221 research outputs found
The Geometry of Slow Structural Fluctuations in a Supercooled Binary Alloy
The liquid structure of a glass-forming binary alloy is studied using
molecular dynamics simulations. The analysis combines common neighbour analysis
with the geometrical approach of Frank and Kasper to establish that the
supercooled liquid contains extended clusters characterised by the same short
range order as the crystal. Fluctuations in these clusters exhibit strong
correlations with fluctuations in the inherent structure energy. The steep
increase in the heat capacity on cooling is, thus, directly coupled to the
growing fluctuations of the Frank-Kasper clusters. The relaxation of particles
in the clusters dominates the slow tail of the self-intermediate scattering
function
Pressure-energy correlations in liquids. V. Isomorphs in generalized Lennard-Jones systems
This series of papers is devoted to identifying and explaining the properties
of strongly correlating liquids, i.e., liquids with more than 90% correlation
between their virial W and potential energy U fluctuations in the NVT ensemble.
Paper IV [N. Gnan et al., J. Chem. Phys. v131, 234504 (2009)] showed that
strongly correlating liquids have "isomorphs", which are curves in the phase
diagram along which structure, dynamics, and some thermodynamic properties are
invariant in reduced units. In the present paper, using the fact that
reduced-unit radial distribution functions are isomorph invariant, we derive an
expression for the shapes of isomorphs in the WU phase diagram of generalized
Lennard-Jones systems of one or more types of particles. The isomorph shape
depends only on the Lennard-Jones exponents; thus all isomorphs of standard
Lennard-Jones systems (with exponents 12 and 6) can be scaled onto to a single
curve. Two applications are given. One is testing the prediction that the
solid-liquid coexistence curve follows an isomorph by comparing to recent
simulations by Ahmed and Sadus [J. Chem. Phys. v131, 174504 (2009)]. Excellent
agreement is found on the liquid side of the coexistence, whereas the agreement
is worse on the solid side. A second application is the derivation of an
approximate equation of state for generalized Lennard-Jones systems by
combining the isomorph theory with the Rosenfeld-Tarazona expression for the
temperature dependence of potential energy on isochores. It is shown that the
new equation of state agrees well with simulations.Comment: 12 pages, 14 figures, Section on solid-liquid coexistence expande
Feasibility of single-order parameter description of equilibrium viscous liquid dynamics
Molecular dynamics results for the dynamic Prigogine-Defay ratio are
presented for two glass-forming liquids, thus evaluating the experimentally
relevant quantity for testing whether metastable-equilibrium liquid dynamics to
a good approximation are described by a single parameter. For the Kob-Andersen
binary Lennard-Jones mixture as well as for an asymmetric dumbbell model liquid
a single-parameter description works quite well. This is confirmed by
time-domain results where it is found that energy and pressure fluctuations are
strongly correlated on the alpha-time scale in the NVT ensemble; in the NpT
ensemble energy and volume fluctuations similarly correlate strongly.Comment: Phys. Rev. E, in pres
Galectin-3 inhibitor GB0139 protects against acute lung injury by inhibiting neutrophil recruitment and activation
Rationale: Galectin-3 (Gal-3) drives fibrosis during chronic lung injury, however, its role in acute lung injury (ALI) remains unknown. Effective pharmacological therapies available for ALI are limited; identifying novel concepts in treatment is essential. GB0139 is a Gal-3 inhibitor currently under clinical investigation for the treatment of idiopathic pulmonary fibrosis. We investigate the role of Gal-3 in ALI and evaluate whether its inhibition with GB0139 offers a protective role. The effect of GB0139 on ALI was explored in vivo and in vitro. Methods: The pharmacokinetic profile of intra-tracheal (i.t.) GB0139 was investigated in C57BL/6 mice to support the daily dosing regimen. GB0139 (1â30 ”g) was then assessed following acute i.t. lipopolysaccharide (LPS) and bleomycin administration. Histology, broncho-alveolar lavage fluid (BALf) analysis, and flow cytometric analysis of lung digests and BALf were performed. The impact of GB0139 on cell activation and apoptosis was determined in vitro using neutrophils and THP-1, A549 and Jurkat E6 cell lines. Results: GB0139 decreased inflammation severity via a reduction in neutrophil and macrophage recruitment and neutrophil activation. GB0139 reduced LPS-mediated increases in interleukin (IL)-6, tumor necrosis factor alpha (TNFα) and macrophage inflammatory protein-1-alpha. In vitro, GB0139 inhibited Gal-3-induced neutrophil activation, monocyte IL-8 secretion, T cell apoptosis and the upregulation of pro-inflammatory genes encoding for IL-8, TNFα, IL-6 in alveolar epithelial cells in response to mechanical stretch. Conclusion: These data indicate that Gal-3 adopts a pro-inflammatory role following the early stages of lung injury and supports the development of GB0139, as a potential treatment approach in ALI
Single-order-parameter description of glass-forming liquids:A one-frequency test
Thermo-viscoelastic linear-response functions are calculated from the master
equation describing viscous liquid inherent dynamics. From the imaginary parts
of the frequency-dependent isobaric specific heat, isothermal compressibility,
and isobaric thermal expansion coefficient, we define a "linear dynamic
Prigogine-Defay ratio" with the property that if this quantity is unity atone
frequency, then it is unity at all frequencies. This happens if and only if
there is a single-order-parameter description of the thermo-viscoelastic linear
responses via an order parameter (which may be non-exponential in time).
Generalizations to other cases of thermodynamic control parameters than
temperature and pressure are treated in an Appendix.Comment: Replaces arXiv:cond-mat/040570
A standard protocol for describing the evaluation of ecological models
Numerical models of ecological systems are increasingly used to address complex environmental and resource management questions. One challenge for scientists, managers, and stakeholders is to appraise how well suited these models are to answer questions of scientific or societal relevance, that is, to perform, communicate, or access transparent evaluations of ecological models. While there have been substantial developments to support standardised descriptions of ecological models, less has been done to standardise and to report model evaluation practices. We present here a general protocol designed to guide the reporting of model evaluation. The protocol is organised in three major parts: the objective(s) of the modelling application, the ecological patterns of relevance and the evaluation methodology proper, and is termed the OPE (objectives, patterns, evaluation) protocol. We present the 25 questions of the OPE protocol which address the many aspects of the evaluation process and then apply them to six case studies based on a diversity of ecological models. In addition to standardising and increasing the transparency of the model evaluation process, we find that going through the OPE protocol helps modellers to think more deeply about the evaluation of their models. From this last point, we suggest that it would be highly beneficial for modellers to consider the OPE early in the modelling process, in addition to using it as a reporting tool and as a reviewing tool.publishedVersio
Hidden scale invariance of metals
Density functional theory (DFT) calculations of 58 liquid elements at their
triple point show that most metals exhibit near proportionality between thermal
fluctuations between virial and potential-energy in the isochoric ensemble.
This demonstrates a general "hidden" scale invariance of metals making the
dense part of the thermodynamic phase diagram effectively one dimensional with
respect to structure and dynamics. DFT computed density scaling exponents,
related to the Gr{\"u}neisen parameter, are in good agreement with experimental
values for 16 elements where reliable data were available. Hidden scale
invariance is demonstrated in detail for magnesium by showing invariance of
structure and dynamics. Computed melting curves of period three metals follow
curves with invariance (isomorphs). The experimental structure factor of
magnesium is predicted by assuming scale invariant inverse power-law (IPL) pair
interactions. However, crystal packings of several transition metals (V, Cr,
Mn, Fe, Nb, Mo, Ta, W and Hg), most post-transition metals (Ga, In, Sn, and Tl)
and the metalloids Si and Ge cannot be explained by the IPL assumption. Thus,
hidden scale invariance can be present even when the IPL-approximation is
inadequate. The virial-energy correlation coefficient of iron and phosphorous
is shown to increase at elevated pressures. Finally, we discuss how scale
invariance explains the Gr{\"u}neisen equation of state and a number of
well-known empirical melting and freezing rules.Comment: 12 pages, 11 figure
GrassPlot v. 2.00 â first update on the database of multi-scale plant diversity in Palaearctic grasslands
Abstract: GrassPlot is a collaborative vegetation-plot database organised by the Eurasian Dry Grassland Group (EDGG) and listed in the Global Index of Vegetation-Plot Databases (GIVD ID EU-00-003). Following a previous Long Database Report (Dengler et al. 2018, Phyto- coenologia 48, 331â347), we provide here the first update on content and functionality of GrassPlot. The current version (GrassPlot v. 2.00) contains a total of 190,673 plots of different grain sizes across 28,171 independent plots, with 4,654 nested-plot series including at least four grain sizes. The database has improved its content as well as its functionality, including addition and harmonization of header data (land use, information on nestedness, structure and ecology) and preparation of species composition data. Currently, GrassPlot data are intensively used for broad-scale analyses of different aspects of alpha and beta diversity in grassland ecosystems
Variation in amount of wild-type transthyretin in different fibril and tissue types in ATTR amyloidosis
Familial transthyretin (TTR) amyloidosis is caused by a mutation in the TTR gene, although wild-type (wt) TTR is also incorporated into the amyloid fibrils. Liver transplantation (LT) is the prevailing treatment of the disease and is performed in order to eliminate the mutant TTR from plasma. The outcome of the procedure is varied; especially problematic is a progressive cardiomyopathy seen in some patients, presumably caused by continued incorporation of wtTTR. What determines the discrepancy in outcome is not clear. We have previously shown that two structurally distinct amyloid fibrils (with or without fragmented ATTR) are found among ATTRV30M patients. In this study, we investigated the proportion of wtATTR in cardiac and adipose amyloid from patients having either fibril type. It was found that cardiac amyloid more easily incorporates wtTTR than adipose amyloid, offering a potential explanation for the vulnerability of cardiac tissue for continued amyloidosis after LT. In cardiac tissue, fibrils with fragmented ATTR contained a higher wt proportion than fibrils without, suggesting that continued incorporation of wtTTR after LT, perhaps, can take place more easily in these patients. In adipose tissue, a rapid increase in wt proportion after LT indicates that a rather fast turnover of the deposits must occur. A difference in wt proportion between the fibril types was seen post-LT but not pre-LT, possibly caused by differences in turnover rate. Conclusively, this study further establishes the basic dissimilarities between the two fibril types and demonstrates that their role in LT outcome needs to be further investigated
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