pinecone/core-2020-05-10-deduplication huggingface dataset:
Exact and efficient calculation of Lagrange multipliers in constrained
  biological polymers: Proteins and nucleic acids as example cases

In order to accelerate molecular dynamics simulations, it is very common to
impose holonomic constraints on their hardest degrees of freedom. In this way,
the time step used to integrate the equations of motion can be increased, thus
allowing, in principle, to reach longer total simulation times. The imposition
of such constraints results in an aditional set of Nc equations (the equations
of constraint) and unknowns (their associated Lagrange multipliers), that must
be solved in one way or another at each time step of the dynamics. In this work
it is shown that, due to the essentially linear structure of typical biological
polymers, such as nucleic acids or proteins, the algebraic equations that need
to be solved involve a matrix which is banded if the constraints are indexed in
a clever way. This allows to obtain the Lagrange multipliers through a
non-iterative procedure, which can be considered exact up to machine precision,
and which takes O(Nc) operations, instead of the usual O(Nc3) for generic
molecular systems. We develop the formalism, and describe the appropriate
indexing for a number of model molecules and also for alkanes, proteins and
DNA. Finally, we provide a numerical example of the technique in a series of
polyalanine peptides of different lengths using the AMBER molecular dynamics
package.Comment: 29 pages, 10 figures, 1 tabl
A Transport Analysis of the BEEM Spectroscopy of Au/Si Schottky Barriers

A systematic transport study of the ballistic electron emission microscopy
(BEEM) of Au/Si(100) and Au/Si(111) Schottky barriers for different thicknesses
of the metal layer and different temperatures is presented. It is shown that
the existing experimental data are compatible with a recently predicted
bandstructure-induced non-forward electron propagation through the Au(111)
layer.Comment: 5 pages, Latex-APS, 1 postscript figure,
  http://www.icmm.csic.es/Pandres/pedro.htm. Phys. Stat. Sol. (b) (to appear),
  HCIS-10 Conf, Berlin 199
General non-rotating perfect-fluid solution with an abelian spacelike
  C_3 including only one isometry

The general solution for non-rotating perfect-fluid spacetimes admitting one
Killing vector and two conformal (non-isometric) Killing vectors spanning an
abelian three-dimensional conformal algebra (C_3) acting on spacelike
hypersurfaces is presented. It is of Petrov type D; some properties of the
family such as matter contents are given. This family turns out to be an
extension of a solution recently given in \cite{SeS} using completely different
methods. The family contains Friedman-Lema\^{\i}tre-Robertson-Walker particular
cases and could be useful as a test for the different FLRW perturbation
schemes. There are two very interesting limiting cases, one with a non-abelian
G_2 and another with an abelian G_2 acting non-orthogonally transitively on
spacelike surfaces and with the fluid velocity non-orthogonal to the group
orbits. No examples are known to the authors in these classes.Comment: Submitted to GRG, Latex fil
Open problems in forward-backward multiplicity correlations in
  hadron-hadron collisions in the TeV region

Continuing previous work on forward-backward multiplicity correlation
properties in proton-proton collisions in the framework of the weighted
superposition model of two components (each one described by a negative
binomial multiplicity distribution) with the addition of the leakage parameter
which controls clan spreading from one hemisphere to the opposite one, we
examine E735 data on the c.m. energy dependence of the total correlation
strength and of the forward variance at fixed total multiplicity. A comparison
with the Chou-Yang approach to the problem is presented and extrapolations of
the mentioned variables at LHC c.m. energy in possible scenarios in the new
energy domain are discussed.Comment: 7 pages, 4 figure
The Mice at play in the CALIFA survey: A case study of a gas-rich major
  merger between first passage and coalescence

We present optical integral field spectroscopy (IFS) observations of the
Mice, a major merger between two massive (>10^11Msol) gas-rich spirals NGC4676A
and B, observed between first passage and final coalescence. The spectra
provide stellar and gas kinematics, ionised gas properties and stellar
population diagnostics, over the full optical extent of both galaxies. The Mice
provide a perfect case study highlighting the importance of IFS data for
improving our understanding of local galaxies. The impact of first passage on
the kinematics of the stars and gas has been significant, with strong bars
likely induced in both galaxies. The barred spiral NGC4676B exhibits a strong
twist in both its stellar and ionised gas disk. On the other hand, the impact
of the merger on the stellar populations has been minimal thus far: star
formation induced by the recent close passage has not contributed significantly
to the global star formation rate or stellar mass of the galaxies. Both
galaxies show bicones of high ionisation gas extending along their minor axes.
In NGC4676A the high gas velocity dispersion and Seyfert-like line ratios at
large scaleheight indicate a powerful outflow. Fast shocks extend to ~6.6kpc
above the disk plane. The measured ram pressure and mass outflow rate
(~8-20Msol/yr) are similar to superwinds from local ULIRGs, although NGC4676A
has only a moderate infrared luminosity of 3x10^10Lsol. Energy beyond that
provided by the mechanical energy of the starburst appears to be required to
drive the outflow. We compare the observations to mock kinematic and stellar
population maps from a merger simulation. The models show little enhancement in
star formation during and following first passage, in agreement with the
observations. We highlight areas where IFS data could help further constrain
the models.Comment: 23 pages, 13 figures, accepted to A&A. A version with a complete set
  of high resolution figures is available here:
  http://www-star.st-and.ac.uk/~vw8/resources/mice_v8_astroph.pd
Thermoelectric DC conductivities from black hole horizons

An analytic expression for the DC electrical conductivity in terms of black
hole horizon data was recently obtained for a class of holographic black holes
exhibiting momentum dissipation. We generalise this result to obtain analogous
expressions for the DC thermoelectric and thermal conductivities. We illustrate
our results using some holographic Q-lattice black holes as well as for some
black holes with linear massless axions, in both $D=4$ and $D=5$ bulk spacetime
dimensions, which include both spatially isotropic and anisotropic examples. We
show that some recently constructed ground states of holographic Q-lattices,
which can be either electrically insulating or metallic, are all thermal
insulators.Comment: 29 pages. Very minor changes; published versio
Top Partner Discovery in the $T\to tZ$ channel at the LHC

In this paper we study the discovery potential of the LHC run II for heavy
vector-like top quarks in the decay channel to a top and a $Z$ boson. Despite
the usually smaller branching ratio compared to charged-current decays, this
channel is rather clean and allows for a complete mass reconstruction of the
heavy top. The latter is achieved in the leptonic decay channel of the $Z$
boson and in the fully hadronic top channel using boosted jet and jet
substructure techniques. To be as model-independent as possible, a simplified
model approach with only two free parameters has been applied. The results are
presented in terms of parameter space regions for $3\sigma$ evidence or
$5\sigma$ discovery for such new states in that channel.Comment: 24 pages, 8 figures, version 2 updated to JHEP 01 (2015) 08
Photoproduction of pi+ pi- pairs in a model with tensor-pomeron and
  vector-odderon exchange

We consider the reaction (gamma p) to (pi+ pi- p) at high energies. Our
description includes dipion production via the resonances rho, omega, rho-prime
and f2, and via non-resonant mechanisms. The calculation is based on a model of
high energy scattering with the exchanges of photon, pomeron, odderon and
reggeons. The pomeron and the C=+1 reggeons are described as effective tensor
exchanges, the odderon and the C=-1 reggeons as effective vector exchanges. We
obtain a gauge-invariant version of the Drell-Soeding mechanism which produces
the skewing of the rho-meson shape. Starting from the explicit formulae for the
matrix element for dipion production we construct an event generator which
comprises all contributions mentioned above and includes all interference
terms. We give examples of total and differential cross sections and discuss
asymmetries which are due to interference of C=+1 and C=-1 exchange
contributions. These asymmetries can be used to search for odderon effects. Our
model is intended to provide all necessary theoretical tools for a detailed
experimental analysis of elastic dipion production for which data exist from
fixed target experiments, from HERA, and are now being collected by LHC
experiments.Comment: 49 page
A chiral SU(N) gauge theory and its non-chiral Spin(8) dual

We study supersymmetric SU(N-4) gauge theories with a symmetric tensor and N antifundamental representations. The theory with W=0 has a dual description in terms of a non-chiral Spin(8) theory with one spinor and N vectors. This duality flows to the SO(N) duality of Seiberg and to a duality proposed by one of us. It also flows to dualities for a number of Spin(m) theories, m\le 8. For N=6, when an {\cal N}=2 SUSY superpotential is added, the singularities of Seiberg and Witten are recovered. For N\le 6, a mass for the spinor generates the branches of SO(8) theories found by Intriligator and Seiberg. Other phenomena include a classical constraint mapped to an anomaly equation under duality and an intricate consistency check on the renormalization group flow
Massive Relativistic Particle Model with Spin and Electric Charge from
  Two-Twistor Dynamics

The sixteen real coordinates of two-twistor space are transformed by a
nonlinear mapping into an enlarged space-time framework. The standard
relativistic phase space of coordinates $(X_\mu, P_\mu)$ is supplemented by a
six-parameter spin phase manifold (two pairs $(\eta_\alpha,\sigma_\alpha)$ and
$(\bar{\eta}_{\dot\alpha}, \bar{\sigma}_{\dot{\alpha}})$ of canonically
conjugated Weyl spinors constrained by two second class constraints) and the
electric charge phase space ($e,\phi$). The free two-twistor classical
mechanics is rewritten in this enlarged relativistic phase space as a model for
a relativistic particle. Definite values for the mass, spin and the electric
charge of the particle are introduced by means of three first class
constraints.Comment: LaTeX, 15 pages. A clarifying comment and a formula added. To appear
  in PL
Field theory limit of branes and gauged supergravities

We discuss the field theory limit of Dp-branes. In this limit, the black Dp-brane solution approaches a solution which is conformal to adS_{p+2} \times S^{8-p}. We argue that the frame in which the conformal factor is equal to one, the dual frame, is a `holographic' frame. The radial coordinate of adS_{p+2} provides a UV/IR connection as in the case of the D3 brane. The gravitational description involves gauged supergravities, typically with non-compact gauge groups. The near-horizon Dp-brane solution becomes a domain-wall solution of the latter
Predictions of striking energy and angular dependence in pp -->
  (pp)_S-wave pi^0 production

A phenomenological calculation from threshold to 800 MeV of the initial
proton beam energy is presented to describe recent data on the reaction pp -->
(pp)_S-wave pi^0 with a low energy cut on the final state diproton excitation
energy. A strong forward dip is obtained in the differential cross section as
in the data from COSY at 800 MeV, although the absolute value of the forward
cross section is too low. Earlier low energy data from CELSIUS are reasonably
well reproduced. In the unexplored energy interval between these two
experiments the model predicts a spectacular energy dependence both in the
forward direction and in the angle-integrated cross section.Comment: 9 pages, 4 figure
A review of energy storage technologie sfor marine current energy systems

Increasing concerns about the depletion of fossil resources and the issue of environment lead to a global need for producing more clean energy from renewable sources. Ocean is appreciated as a vast source of renewable energies. Considering marine renewable energies, it can be noticed that significant electrical power can be extracted from marine tidal currents. However, the power harnessed from marine tidal currents is highly fluctuant due to the swell effect and the periodicity of the tidal phenomenon. To improve the power quality and make the marine generation system more reliable, energy storage systems can play a crucial role. In this paper, an overview and the state of art of energy storage technologies are presented. Characteristics of various energy storage technologies are analyzed and compared for this particular application. The comparison shows that high-energy batteries like sodium–sulphur battery and flow battery are favorable for smoothing the long-period power fluctuation due to the tide phenomenon while supercapacitor and flywheel are more suitable for eliminating short-period power disturbances due to swell or turbulence phenomena. This means that hybrid storage technologies are needed for achieving optimal results in tidal marine current energy applications.This work was funded by BMO (Brest Métropole Océane
'Exotic vector-like pair' of color-triplet scalars

We propose a minimal extension of Standard Model, generating a Majorana mass
for neutron, connected with a mechanism of Post-Sphaleron Baryogenesis. We
consider an `exotic vector-like pair' of color-triplet scalars, an extra
Majorana fermion $\psi$, and a scalar field $\phi$, giving mass to $\psi$. The
vector-like pair is defined `exotic' because of a peculiar mass term of the
color-triplet scalars, violating Baryon number as $\Delta B=1$. A
Post-Sphaleron Baryogenesis is realized through $\phi$-decays into six quarks
(antiquarks), or through $\psi$-decays into three quarks (antiquarks). This
model suggests some intriguing B-violating signatures, testable in the next
future, in Neutron-Antineutron physics and LHC. We also discuss limits from
FCNC.
  Sterile fermion can also be light as $1-100\, \rm GeV$. In this case, the
sterile fermion could be (meta)-stable and $n-\bar{n}$ oscillation can be
indirectly generated by two $n-\psi$, $\psi-\bar{n}$ oscillations, without
needing of an effective Majorana mass for neutron. Majorana fermion $\psi$ can
be a good candidate for WIMP-like dark matter.Comment: Sections 2.1 and 3 revisited; New Fig.5 of jj+Missing Energy channel;
  more references about LHC and FCNCs. Essential results on Neutron-Antineutron
  oscillations and Post-Sphaleron Baryogenesis are the same. More comments
  about string-inspred models. Accepted by JHE
Search for a CP-odd Higgs boson decaying to $Zh$ in $pp$ collisions at
  $\sqrt{s} = 8$ TeV with the ATLAS detector

A search for a heavy, CP-odd Higgs boson, $A$, decaying into a $Z$ boson and
a 125 GeV Higgs boson, $h$, with the ATLAS detector at the LHC is presented.
The search uses proton--proton collision data at a centre-of-mass energy of 8
TeV corresponding to an integrated luminosity of 20.3 fb$^{-1}$. Decays of
CP-even $h$ bosons to $\tau\tau$ or $bb$ pairs with the $Z$ boson decaying to
electron or muon pairs are considered, as well as $h \rightarrow bb$ decays
with the $Z$ boson decaying to neutrinos. No evidence for the production of an
$A$ boson in these channels is found and the 95% confidence level upper limits
derived for $\sigma (gg\rightarrow A) \times \mbox{BR}(A \rightarrow Zh) \times
\mbox{BR}(h \rightarrow f\bar{f})$ are 0.098--0.013 pb for $f=\tau$ and
0.57--0.014 pb for $f=b$ in a range of $m_A =$ 220--1000 GeV. The results are
combined and interpreted in the context of two-Higgs doublet models.Comment: 13 pages plus author list + cover pages (30 pages total), 5 figures,
  2 tables, submitted to Phys. Lett. B, All figures including auxiliary figures
  are available at
  https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HIGG-2013-06
Search for a pseudoscalar boson decaying into a Z boson and the 125 GeV
  Higgs boson in llbb final states

Results are reported on a search for decays of a pseudoscalar A boson into a
Z boson and a light scalar h boson, where the Z boson decays into a pair of
oppositely-charged electrons or muons, and the h boson decays into b anti-b.
The search is based on data from proton-proton collisions at a center-of-mass
energy sqrt(s)=8 TeV collected with the CMS detector, corresponding to an
integrated luminosity of 19.7 inverse femtobarns. The h boson is assumed to be
the standard model-like Higgs boson with a mass of 125 GeV. With no evidence
for signal, upper limits are obtained on the product of the production cross
section and the branching fraction of the A boson in the Zh channel. Results
are also interpreted in the context of two Higgs doublet models.Comment: Replaced with published version. Added journal referenc
Quantization of BMS$_3$ orbits: a perturbative approach

We compute characters of the BMS group in three dimensions. The approach is
the same as that performed by Witten in the case of coadjoint orbits of the
Virasoro group in the eighties, within the large central charge approximation.
The procedure involves finding a Poisson bracket between classical variables
and the corresponding commutator of observables in a Hilbert space, explaining
why we call this a quantization. We provide first a pedagogical warm up by
applying the method to both SL(2,R) and Poincar\'{e}3 groups. As for BMS3, our
results coincide with the characters of induced representations recently
studied in the literature. Moreover, we relate the 'coadjoint representations'
to the induced representations.Comment: 17 pages. v2: references added. v3: minor changes and published in
  Nucelar Physics
Alpha induced reaction cross section measurements on 162Er for the astrophysical ?? process

Funding Details: NSF, National Science Foundation. ??2014 Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/). Funded by SCOAP3The cross sections of the Er162(??,??)Yb166 and Er162(??,n)Yb165 reactions have been measured for the first time. The radiative alpha capture reaction cross section was measured from Ec.m.=16.09MeV down to Ec.m.=11.21MeV, close to the astrophysically relevant region (which lies between 7.8 and 11.48 MeV at 3 GK stellar temperature). The Er162(??,n)Yb165 reaction was studied above the reaction threshold between Ec.m.=12.19 and 16.09MeV. The fact that the Er162(??,??)Yb166 cross sections were measured below the (??,n) threshold at first time in this mass region opens the opportunity to study directly the ??-widths required for the determination of astrophysical reaction rates. The data clearly show that compound nucleus formation in this reaction proceeds differently than previously predicted. ?? 2014 Elsevier B.V
WASP-52b, WASP-58b, WASP-59b, and WASP-60b : four new transiting close-in giant planets

The research leading to these results received funding from the European Communitys Seventh Framework Programme (FP7/2007-2013) under grant agreement number RG226604 (OPTICON), as well as the Programme National de Planétologie (PNP) of CNRS/INSU (France).We present the discovery of four new transiting hot Jupiters, detected mainly from SuperWASP-North and SOPHIE observations. These new planets, WASP-52b, WASP-58b, WASP-59b, and WASP-60b, have orbital periods ranging from 1.7 to 7.9 days, masses between 0.46 and 0.94 MJup, and radii between 0.73 and 1.49 RJup. Their G1 to K5 dwarf host stars have V magnitudes in the range 11.7−13.0. The depths of the transits are between 0.6 and 2.7%, depending on the target. With their large radii, WASP-52b and WASP-58b are new cases of low-density, inflated planets, whereas WASP-59b is likely to have a large, dense core. WASP-60 shows shallow transits. In the case of WASP-52 we also detected the Rossiter-McLaughlin anomaly via time-resolved spectroscopy of a transit. We measured the sky-projected obliquity λ = 24° +17-9, indicating that WASP-52b orbits in the same direction as its host star is rotating and that this prograde orbit is slightly misaligned with the stellar equator. These four new planetary systems increase our statistics on hot Jupiters and provide new targets for follow-up studies.Publisher PDFPeer reviewe
Psychophysiology, task complexity, and team factors determine emergency response teams' shared beliefs

In field settings where the objective truth is not known, the extent to which you have the same understanding of the situation as your team leader may be used as an indicator for a team’s situation awareness. Two experiments showed emergency response team members’ degree of shared beliefs (measured as a ‘similarity index’) to be associated with which team they are in, but not with which position they have in the team. This indicates that factors specific to the teams, e.g. the leader’s behavior, the team’s shared experience, or communication patterns, are important for a team’s situation awareness. In the second experiment, task complexity was manipulated with a scripted scenario design and heart rate variability was measured as an indicator of executive function. Shared beliefs were shown to be associated with the degree of high frequency modulation of heart rate variability. Further, shared beliefs were associated with the designed task complexity for some teams. The experiments showed no association between the measure of shared beliefs and subjective reports of situation awareness
TEM and XPS studies of nanocrystals and clusters in nanostructured materials used for memory storage applications

Nanoscaled electronic devices have attracted much attention due to their optical and electronic properties, especially related to MOS (Metal-Oxide-Semiconductor) devices used for memory storage applications. Improved electrical properties, longer retention, lower gate voltage and lower power consumption are assumed to be possible when replacing bulk floating gate in flash memory devices with nanocrystals. Multilayer samples with Si, Ge, Er-oxide, and Pd nanocrystals and clusters were studied in detail. The nucleation, distribution, defects, composition, and atomic and electronic structure are important factors to understand in order to improve performance of memory storage devices. These parameters were studied by high resolution transmission electron microscopy, energy filtered transmission electron microscopy, electron energy loss spectroscopy, X-ray photoelectron spectroscopy, energy dispersive spectroscopy, and secondary ion-mass spectrometry
The C-terminal domain of eukaryotic initiation factor 5 promotes start codon recognition by its dynamic interplay with eIF1 and eIF2 beta

Recognition of the proper start codon on mRNAs is essential for protein synthesis, which requires scanning and involves eukaryotic initiation factors (eIFs) eIF1, eIF1A, eIF2, and eIF5. The carboxyl terminal domain (CTD) of eIF5 stimulates 43S preinitiation complex (PIC) assembly; however, its precise role in scanning and start codon selection has remained unknown. Using nuclear magnetic resonance (NMR) spectroscopy, we identified the binding sites of eIF1 and eIF2β on eIF5-CTD and found that they partially overlapped. Mutating select eIF5 residues in the common interface specifically disrupts interaction with both factors. Genetic and biochemical evidence indicates that these eIF5-CTD mutations impair start codon recognition and impede eIF1 release from the PIC by abrogating eIF5-CTD binding to eIF2β. This study provides mechanistic insight into the role of eIF5-CTD's dynamic interplay with eIF1 and eIF2β in switching PICs from an open to a closed state at start codons