1,170 research outputs found
Thin-Film Metamaterials called Sculptured Thin Films
Morphology and performance are conjointed attributes of metamaterials, of
which sculptured thin films (STFs) are examples. STFs are assemblies of
nanowires that can be fabricated from many different materials, typically via
physical vapor deposition onto rotating substrates. The curvilinear--nanowire
morphology of STFs is determined by the substrate motions during fabrication.
The optical properties, especially, can be tailored by varying the morphology
of STFs. In many cases prototype devices have been fabricated for various
optical, thermal, chemical, and biological applications.Comment: to be published in Proc. ICTP School on Metamaterials (Augsut 2009,
Sibiu, Romania
HARES: an efficient method for first-principles electronic structure calculations of complex systems
We discuss our new implementation of the Real-space Electronic Structure
method for studying the atomic and electronic structure of infinite periodic as
well as finite systems, based on density functional theory. This improved
version which we call HARES (for High-performance-fortran Adaptive grid
Real-space Electronic Structure) aims at making the method widely applicable
and efficient, using high performance Fortran on parallel architectures. The
scaling of various parts of a HARES calculation is analyzed and compared to
that of plane-wave based methods. The new developments that lead to enhanced
performance, and their parallel implementation, are presented in detail. We
illustrate the application of HARES to the study of elemental crystalline
solids, molecules and complex crystalline materials, such as blue bronze and
zeolites.Comment: 17 two-column pages, including 9 figures, 5 tables. To appear in
Computer Physics Communications. Several minor revisions based on feedbac
Salerno's model of DNA reanalysed: could solitons have biological significance?
We investigate the sequence-dependent behaviour of localised excitations in a
toy, nonlinear model of DNA base-pair opening originally proposed by Salerno.
Specifically we ask whether ``breather'' solitons could play a role in the
facilitated location of promoters by RNA polymerase. In an effective potential
formalism, we find excellent correlation between potential minima and {\em
Escherichia coli} promoter recognition sites in the T7 bacteriophage genome.
Evidence for a similar relationship between phage promoters and downstream
coding regions is found and alternative reasons for links between AT richness
and transcriptionally-significant sites are discussed. Consideration of the
soliton energy of translocation provides a novel dynamical picture of sliding:
steep potential gradients correspond to deterministic motion, while ``flat''
regions, corresponding to homogeneous AT or GC content, are governed by random,
thermal motion. Finally we demonstrate an interesting equivalence between
planar, breather solitons and the helical motion of a sliding protein
``particle'' about a bent DNA axis.Comment: Latex file 20 pages, 5 figures. Manuscript of paper to appear in J.
Biol. Phys., accepted 02/09/0
Golgi Outpost Synthesis Impaired by Toxic Polyglutamine Proteins Contributes to Dendritic Pathology in Neurons
Dendrite aberration is a common feature of neurodegenerative diseases caused by protein toxicity, but the underlying mechanisms remain largely elusive. Here, we show that nuclear polyglutamine (polyQ) toxicity resulted in defective terminal dendrite elongation accompanied by a loss of Golgi outposts (GOPs) and a decreased supply of plasma membrane (PM) in Drosophila class IV dendritic arborization (da) (C4 da) neurons. mRNA sequencing revealed that genes downregulated by polyQ proteins included many secretory pathway-related genes, including COPII genes regulating GOP synthesis. Transcription factor enrichment analysis identified CREB3L1/CrebA, which regulates COPII gene expression. CrebA overexpression in C4 da neurons restores the dysregulation of COPII genes, GOP synthesis, and PM supply. Chromatin immunoprecipitation (ChIP)-PCR revealed that CrebA expression is regulated by CREB-binding protein (CBP), which is sequestered by polyQ proteins. Furthermore, co-overexpression of CrebA and Rac1 synergistically restores the polyQ-induced dendrite pathology. Collectively, our results suggest that GOPs impaired by polyQ proteins contribute to dendrite pathology through the CBP-CrebA-COPII pathway. ? 2017 The Author(s)113Ysciescopu
SETD2 haploinsufficiency for microtubule methylation is an early driver of genomic instability in renal cell carcinoma
Loss of the short arm of chromosome 3 (3p) occurs early in >95% of clear cell renal cell carcinoma (ccRCC). Nearly ubiquitous 3p loss in ccRCC suggests haploinsufficiency for 3p tumor suppressors as early drivers of tumorigenesis. We previously reported methyltransferase SETD2, which trimethylates H3 histones on lysine 36 (H3K36me3) and is located in the 3p deletion, to also trimethylate microtubules on lysine 40 (aTubK40me3) during mitosis, with aTubK40me3 required for genomic stability. We now show that monoallelic, Setd2-deficient cells retaining H3K36me3, but not aTubK40me3, exhibit a dramatic increase in mitotic defects and micronuclei count, with increased viability compared with biallelic loss. In SETD2-inactivated human kidney cells, rescue with a pathogenic SETD2 mutant deficient for microtubule (aTubK40me3), but not histone (H3K36me3) methylation, replicated this phenotype. Genomic instability (micronuclei) was also a hallmark of patient-derived cells from ccRCC. These data show that the SETD2 tumor suppressor displays a haploinsufficiency phenotype disproportionately impacting microtubule methylation and serves as an early driver of genomic instability. Significance: Loss of a single allele of a chromatin modifier plays a role in promoting oncogenesis, underscoring the growing relevance of tumor suppressor haploinsufficiency in tumorigenesis
Observation of the Charmed Baryon Decays to , , and
We have observed two new decay modes of the charmed baryon into
and using data collected with the
CLEO II detector. We also present the first measurement of the branching
fraction for the previously observed decay mode . The branching fractions for these three modes relative to
are measured to be , , and , respectively.Comment: 12 page uuencoded postscript file, postscript file also available
through http://w4.lns.cornell.edu/public/CLN
Dilepton mass spectra in p+p collisions at sqrt(s)= 200 GeV and the contribution from open charm
The PHENIX experiement has measured the electron-positron pair mass spectrum
from 0 to 8 GeV/c^2 in p+p collisions at sqrt(s)=200 GeV. The contributions
from light meson decays to e^+e^- pairs have been determined based on
measurements of hadron production cross sections by PHENIX. They account for
nearly all e^+e^- pairs in the mass region below 1 GeV/c^2. The e^+e^- pair
yield remaining after subtracting these contributions is dominated by
semileptonic decays of charmed hadrons correlated through flavor conservation.
Using the spectral shape predicted by PYTHIA, we estimate the charm production
cross section to be 544 +/- 39(stat) +/- 142(syst) +/- 200(model) \mu b, which
is consistent with QCD calculations and measurements of single leptons by
PHENIX.Comment: 375 authors from 57 institutions, 18 pages, 4 figures, 2 tables.
Submitted to Physics Letters B. v2 fixes technical errors in matching authors
to institutions. Plain text data tables for the points plotted in figures for
this and previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
Inclusive cross section and double helicity asymmetry for \pi^0 production in p+p collisions at sqrt(s)=200 GeV: Implications for the polarized gluon distribution in the proton
The PHENIX experiment presents results from the RHIC 2005 run with polarized
proton collisions at sqrt(s)=200 GeV, for inclusive \pi^0 production at
mid-rapidity. Unpolarized cross section results are given for transverse
momenta p_T=0.5 to 20 GeV/c, extending the range of published data to both
lower and higher p_T. The cross section is described well for p_T < 1 GeV/c by
an exponential in p_T, and, for p_T > 2 GeV/c, by perturbative QCD. Double
helicity asymmetries A_LL are presented based on a factor of five improvement
in uncertainties as compared to previously published results, due to both an
improved beam polarization of 50%, and to higher integrated luminosity. These
measurements are sensitive to the gluon polarization in the proton, and exclude
maximal values for the gluon polarization.Comment: 375 authors, 7 pages, 3 figures. Submitted to Phys. Rev. D, Rapid
Communications. Plain text data tables for the points plotted in figures for
this and previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
System Size and Energy Dependence of Jet-Induced Hadron Pair Correlation Shapes in Cu+Cu and Au+Au Collisions at sqrt(s_NN) = 200 and 62.4 GeV
We present azimuthal angle correlations of intermediate transverse momentum
(1-4 GeV/c) hadrons from {dijets} in Cu+Cu and Au+Au collisions at sqrt(s_NN) =
62.4 and 200 GeV. The away-side dijet induced azimuthal correlation is
broadened, non-Gaussian, and peaked away from \Delta\phi=\pi in central and
semi-central collisions in all the systems. The broadening and peak location
are found to depend upon the number of participants in the collision, but not
on the collision energy or beam nuclei. These results are consistent with sound
or shock wave models, but pose challenges to Cherenkov gluon radiation models.Comment: 464 authors from 60 institutions, 6 pages, 3 figures, 2 tables.
Submitted to Physical Review Letters. Plain text data tables for the points
plotted in figures for this and previous PHENIX publications are (or will be)
publicly available at http://www.phenix.bnl.gov/papers.htm
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