126 research outputs found
Testing "microscopic" theories of glass-forming liquids
We assess the validity of "microscopic" approaches of glass-forming liquids
based on the sole k nowledge of the static pair density correlations. To do so
we apply them to a benchmark provided by two liquid models that share very
similar static pair density correlation functions while disp laying distinct
temperature evolutions of their relaxation times. We find that the approaches
are unsuccessful in describing the difference in the dynamical behavior of the
two models. Our study is not exhausti ve, and we have not tested the effect of
adding corrections by including for instance three-body density correlations.
Yet, our results appear strong enough to challenge the claim that the slowd own
of relaxation in glass-forming liquids, for which it is well established that
the changes of the static structure factor with temperature are small, can be
explained by "microscopic" appr oaches only requiring the static pair density
correlations as nontrivial input.Comment: 10 pages, 7 figs; Accepted to EPJE Special Issue on The Physics of
Glasses. Arxiv version contains an addendum to the appendix which does not
appear in published versio
The nature of slow dynamics in a minimal model of frustration-limited domains
We present simulation results for the dynamics of a schematic model based on
the frustration-limited domain picture of glass-forming liquids. These results
are compared with approximate theoretical predictions analogous to those
commonly used for supercooled liquid dynamics. Although model relaxation times
increase by several orders of magnitude in a non-Arrhenius manner as a
microphase separation transition is approached, the slow relaxation is in many
ways dissimilar to that of a liquid. In particular, structural relaxation is
nearly exponential in time at each wave vector, indicating that the mode
coupling effects dominating liquid relaxation are comparatively weak within
this model. Relaxation properties of the model are instead well reproduced by
the simplest dynamical extension of a static Hartree approximation. This
approach is qualitatively accurate even for temperatures at which the mode
coupling approximation predicts loss of ergodicity. These results suggest that
the thermodynamically disordered phase of such a minimal model poorly
caricatures the slow dynamics of a liquid near its glass transition
Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6
The Jumonji domain-containing protein JMJD6 is a 2-oxoglutarate-dependent dioxygenase associated with a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing, and cotranscriptional processing. Although not all studies agree, JMJD6 has been reported to catalyze both hydroxylation of lysine residues and demethylation of arginine residues. However, despite extensive study and indirect evidence for JMJD6 catalysis in many cellular processes, direct assignment of JMJD6 catalytic substrates has been limited. Examination of a reported site of proline hydroxylation within a lysine-rich region of the tandem bromodomain protein BRD4 led us to conclude that hydroxylation was in fact on lysine and catalyzed by JMJD6. This prompted a wider search for JMJD6-catalyzed protein modifications deploying mass spectrometric methods designed to improve the analysis of such lysine-rich regions. Using lysine derivatization with propionic anhydride to improve the analysis of tryptic peptides and nontryptic proteolysis, we report 150 sites of JMJD6-catalyzed lysine hydroxylation on 48 protein substrates, including 19 sites of hydroxylation on BRD4. Most hydroxylations were within lysine-rich regions that are predicted to be unstructured; in some, multiple modifications were observed on adjacent lysine residues. Almost all of the JMJD6 substrates defined in these studies have been associated with membraneless organelle formation. Given the reported roles of lysine-rich regions in subcellular partitioning by liquid-liquid phase separation, our findings raise the possibility that JMJD6 may play a role in regulating such processes in response to stresses, including hypoxia
Distributed flow optimization and cascading effects in weighted complex networks
We investigate the effect of a specific edge weighting scheme on distributed flow efficiency and robustness to cascading
failures in scale-free networks. In particular, we analyze a simple, yet
fundamental distributed flow model: current flow in random resistor networks.
By the tuning of control parameter and by considering two general cases
of relative node processing capabilities as well as the effect of bandwidth, we
show the dependence of transport efficiency upon the correlations between the
topology and weights. By studying the severity of cascades for different
control parameter , we find that network resilience to cascading
overloads and network throughput is optimal for the same value of over
the range of node capacities and available bandwidth
The Theory of Brown Dwarfs and Extrasolar Giant Planets
Straddling the traditional realms of the planets and the stars, objects below
the edge of the main sequence have such unique properties, and are being
discovered in such quantities, that one can rightly claim that a new field at
the interface of planetary science and and astronomy is being born. In this
review, we explore the essential elements of the theory of brown dwarfs and
giant planets, as well as of the new spectroscopic classes L and T. To this
end, we describe their evolution, spectra, atmospheric compositions, chemistry,
physics, and nuclear phases and explain the basic systematics of
substellar-mass objects across three orders of magnitude in both mass and age
and a factor of 30 in effective temperature. Moreover, we discuss the
distinctive features of those extrasolar giant planets that are irradiated by a
central primary, in particular their reflection spectra, albedos, and transits.
Aspects of the latest theory of Jupiter and Saturn are also presented.
Throughout, we highlight the effects of condensates, clouds, molecular
abundances, and molecular/atomic opacities in brown dwarf and giant planet
atmospheres and summarize the resulting spectral diagnostics. Where possible,
the theory is put in its current observational context.Comment: 67 pages (including 36 figures), RMP RevTeX LaTeX, accepted for
publication in the Reviews of Modern Physics. 30 figures are color. Most of
the figures are in GIF format to reduce the overall size. The full version
with figures can also be found at:
http://jupiter.as.arizona.edu/~burrows/papers/rm
Marine Toxins: Chemistry, Toxicity, Occurrence and Detection, with Special Reference to the Dutch Situation
Various species of algae can produce marine toxins under certain circumstances. These toxins can then accumulate in shellfish such as mussels, oysters and scallops. When these contaminated shellfish species are consumed severe intoxication can occur. The different types of syndromes that can occur after consumption of contaminated shellfish, the corresponding toxins and relevant legislation are discussed in this review. Amnesic Shellfish Poisoning (ASP), Paralytic Shellfish Poisoning (PSP), Diarrheic Shellfish Poisoning (DSP) and Azaspiracid Shellfish Poisoning (AZP) occur worldwide, Neurologic Shellfish Poisoning (NSP) is mainly limited to the USA and New Zealand while the toxins causing DSP and AZP occur most frequently in Europe. The latter two toxin groups are fat-soluble and can therefore also be classified as lipophilic marine toxins. A detailed overview of the official analytical methods used in the EU (mouse or rat bioassay) and the recently developed alternative methods for the lipophilic marine toxins is given. These alternative methods are based on functional assays, biochemical assays and chemical methods. From the literature it is clear that chemical methods offer the best potential to replace the animal tests that are still legislated worldwide. Finally, an overview is given of the situation of marine toxins in The Netherlands. The rat bioassay has been used for monitoring DSP and AZP toxins in The Netherlands since the 1970s. Nowadays, a combination of a chemical method and the rat bioassay is often used. In The Netherlands toxic events are mainly caused by DSP toxins, which have been found in Dutch shellfish for the first time in 1961, and have reoccurred at irregular intervals and in varying concentrations. From this review it is clear that considerable effort is being undertaken by various research groups to phase out the animal tests that are still used for the official routine monitoring programs
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