal dynamics of catenanes is affected too. Going from flexible to rigid rings causes a several-fold slowing of different processes, from segmental rotations and size fluctuations to Rouse modes. Finally, by considering the statics and dynamics of crowded solutions of catenanes, we isolate another emergent property controlled by the rigidity of the rings. Specifically, we show that catenanes with rigid rings hinder each other's motion more than those with flexible rings. Thus, in equally crowded solutions, the diffusion coefficient is smaller for catenanes with stiffer rings
Work fluctuations of self-propelled particles in the phase separated state
Full text linkWe study the large deviations of the distributionP(W-tau) of the work associated with the propulsion of individual active Brownian particles in a time interval tau, in the region of the phase diagram where macroscopic phase separation takes place.P(W-tau) is characterised by two peaks, associated to particles in the gaseous and in the clusterised phases, and two separate non-convex branches. Accordingly, the generating function ofW(tau)'s cumulants displays a double singularity. We discuss the origin of such non-convex branches in terms of the peculiar dynamics of the system phases, and the relation between the observation time tau and the typical persistence times of the particles in the two phases
Work fluctuations of self-propelled particles in the phase separated state
Full text linkWe study the large deviations of the distribution P(W τ ) of the work associated with the propulsion of individual active Brownian particles in a time interval τ, in the region of the phase diagram where macroscopic phase separation takes place. P(W τ ) is characterised by two peaks, associated to particles in the gaseous and in the clusterised phases, and two separate non-convex branches. Accordingly, the generating function of W τ 's cumulants displays a double singularity. We discuss the origin of such non-convex branches in terms of the peculiar dynamics of the system phases, and the relation between the observation time τ and the typical persistence times of the particles in the two phases
RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration
Full text linkWe use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide-long xrRNA from the Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on time scales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, for both activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings provide a useful reference to interpret and design future theoretical and experimental studies of RNA translocation
RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration
Full text linkWe use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide-long xrRNA from the Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on time scales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, for both activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings provide a useful reference to interpret and design future theoretical and experimental studies of RNA translocation
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
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