pinecone/core-2020-05-10-deduplication huggingface dataset:
Rotation misorientated graphene moire superlattices on Cu(111):
  classical molecular dynamics simulations and scanning tunneling microscopy
  studies

Graphene on copper is a system of high technological relevance, as Cu is one
of the most widely used substrates for the CVD growth of graphene. However,
very little is known about the details of their interaction. One approach to
gain such information is studying the superlattices emerging due to the
mismatch of the two crystal lattices. However, graphene on copper is a
low-corrugated system making both their experimental and theoretical study
highly challenging. Here, we report the observation of a new rotational Moire
superlattice of CVD graphene on Cu (111), characterized by a periodicity of
$1.5 \pm 0.05$ nm and corrugation of $0.15 \pm 0.05$ $\hbox{\AA}$ , as measured
by Scanning Tunneling Microscopy. To understand the observed superlattice we
have developed a newly parameterized Tersoff-potential for the graphene/Cu
(111) interface fitted to nonlocal van der Waals density functional theory
(DFT) calculations. The interfacial force field with time-lapsed CMD provides
superlattices in good quantitative agreement with the experimental results, for
a misorientation angle of $10.4 \pm 0.5,^{\circ}$ without any further parameter
adjustment. Furthermore, the CMD simulations predict the existence of two
non-equivalent high-symmetry directions of the Moir\'e pattern that could also
be identified in the experimental STM images.Comment: 7 pages, 2 figures, 2 table
Impact factors for Reggeon-gluon transition in N = 4 SYM with large
  number of colours

We calculate impact factors for Reggeon-gluon transition in supersymmetric
Yang-Mills theory with four supercharges at large number of colours Nc. In the
next-to-leading order impact factors are not uniquely defined and must accord
with BFKL kernels and energy scales. We obtain the impact factor corresponding
to the kernel and the energy evolution parameter, which is invariant under
Moebius transformation in momentum space, and show that it is also Moebius
invariant up to terms taken into account in the BDS ansatz.Comment: 13 page
Improved Epstein-Glaser renormalization in $x$-space versus differential
  renormalization

Renormalization of massless Feynman amplitudes in $x$-space is reexamined
here, using almost exclusively real-variable methods. We compute a wealth of
concrete examples by means of recursive extension of distributions. This allows
us to show perturbative expansions for the four-point and two-point functions
at several loop order. To deal with internal vertices, we expound and expand on
convolution theory for log-homogeneous distributions. The approach has much in
common with differential renormalization as given by Freedman, Johnson and
Latorre; but differs in important details.Comment: Latex, 47 pages. v2: Some reorganization, minor improvements, 4 added
  references. v3: Minor corrections to match published version v4: Appendix B
  completed (with respect to the published version) by supplying a missing
  contribution to the two-point function, following a suggestion of Schnetz
  [26]; and a few misprints correcte
Anisotropic plasma at finite $U(1)$ chemical potential

We present a type IIB supergravity solution dual to a spatially anisotropic
$\mathcal{N}=4$ super Yang-Mills plasma at finite $U(1)$ chemical potential and
finite temperature. The effective five-dimensional gravitational theory is a
consistent Einstein-Maxwell-dilaton-Axion truncation of the gauged
supergravity. We obtain the solutions both numerically and analytically. We
study the phase structure and thermodynamic instabilities of the solution, and
find new instabilities independent of the renormalization scheme.Comment: 1+50 pages, 31 figures. typos corrected. published version. arXiv
  admin note: text overlap with arXiv:1106.1637 by other author
Construction of BRST invariant states in G/H WZNW models

We study the cohomology arising in the BRST formulation of G/H gauged WZNW models, i.e. in which the states of the gauged theory are projected out from the ungauged one by means of a BRST condition. We will derive for a general simple group H with arbitrary level, conditions for which the cohomology is non-trivial. We show, by introducing a small perturbation due to Jantzen, in the highest weights of the representations, how states in the cohomology, "singlet pairs", arise from unphysical states, "Kugo-Ojima quartets", as the perturbation is set to zero. This will enable us to identify and construct states in the cohomology. The ghost numbers that will occur are \pm p, with p uniquely determined by the representations of the algebras involved. Our construction is given in terms of the current modes and relies on the explicit form of highest weight null-states given by Malikov, Feigen and Fuchs
The ROSAT BRIGHT survey; 1, Identification of an AGN sample with hard ROSAT X-ray spectra

The ROSAT Bright Survey (RBS) aims to completely optically identify the more than 2000 brightest sources detected in the ROSAT all-sky survey at galactic latitudes |b| > 30 degr (excluding LMC, SMC, Virgo cluster). This paper presents a subsample of 66 bright point-like ROSAT survey sources with almost hard PSPC spectra, the hardness ratio HR1 is > 0.5 for most of the sources. The subsample could be nearly completely identified by low-resolution optical spectroscopy with the following breakdown into object classes: 31 Seyfert galaxies, 22 BL Lac candidates, 5 clusters of galaxies 1 cataclysmic variable, and 5 bright stars. Only one object remained unidentified and one X-ray source was a spurious detect ion. The redshift distribution peaks around 0.06 for the Seyferts and around 0.13 for the BL Lac candidates. Observations with medium spectral resolution were obtained for most of the new S eyfert galaxies. A large fraction (20 objects) are type 1 Seyfert galaxies, the other fraction includes Seyfert galaxies of type 1.5 - 1.8 (5 objects), two LINERs, and 4 possible narrow-line Seyfert 1 galaxies (NLS1). About one third of the new Seyfert's have nearby companion galaxies displaying either emission or absorption lines at the same redshift. Among them are a couple of systems showing direct morphological evidence for interaction. The large fraction of interacting galaxies among our sample suggests a scenario where interaction is the main trigger of AGN activity
Rotating NS5-brane solution and its exact string theoretical description

We construct the most general solution in type-II string theory that represents N coincident non-extremal rotating NS5-branes and determine the relevant thermodynamic quantities. We show that in the field theory limit, it has an exact description. In particular, it can be obtained by an O(3,3) duality transformation on the exact string background for the coset model SL(2,R)_{-N}/U(1) \times SU(2)_N. In the extreme supersymmetric limit we recover the multicenter solution, with a ring singularity structure, that has been discussed recently
Construction of BRST invariant states in $G/H$ WZNW models.

We study the cohomology arising in the BRST formulation of G/H gauged WZNW
models, i.e. in which the states of the gauged theory are projected out from
the ungauged one by means of a BRST condition. We will derive for a general
simple group $H$ with arbitrary level, conditions for which the cohomology is
non-trivial. We show, by introducing a small perturbation due to Jantzen, in
the highest weights of the representations, how states in the cohomology,
"singlet pairs", arise from unphysical states, "Kugo-Ojima quartets", as the
perturbation is set to zero. This will enable us to identify and construct
states in the cohomology. The ghost numbers that will occur are $\pm p$, with
$p$ uniquely determined by the representations of the algebras involved. Our
construction is given in terms of the current modes and relies on the explicit
form of highest weight null-states given by Malikov, Feigen and Fuchs.Comment: 12 pages, late
Matrix String Partition Functions

We evaluate quasi-classically the Ramond partition function of Euclidean D=10
U(N) super-Yang--Mills theory reduced to a two-dimensional torus. The result
can be interpreted in terms of free strings wrapping the space-time torus, as
expected from the point of view of Matrix string theory. We demonstrate that,
when extrapolated to the ultraviolet limit (small area of the torus), the
quasi-classical expressions reproduce exactly the recently obtained expression
for the partition of the completely reduced SYM theory, including the overall
numerical factor. This is an evidence that our quasi-classical calculation
might be exact.Comment: harvmac (b), 15 pages. v2 Cosmetic changes in the text and references
  adde
Topology and Phase Transitions I. Preliminary Results

In this first paper, we demonstrate a theorem that establishes a first step
toward proving a necessary topological condition for the occurrence of first or
second order phase transitions: we prove that the topology of certain
submanifolds of configuration space must necessarily change at the phase
transition point. The theorem applies to smooth, finite-range and confining
potentials V bounded below, describing systems confined in finite regions of
space with continuously varying coordinates. The relevant configuration space
submanifolds are both the level sets {\Sigma_v := V_N^{-1} (v)}_{v \in R} of
the potential function V_N and the configuration space submanifolds enclosed by
the \Sigma_{v} defined by {M_v := V_N^{-1} ((-\infty,v])}_{v \in R}, which are
labeled by the potential energy value v, and where N is the number of degrees
of freedom. The proof of the theorem proceeds by showing that, under the
assumption of diffeomorphicity of the equipotential hypersurfaces {\Sigma_v}_{v
\in R}, as well as of the ${M_v}_{v \in R}, in an arbitrary interval of values
for \vb=v/N, the Helmoltz free energy is uniformly convergent in N to its
thermodynamic limit, at least within the class of twice differentiable
functions, in the corresponding interval of temperature. This preliminary
theorem is essential to prove another theorem - in paper II - which makes a
stronger statement about the relevance of topology for phase transitions.Comment: 35 pages. This is an improved version of math-ph/0305032. Added minor
  chances: Title, Abstract, Introductio
Peptide adsorption to lipid bilayers : slow processes revealed by linear dichroism spectroscopy.

The adsorption and insertion kinetics for the association of two 34-residue cyclic peptides with phosphocholine membranes have been studied using circular and linear dichroism approaches. The two peptides studied are identical with the exception of two residues, which are both tyrosine in one of the peptides and tryptophan in the other. Both peptides adopt random coil conformations in solution in the absence of membranes and do not aggregate at concentrations below 20 PM. After addition to liposome dispersions, circular dichroism spectroscopy indicated that both peptides undergo an extremely rapid transformation to a beta-conformation that remains unchanged throughout the remainder of the experiment. Linear dichroism (LD) spectroscopy was used to study the kinetics of membrane adsorption and insertion. The data were analyzed by nonlinear least squares approaches, leading to identification of a number of bound states and their corresponding LD spectra. Two pseudo-first order processes could be identified that were common to both peptides. The first occurred with a time constant of the order of 1 min and led to a bound state characterized by weak LD signals, with significant bands corresponding to the transitions of aromatic side chains. The second process occurred with an unusually long time constant of between 75 and 100 min, forming a state with considerably stronger positive LD absorbance in the far-ultraviolet region of the spectrum. For the tyrosine-substituted peptide, a third slow process with a long time constant (76 min) could also be delineated and was attributed to rearrangements of the peptide within the membrane
Affine Toda field theories related to Coxeter groups of noncrystallographic type

We propose affine Toda field theories related to the non-crystallographic Coxeter groups H_2, H_3 and H_4. The classical mass spectrum, the classical three-point couplings and the one-loop corrections to the mass renormalisation are determined. The construction is carried out by means of a reduction procedure from crystallographic to non-crystallographic Coxeter groups. The embedding structure explains for various affine Toda field theories that their particles can be organised in pairs, such that their relative masses differ by the golden ratio
Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of on- going abnormal mutational processes, consistent with field-effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissue or between different ERG-lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases
Mapping the energy and diffusion landscapes of membrane proteins at the
  cell surface using high-density single-molecule imaging and Bayesian
  inference: application to the multi-scale dynamics of glycine receptors in
  the neuronal membrane

Protein mobility is conventionally analyzed in terms of an effective
diffusion. Yet, this description often fails to properly distinguish and
evaluate the physical parameters (such as the membrane friction) and the
biochemical interactions governing the motion. Here, we present a method
combining high-density single-molecule imaging and statistical inference to
separately map the diffusion and energy landscapes of membrane proteins across
the cell surface at ~100 nm resolution (with acquisition of a few minutes).
When applying these analytical tools to glycine neurotransmitter receptors
(GlyRs) at inhibitory synapses, we find that gephyrin scaffolds act as shallow
energy traps (~3 kBT) for GlyRs, with a depth modulated by the biochemical
properties of the receptor-gephyrin interaction loop. In turn, the inferred
maps can be used to simulate the dynamics of proteins in the membrane, from the
level of individual receptors to that of the population, and thereby, to model
the stochastic fluctuations of physiological parameters (such as the number of
receptors at synapses). Overall, our approach provides a powerful and
comprehensive framework with which to analyze biochemical interactions in
living cells and to decipher the multi-scale dynamics of biomolecules in
complex cellular environments.Comment: 23 pages, 4 figure
Associated $W^{\pm}D^{(*)}$ production at the LHC and prospects to
  observe double parton interactions

Associated production of charged gauge bosons and charged charmed mesons at
the LHC is considered in the framework of $k_T$-factorization approach.
Theoretical predictions are compared with ATLAS data, and reasonably good
agreement is found. Predictions on the same-sign $W^{\pm}D^{\pm}$
configurations are presented including single parton scattering and double
parton scattering contributions. The latter are shown to dominate over the
former, thus giving evidence that the proposed process can serve as another
indicator of double parton interactions.Comment: 5 pages, 1 figur
Chern-Simons-Higgs Theory with Visible and Hidden Sectors and its ${\cal
  N}=2$ SUSY Extension

We study vortex solutions in Abelian Chern-Simons-Higgs theories with visible
and hidden sectors. We first consider the case in which the two sectors are
connected through a BF-like gauge mixing term with no explicit interaction
between the the two scalars. Since first order Bogomolny equations do not exist
in this case, we derive the second order field equations. We then proceed to an
${\cal N}=2$ supersymmetric extension including a Higgs portal mixing among the
visible and hidden charged scalars. As expected, Bogomolnyi equations do exist
in this case and we study their string-like solutions numerically.Comment: 10 pages, 12 figures. Several typos fixed and the Gauss law is
  explicitly written, figures correctly shown. Accepted in PL
The 106Cd(??, ??)106Cd elastic scattering in a wide energy range for ?? process studies

Date of Acceptance: 15/04/2015Alpha elastic scattering angular distributions of the <sup>106</sup>Cd(??, ??)<sup>106</sup>Cd reaction were measured at three energies around the Coulomb barrier to provide a sensitive test for the ?? + nucleus optical potential parameter sets. Furthermore, the new high precision angular distributions, together with the data available from the literature were used to study the energy dependence of the locally optimized ?? + nucleus optical potential in a wide energy region ranging from E<inf>Lab</inf>=27.0MeV down to 16.1 MeV.The potentials under study are a basic prerequisite for the prediction of ??-induced reaction cross sections and thus, for the calculation of stellar reaction rates used for the astrophysical ?? process. Therefore, statistical model predictions using as input the optical potentials discussed in the present work are compared to the available <sup>106</sup>Cd + alpha cross section data
The TREAT-NMD DMD Global Database: analysis of more than 7,000 Duchenne muscular dystrophy mutations.

Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations)
A density spike on astrophysical scales from an N -field waterfall transition

Hybrid inflation models are especially interesting as they lead to a spike in the density power spectrum on small scales, compared to the CMB, while also satisfying current bounds on tensor modes. Here we study hybrid inflation with N waterfall fields sharing a global SO(N) symmetry. The inclusion of many waterfall fields has the obvious advantage of avoiding topologically stable defects for N>3 . We find that it also has another advantage: it is easier to engineer models that can simultaneously (i) be compatible with constraints on the primordial spectral index, which tends to otherwise disfavor hybrid models, and (ii) produce a spike on astrophysically large length scales. The latter may have significant consequences, possibly seeding the formation of astrophysically large black holes. We calculate correlation functions of the time-delay, a measure of density perturbations, produced by the waterfall fields, as a convergent power series in both 1/N and the field's correlation function Δ(x) . We show that for large N , the two-point function is 〈δt(x)δt(0)〉∝Δ2(|x|)/N and the three-point function is 〈δt(x)δt(y)δt(0)〉∝Δ(|x−y|)Δ(|x|)Δ(|y|)/N2 . In accordance with the central limit theorem, the density perturbations on the scale of the spike are Gaussian for large N and non-Gaussian for small N
On the relationship between hierarchy and type morphisms

23 páginas, 1 figura.-- El pdf del artículo es el documento de trabajo.Here, we establish a relationship between hierarchy and type morphisms. Both concepts have been used to relate the types in one structure to types in a second "larger" structure. In general, the two concepts may differ, in the sense that a hierarchy morphism need not be a type morphism. We provide a necessary and sufficient condition under which the two concepts coincide. We go on to provide situations under which this condition must be satisfiedMeier was supported by the Spanish Ministerio de Educación y Ciencia via a Ramon y Cajal\ud
Fellowship (IAE-CSIC) and Research Grant SEJ 2006-02079
Integrating biological information for enhanced function annotation of serine proteases in Drosophila melanogaster

Uncovering functional associations for genes and gene products is a significant challenge. Studies have emerged that employ knowledge-based procedures to extract functional data for genes from a variety of biological sources. However, data derived from a single biological resource often provides only a limited perspective on their functional associations largely due to systematic bias in the underlying data. The post-genomic era has seen the emergence of studies that aim to infer functional associations by combining many biological evidence types. These are expected to provide better insights into the functional aspects of diverse genes, genomes and networks.PRIB 2008 proceedings found at: http://dx.doi.org/10.1007/978-3-540-88436-
Using signature sequences to classify intersection curves of two quadrics

We present a method that uses signature sequences to classify the intersection curve of two quadrics (QSIC) or, equivalently, quadric pencils in PR3 (3D real projective space), in terms of the shape, topological properties, and algebraic properties of the QSIC. Specifically, for a QSIC we consider its singularity, reducibility, the number of its components, and the degree of each irreducible component, etc. There are in total 35 different types of non-degenerate quadric pencils. For each of the 35 types of QSICs given by these non-degenerate pencils, through a detailed study of the eigenvalue curve and the index function jump we establish a characterizing algebraic condition expressed in terms of the Segre characteristics and the signature sequence of the quadric pencil. We show how to compute a signature sequence with rational arithmetic and use it to determine the type of the intersection curve of any two quadrics which form a non-degenerate pencil. As an example of application, we discuss how to apply our results to collision detection of cones in 3D affine space. © 2008.preprin