1,720,956 research outputs found
Early prediction of spinodal-like relaxation events in supercooled liquid water
No full textSeveral computational studies on different water models reported evidence of a phase transition in supercooled conditions between two liquid states of water differing in density: the high-density liquid (HDL) and the low-density liquid (LDL). Yet, conclusive experimental evidence of the existence of a phase transition between the two liquid water phases could not be obtained due to fast crystallization in the region where the phase transition should occur. For the same reason, the investigation of possible transition mechanisms between the two phases is committed to computational investigations. In this work, we simulate an out-of-equilibrium temperature-induced transition from the LDL to the HDL-like state in the TIP4P/2005 water model. To structurally characterize the system relaxation, we use the node total communicability (NTC) we recently proposed as an effective order parameter to discriminate the two liquid phases differing in density. We find that the relaxation process is compatible with a spinodal-like scenario. We observe the formation of HDL-like domains in the LDL phase and we characterize their fluctuating behavior and subsequent coarsening and stabilization. Furthermore, we find that the formation of stable HDL-like domains is favored in the regions where the early formation of small patches of highly connected HDL-like molecules (i.e., with very high NTC values) is observed. Besides characterizing the LDL- to HDL-like relaxation from a structural point of view, these results also show that the NTC order parameter can serve as an early-time predictor of the regions from which the transition process initiates
Protein Secondary Structure Patterns in Short‐Range Cross‐Link Atlas
Full text linkCross-linking mass spectrometry (XL-MS) has become a powerful tool in structural biology for investigating protein structure, dynamics, and interactomics. However, short-range cross-links, defined as those connecting residues fewer than 20 positions apart, have traditionally been considered less informative and largely overlooked, leaving significant data unexplored in a systematic manner. Here, we present a system-wide analysis of short-range cross-links, demonstrating their intrinsic correlation with protein secondary structure. We introduce the X-SPAN (Cross-link Structural Pattern Analyzer) software, which integrates publicly available XL-MS datasets from system-wide experiments with AlphaFold-predicted protein structures. Our analysis reveals distinct cross-linking patterns that reflect the spatial constraints imposed by secondary structural elements. Specifically, α-helices exhibit periodic cross-linking patterns consistent with their characteristic helical pitch, whereas coils and β-strands display nearly monotonic distributions. A context-dependent protein grammar reinforces short-range cross-link specificity. Short-range cross-links can enhance the statistical inference of secondary structures within integrative modeling workflows. Additionally, our work establishes a framework for benchmarking AlphaFold's local prediction accuracy and provides novel quality control criteria for XL-MS experiments. We anticipate that X-SPAN and our short-range cross-link database will serve as a valuable resource for exploring local secondary structure rearrangements and their potential roles in protein function and allosteric regulation
Enhanced connectivity and mobility in liquid water : implications for the high density liquid structure and its onset
Full text linkIn this work, we investigate simulated liquid water at ambient pressure in both stable and metastable supercooled conditions by means of a new order parameter we recently proposed, namely the node total communicability (NTC), based on graph theory concepts. We show that this order parameter is able to identify the two liquid states differing in density, the LDL- and HDL-like states, in simulation conditions at which both states coexist. We also show that NTC is able to capture both the structural and dynamic differences between the two states, being correlated with both the local density and the mobility of water molecules within the network. In addition, we further investigate the high connectivity patches we previously identified as characteristic of the HDL-like states. We show that these extended patches are composed of molecules with an increased local density and mobility, packed in a highly connected network. The formation of these highly connected networks is characterized by a fast dynamics, with mobile molecules entering and exiting the patches. Interestingly, we observe small highly connected patches also at low temperatures, where the prevailing states is LDL-like. We show that the small-to-large patches transition is related to the Widom line crossing and we suggest that the small highly connected patches at low temperatures might function as initial sites for the formation of extended HDL-like regions characteristic of the highest temperatures
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
Size-dependent effect of nano-confinement of water in an ionic liquid matrix at low temperature
Full text linkOne of the leading hypotheses explaining water's anomalies is a metastable liquid-liquid phase transition (LLPT) at high pressure and low temperatures, which remains experimentally elusive due to homogeneous nucleation. Infrared spectroscopy experiments have shown that adding hydrazinium trifluoroacetate to water induces a sharp, reversible LLPT at ambient pressure, potentially originating from the same underlying mechanism as in pure water. In a previous work, we demonstrated that this transition can be attributed to the behavior of pure water only when nanosegregation of the aqueous component is brought into play. Here, by means of molecular dynamics simulations and the structural order parameter ζ, we explicitly analyze the effect of the ionic compound on the structure of liquid water at low temperature, both in a mixed solution and nanoconfined in spherical clusters of varying size. Our findings indicate that the ions surrounding the water induce structural perturbations that disrupt the water hydrogen-bond network up to a depth of approximately 0.70-0.75 nm from the surface toward the center of the sphere. This suggests that, in order to preserve a low-density liquid state within this ionic matrix, and more in general highly ionic matrices, water must be confined within pockets with radii greater than approximately 0.70-0.75 nm
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