483 research outputs found
Transparent dense sodium
Under pressure, metals exhibit increasingly shorter interatomic distances.
Intuitively, this response is expected to be accompanied by an increase in the
widths of the valence and conduction bands and hence a more pronounced
free-electron-like behaviour. But at the densities that can now be achieved
experimentally, compression can be so substantial that core electrons overlap.
This effect dramatically alters electronic properties from those typically
associated with simple free-electron metals such as lithium and sodium, leading
in turn to structurally complex phases and superconductivity with a high
critical temperature. But the most intriguing prediction - that the seemingly
simple metals Li and Na will transform under pressure into insulating states,
owing to pairing of alkali atoms - has yet to be experimentally confirmed. Here
we report experimental observations of a pressure-induced transformation of Na
into an optically transparent phase at 200 GPa (corresponding to 5.0-fold
compression). Experimental and computational data identify the new phase as a
wide bandgap dielectric with a six-coordinated, highly distorted
double-hexagonal close-packed structure. We attribute the emergence of this
dense insulating state not to atom pairing, but to p-d hybridizations of
valence electrons and their repulsion by core electrons into the lattice
interstices. We expect that such insulating states may also form in other
elements and compounds when compression is sufficiently strong that atomic
cores start to overlap strongly.Comment: Published in Nature 458, 182-185 (2009
Effect of small scale density perturbations on the formation of dark matter halo profiles
With help of a set of toy N-body models of dark halo formation we study the
impact of small scale initial perturbations on the inner density profiles of
haloes. We find a significant flattening of the inner slope to in some range of scales and amplitudes
of the perturbations (while in the case of absence of these perturbations the
NFW profile with is reproduced). This effect may be responsible for
the formation of cuspless galactic haloes.Comment: 5 pages, 2 figures, accepted for publication in MNRAS Letter
Importance of Itinerancy and Quantum Fluctuations for the Magnetism in Iron Pnictides
By applying density functional theory, we find strong evidence for an
itinerant nature of magnetism in two families of iron pnictides. Furthermore,
by employing dynamical mean field theory with continuous time quantum Monte
Carlo as an impurity solver, we observe that the antiferromagnetic metal with
small magnetic moment naturally arises out of coupling between unfrustrated and
frustrated bands. Our results point to a possible scenario for magnetism in
iron pnictides where magnetism originates from a strong instability at the
momentum vector (, , ) while it is reduced by quantum
fluctuations due to the coupling between weakly and strongly frustrated bands.Comment: 4 pages, 4 figure
A Unifying Model of Genome Evolution Under Parsimony
We present a data structure called a history graph that offers a practical
basis for the analysis of genome evolution. It conceptually simplifies the
study of parsimonious evolutionary histories by representing both substitutions
and double cut and join (DCJ) rearrangements in the presence of duplications.
The problem of constructing parsimonious history graphs thus subsumes related
maximum parsimony problems in the fields of phylogenetic reconstruction and
genome rearrangement. We show that tractable functions can be used to define
upper and lower bounds on the minimum number of substitutions and DCJ
rearrangements needed to explain any history graph. These bounds become tight
for a special type of unambiguous history graph called an ancestral variation
graph (AVG), which constrains in its combinatorial structure the number of
operations required. We finally demonstrate that for a given history graph ,
a finite set of AVGs describe all parsimonious interpretations of , and this
set can be explored with a few sampling moves.Comment: 52 pages, 24 figure
Temperature and pressure evolution of the crystal structure of Ax(Fe1-ySe)2 (A = Cs, Rb, K) studied by synchrotron powder diffraction
Temperature-dependent synchrotron powder diffraction on Cs0.83(Fe0.86Se)2
revealed first order I4/m to I4/mmm structural transformation around 216{\deg}C
associated with the disorder of the Fe vacancies. Irreversibility observed
during the transition is likely associated with a mobility of intercalated
Alkali atoms. Pressure-dependent synchrotron powder diffraction on
Cs0.83(Fe1-ySe)2, Rb0.85(Fe1-ySe)2 and K0.8(Fe1-ySe)2 (y ~ 0.14) indicated that
the I4/m superstructure reflections are present up to pressures of 120 kbar.
This may indicate that the ordering of the Fe vacancies is present in both
superconducting and non-superconductive states.Comment: 11 pages, 5 figures, 1 tabl
Lepton Acceleration in Pulsar Wind Nebulae
Pulsar Wind Nebulae (PWNe) act as calorimeters for the relativistic pair
winds emanating from within the pulsar light cylinder. Their radiative
dissipation in various wavebands is significantly different from that of their
pulsar central engines: the broadband spectra of PWNe possess characteristics
distinct from those of pulsars, thereby demanding a site of lepton acceleration
remote from the pulsar magnetosphere. A principal candidate for this locale is
the pulsar wind termination shock, a putatively highly-oblique,
ultra-relativistic MHD discontinuity. This paper summarizes key characteristics
of relativistic shock acceleration germane to PWNe, using predominantly Monte
Carlo simulation techniques that compare well with semi-analytic solutions of
the diffusion-convection equation. The array of potential spectral indices for
the pair distribution function is explored, defining how these depend
critically on the parameters of the turbulent plasma in the shock environs.
Injection efficiencies into the acceleration process are also addressed.
Informative constraints on the frequency of particle scattering and the level
of field turbulence are identified using the multiwavelength observations of
selected PWNe. These suggest that the termination shock can be comfortably
invoked as a principal injector of energetic leptons into PWNe without
resorting to unrealistic properties for the shock layer turbulence or MHD
structure.Comment: 19 pages, 5 figures, invited review to appear in Proc. of the
inaugural ICREA Workshop on "The High-Energy Emission from Pulsars and their
Systems" (2010), eds. N. Rea and D. Torres, (Springer Astrophysics and Space
Science series
Evolution of tetragonal phase in the FeSe wire fabricated by a novel chemical-transformation PIT process
We fabricated superconducting FeSe wires by the chemical-transformation PIT
process. The obvious correlation between annealing temperature and phase
transformation was observed. Annealing above 500^{\circ}C produced wire-core
transformation from hexagonal to tetragonal phase. Furthermore the hexagonal
phase completely transformed into the tetragonal phase by annealing at
1000^{\circ}C. With increasing annealing temperature, the superconducting
property was dramatically improved, associated with the evolution of the
tetragonal phase.Comment: 14 pages, 6 figure
Reconstructing cancer genomes from paired-end sequencing data
<p>Abstract</p> <p>Background</p> <p>A cancer genome is derived from the germline genome through a series of somatic mutations. Somatic structural variants - including duplications, deletions, inversions, translocations, and other rearrangements - result in a cancer genome that is a scrambling of intervals, or "blocks" of the germline genome sequence. We present an efficient algorithm for reconstructing the block organization of a cancer genome from paired-end DNA sequencing data.</p> <p>Results</p> <p>By aligning paired reads from a cancer genome - and a matched germline genome, if available - to the human reference genome, we derive: (i) a partition of the reference genome into intervals; (ii) adjacencies between these intervals in the cancer genome; (iii) an estimated copy number for each interval. We formulate the Copy Number and Adjacency Genome Reconstruction Problem of determining the cancer genome as a sequence of the derived intervals that is consistent with the measured adjacencies and copy numbers. We design an efficient algorithm, called Paired-end Reconstruction of Genome Organization (PREGO), to solve this problem by reducing it to an optimization problem on an interval-adjacency graph constructed from the data. The solution to the optimization problem results in an Eulerian graph, containing an alternating Eulerian tour that corresponds to a cancer genome that is consistent with the sequencing data. We apply our algorithm to five ovarian cancer genomes that were sequenced as part of The Cancer Genome Atlas. We identify numerous rearrangements, or structural variants, in these genomes, analyze reciprocal vs. non-reciprocal rearrangements, and identify rearrangements consistent with known mechanisms of duplication such as tandem duplications and breakage/fusion/bridge (B/F/B) cycles.</p> <p>Conclusions</p> <p>We demonstrate that PREGO efficiently identifies complex and biologically relevant rearrangements in cancer genome sequencing data. An implementation of the PREGO algorithm is available at <url>http://compbio.cs.brown.edu/software/</url>.</p
Characterization analysis and polymorphism detection of the porcine Myd88 gene
The myeloid differentiation primary response protein 88 (Myd88) is an essential adaptor protein, which mediates in all Toll-like receptor (TLR) members signal transduction, except for TLR3. In this study, the 4464 bp genomic sequence of porcine Myd88 was first isolated, whereupon tissue distribution, chromosome mapping and single nucleotide polymorphism (SNP) were analyzed. Our results revealed that porcine Myd88 gene, which was located at chromosome 13 linked with marker S0288 (distance = 40 cR; LOD = 8.66), was widely expressed in all the examined tissues. There were 16 potential SNPs in the isolated genome fragment. SNP 797T/C in the first intron was studied, with no significant association being found between the genotype and immune traits in pigs (p > 0.05). The porcine Myd88 protein contained both the death domain (DD) and the Toll/IL-1 receptor domain (TIR). Leu residues, essential for its structure, were the most abundant encountered in the DD. The TIR contained two conserved motifs which may play important roles in the Myd88 function
Disentangling astroglial physiology with a realistic cell model in silico
Electrically non-excitable astroglia take up neurotransmitters, buffer extracellular K+ and generate Ca2+ signals that release molecular regulators of neural circuitry. The underlying machinery remains enigmatic, mainly because the sponge-like astrocyte morphology has been difficult to access experimentally or explore theoretically. Here, we systematically incorporate multi-scale, tri-dimensional astroglial architecture into a realistic multi-compartmental cell model, which we constrain by empirical tests and integrate into the NEURON computational biophysical environment. This approach is implemented as a flexible astrocyte-model builder ASTRO. As a proof-of-concept, we explore an in silico astrocyte to evaluate basic cell physiology features inaccessible experimentally. Our simulations suggest that currents generated by glutamate transporters or K+ channels have negligible distant effects on membrane voltage and that individual astrocytes can successfully handle extracellular K+ hotspots. We show how intracellular Ca2+ buffers affect Ca2+ waves and why the classical Ca2+ sparks-and-puffs mechanism is theoretically compatible with common readouts of astroglial Ca2+ imaging
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