1,720,965 research outputs found
Heterogeneous nucleation of ice on carbon surfaces
No full textAtmospheric aerosols can promote the heterogeneous nucleation of ice, impacting the radiative properties of clouds and Earth's climate. The experimental investigation of heterogeneous freezing of water droplets by carbonaceous particles reveals widespread ice freezing temperatures. It is not known which structural and chemical characteristics of soot account for the variability in ice nucleation efficiency. Here we use molecular dynamics simulations to investigate the nucleation of ice from liquid water in contact with graphitic surfaces. We find that atomically flat carbon surfaces promote heterogeneous nucleation of ice, while molecularly rough surfaces with the same hydrophobicity do not. Graphitic surfaces and other surfaces that promote ice nucleation induce layering in the interfacial water, suggesting that the order imposed by the surface on liquid water may play an important role in the heterogeneous nucleation mechanism. We investigate a large set of graphitic surfaces of various dimensions and radii of curvature and find that variations in nanostructures alone could account for the spread in the freezing temperatures of ice on soot in experiments. We conclude that a characterization of the nanostructure of soot is needed to predict its ice nucleation efficiency
Free energy contributions and structural characterization of stacking disordered ices
No full textCrystallization of ice from deeply supercooled water and amorphous ices - a process of fundamental importance in the atmosphere, interstellar space, and cryobiology - results in stacking disordered ices with a wide range of metastabilities with respect to hexagonal ice. The structural origin of this high variability, however, has not yet been elucidated. Here we use molecular dynamics simulations with the mW water model to characterize the structure of ice freshly grown from supercooled water at temperatures from 210 to 270 K, the thermodynamics of stacking faults, line defects, and interfaces, and to elucidate the interplay between kinetics and thermodynamics in determining the structure of ice. In agreement with experiments, the ice grown in the simulations is stacking disordered with a random distribution of cubic and hexagonal layers, and a cubicity that decreases with growth temperature. The former implies that the cubicity of ice is determined by processes at the ice/liquid interface, without memory of the structure of buried ice layers. The latter indicates that the probability of building a cubic layer at the interface decreases upon approaching the melting point of ice, which we attribute to a more efficient structural equilibration of ice at the liquid interface as the driving force for growth wanes. The free energy cost for creating a pair of cubic layers in ice is 8.0 J mol(-1) in experiments, and 9.7 ± 1.9 J mol(-1) for the mW water model. This not only validates the simulations, but also indicates that dispersion in cubicity is not sufficient to explain the large energetic variability of stacking disordered ices. We compute the free energy cost of stacking disorder, line defects, and interfaces in ice and conclude that a characterization of the density of these defects is required to predict the degree of metastability and vapor pressure of atmospheric ices
Role of stacking disorder in ice nucleation
No full textThe freezing of water affects the processes that determine Earth's climate. Therefore, accurate weather and climate forecasts hinge on good predictions of ice nucleation rates. Such rate predictions are based on extrapolations using classical nucleation theory, which assumes that the structure of nanometre-sized ice crystallites corresponds to that of hexagonal ice, the thermodynamically stable form of bulk ice. However, simulations with various water models find that ice nucleated and grown under atmospheric temperatures is at all sizes stacking-disordered, consisting of random sequences of cubic and hexagonal ice layers. This implies that stacking-disordered ice crystallites either are more stable than hexagonal ice crystallites or form because of non-equilibrium dynamical effects. Both scenarios challenge central tenets of classical nucleation theory. Here we use rare-event sampling and free energy calculations with the mW water model to show that the entropy of mixing cubic and hexagonal layers makes stacking-disordered ice the stable phase for crystallites up to a size of at least 100,000 molecules. We find that stacking-disordered critical crystallites at 230 kelvin are about 14 kilojoules per mole of crystallite more stable than hexagonal crystallites, making their ice nucleation rates more than three orders of magnitude higher than predicted by classical nucleation theory. This effect on nucleation rates is temperature dependent, being the most pronounced at the warmest conditions, and should affect the modelling of cloud formation and ice particle numbers, which are very sensitive to the temperature dependence of ice nucleation rates. We conclude that classical nucleation theory needs to be corrected to include the dependence of the crystallization driving force on the size of the ice crystallite when interpreting and extrapolating ice nucleation rates from experimental laboratory conditions to the temperatures that occur in clouds
Doctor of Philosophy
No full textdissertationThe processes at the surface of ice modulate crystal growth, atmospheric and biologically relevant adsorption of solutes, and chemical reactions. These processes are not well characterized, in part, due to lack of spatial and temporal resolution of the existing experimental techniques. In this dissertation, we use molecular modeling to study the role of structure and thermodynamics of ice/liquid and ice/vapor interfaces in determining the morphology of water-salt ultrafine aerosols, polymorph of ice that grows from liquid or water vapor uptake, and the behavior of ions, organics, and biological molecules at the interfaces of ice. We find that the crystallized water-salt aerosols adopt a spherical cap morphology in which the ice nanophase is exposed to vapor. Our analysis indicates that change of liquid/vapor surface tension with solute concentration is the key thermodynamic predictor that determines the morphology of crystallized binary aqueous aerosols. We find that the ice growth from liquid water and from vapor results in the stacking disordered and hexagonal ice, respectively. This can be attributed to distinct thermodynamics and kinetics of processes modulating ice growth at the ice/liquid and ice/vapor interface. Investigation of the ice/vapor interface reveals solvation properties that are distinctly different from that of bulk liquid. We find that strongly hydrophilic solutes that increase the liquidity of the ice surface experiences a water-driven long-ranged attraction at the surface of ice, resulting in solvent-separated ion clusters. iv This dissertation elucidates the molecular mechanism of ice recognition and binding by antifreeze and ice-nucleating proteins. We find two distinct ice-binding sites for the ice-nucleating protein of Pseudomonas syringae. We find that the hyperactive insect antifreeze proteins bind to ice through an ice-plane-specific anchored clathrate motif. The water at the ice-binding site of the antifreeze protein is not preordered in solution, in contradiction to the widely prevailing "preordering-binding" hypothesis. Instead, ice recognition and binding occur by slow diffusive dynamics of the protein at the surface of ice to find the appropriate orientations, followed by a fast reorganization of water at the binding site that latches the protein to ice
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
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HIV-1 capsid shape, orientation, and entropic elasticity regulate translocation into the nuclear pore complex
Full text linkNuclear import and uncoating of the viral capsid are critical steps in the HIV-1 life cycle that serve to transport and release genomic material into the nucleus. Viral core import involves translocating the HIV-1 capsid at the nuclear pore complex (NPC). Notably, the central channel of the NPC appears to often accommodate and allow passage of intact HIV-1 capsid, though mechanistic details of the process remain to be fully understood. Here, we investigate the molecular interactions that operate in concert between the HIV-1 capsid and the NPC that regulate capsid translocation through the central channel. To this end, we develop a “bottom-up” coarse-grained (CG) model of the human NPC from recently released cryo-electron tomography structure and then construct composite membrane-embedded CG NPC models. We find that successful translocation from the cytoplasmic side to the NPC central channel is contingent on the compatibility of the capsid morphology and channel dimension and the proper orientation of the capsid approach to the channel from the cytoplasmic side. The translocation dynamics is driven by maximizing the contacts between phenylalanine-glycine nucleoporins at the central channel and the capsid. For the docked intact capsids, structural analysis reveals correlated striated patterns of lattice disorder likely related to the intrinsic capsid elasticity. Uncondensed genomic material inside the docked capsid augments the overall lattice disorder of the capsid. Our results suggest that the intrinsic “elasticity” can also aid the capsid to adapt to the stress and remain structurally intact during translocation
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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