pinecone/core-2020-05-10-deduplication huggingface dataset:
Kinetics of microribbon formation in a simplified model of amelogenin
  biomacromolecules

We show that the kinetics of microribbon formation of amelogenin molecules is
well described by a combination of translational and rotational diffusion of a
simplified anisotropic bipolar model consisting of hydrophobic spherical
colloid particles and a point charge located on each particle surface. The
colloid particles interact via a standard depletion attraction while the point
charges interact through a screened Coulomb repulsion. We study the kinetics
via a Brownian dynamics simulation of both translational and rotational motions
and show that the anisotropy brought in by the charge dramatically affects the
kinetic pathway of cluster formation and our simple model captures the main
features of the experimental observations.Comment: 4 pages, 5 figure
A jet-disk symbiosis model for Gamma Ray Bursts: fluence distribution,
  CRs and $\nu$'s

We consider a jet-disk symbiosis model to explain Gamma Ray Bursts and their
afterglows. It is proposed that GRBs are created inside a pre-existing jet from
a neutron star in a binary system which collapses to a black hole due to
accretion. In our model we assume that a fraction of the initial energy due to
this transition is deposited in the jet by magnetic fields. The observed
emission is then due to an ultrarelativistic shock wave propagating along the
jet. Good agreement with observational data can be obtained for systems such as
the Galactic jet source SS433. Specifically, we are able to reproduce the
typical observed afterglow emission flux, its spectrum as a function of time,
and the fluence distribution of the corrected data for the 4B BATSE catalogue.
We also studied the relation between the cosmological evolution of our model
and the cosmic ray energy distribution. We used the Star Formation Rate (SFR)
as a function of redshift to obtain the distribution in fluences of GRBs in our
model. The fluence in the gamma ray band has been used to calculate the energy
in cosmic rays both in our Galaxy and at extragalactic distances. This energy
input has been compared with the Galactic and extragalactic spectrum of cosmic
rays and neutrinos. We found that in the context of our model it is not
possible to have any contribution from GRBs to either the extragalactic or the
Galactic cosmic ray spectra.Comment: 5 pages, 2 pictures, to appear in Proceedings of the 10th Annual
  October Astrophysics Conference in Maryland: Cosmic Explosion
Theory of tunable pH sensitive vesicles of anionic and cationic lipids
  or anionic and neutral lipids

The design of vesicles which become unstable at an easily tuned value of pH
is of great interest for targeted drug delivery. We present a microscopic
theory for two forms of such vesicles. A model of lipids introduced by us
previously is applied to a system of ionizable, anionic lipid, and permanently
charged, cationic lipid. We calculate the pH at which the lamellar phase
becomes unstable with respect to an inverted hexagonal one, a value which
depends continuously on the system composition. Identifying this instability
with that displayed by unilamellar vesicles undergoing fusion, we obtain very
good agreement with the recent experimental data of Hafez et al., Biophys. J.
2000 79: 1438-1446, on the pH at which fusion occurs vs. vesicle composition.
We explicate the mechanism in terms of the role of the counter ions. This
understanding suggests that a system of a neutral, non lamellar forming lipid
stabilized by an anionic lipid would serve equally well for preparing tunable,
pH sensitive vesicles. Our calculations confirm this. Further, we show that
both forms of vesicle have the desirable feature of exhibiting a regime in
which the pH at instability is a rapidly varying function of the vesicle
composition.Comment: five figures, to appear in Biophys.
Sharp bounds on $2m/r$ of general spherically symmetric static objects

In 1959 Buchdahl \cite{Bu} obtained the inequality $2M/R\leq 8/9$ under the
assumptions that the energy density is non-increasing outwards and that the
pressure is isotropic. Here $M$ is the ADM mass and $R$ the area radius of the
boundary of the static body. The assumptions used to derive the Buchdahl
inequality are very restrictive and e.g. neither of them hold in a simple soap
bubble. In this work we remove both of these assumptions and consider
\textit{any} static solution of the spherically symmetric Einstein equations
for which the energy density $\rho\geq 0,$ and the radial- and tangential
pressures $p\geq 0$ and $p_T,$ satisfy $p+2p_T\leq\Omega\rho, \Omega>0,$ and we
show that $$\sup_{r>0}\frac{2m(r)}{r}\leq
\frac{(1+2\Omega)^2-1}{(1+2\Omega)^2},$$ where $m$ is the quasi-local mass, so
that in particular $M=m(R).$ We also show that the inequality is sharp. Note
that when $\Omega=1$ the original bound by Buchdahl is recovered. The
assumptions on the matter model are very general and in particular any model
with $p\geq 0$ which satisfies the dominant energy condition satisfies the
hypotheses with $\Omega=3.$Comment: 28 pages, typos corrected and the analogy in section 4 is presented
  slightly differentl
Heavy Quark Parameters and Vcb from Spectral Moments in Semileptonic B
  Decays

We extract the heavy quark masses and non-perturbative parameters from the
Delphi preliminary measurements of the first three moments of the charged
lepton energy and hadronic mass distributions in semileptonic B decays, using a
multi-parameter fit. We adopt two formalisms, one of which does not rely on a
1/mc expansion and makes use of running quark masses. The data are consistent
and the level of accuracy of the experimental inputs largely determines the
present sensitivity. The results allow to improve on the uncertainty in the
extraction of Vcb.Comment: 13 pages, 2 figure
Decay Constants of $D_{sJ}^*$(2317) and $D_{sJ}$(2460)

The resonances $D_{sJ}^*$(2317) and $D_{sJ}$(2460) which are considered to be
the $(0^+,1^+)$ doublet composed of charm and strange quarks have been
discovered recently. Using the method of Rosner which is based on the
factorization hypothesis, we calculate the lower bounds of the decay constants
of these states from the branching ratios of $B\to D D_{sJ}$ measured by Belle
and Babar.Our result shows that the decay constant of $D_{sJ}$(2460) is about
twice that of $D_{sJ}^*$(2317) on the contrary to the naive expectation of the
heavy quark symmetry which gives their equality. We show that this big
deviation originates from the large internal motion of quarks inside these
$P$-wave states and that our result is in good accord with the relativistic
quark model calculation
A relative Szemer\'edi theorem

The celebrated Green-Tao theorem states that there are arbitrarily long
arithmetic progressions in the primes. One of the main ingredients in their
proof is a relative Szemer\'edi theorem which says that any subset of a
pseudorandom set of integers of positive relative density contains long
arithmetic progressions.
  In this paper, we give a simple proof of a strengthening of the relative
Szemer\'edi theorem, showing that a much weaker pseudorandomness condition is
sufficient. Our strengthened version can be applied to give the first relative
Szemer\'edi theorem for $k$-term arithmetic progressions in pseudorandom
subsets of $\mathbb{Z}_N$ of density $N^{-c_k}$.
  The key component in our proof is an extension of the regularity method to
sparse pseudorandom hypergraphs, which we believe to be interesting in its own
right. From this we derive a relative extension of the hypergraph removal
lemma. This is a strengthening of an earlier theorem used by Tao in his proof
that the Gaussian primes contain arbitrarily shaped constellations and, by
standard arguments, allows us to deduce the relative Szemer\'edi theorem.Comment: 22 page
Morphological Parameters of Spitzer Survey of Stellar Structure in
  Galaxies (S4G)

The morphology of galaxies can be quantified to some degree using a set of
scale-invariant parameters. Concentration (C), Asymmetry (A), Smoothness (S),
the Gini index (G), relative contribution of the brightest pixels to the second
order moment of the flux (M20), ellipticity (E), and the Gini index of the
second order moment (GM) have all been applied to morphologically classify
galaxies at various wavelengths. Here we present a catalog of these parameters
for the Spitzer Survey of Stellar Structure in Galaxies (S4G), a volume-limited
near-infrared imaging survey of nearby galaxies using the 3.6 and 4.5 micron
channels of the IRAC camera. Our goal is to provide a reference catalog of
near-infrared quantified morphology for high-redshift studies and galaxy
evolution models with enough detail to resolve stellar mass morphology.
  We explore where normal, non-interacting galaxies -those typically found on
the Hubble tuning fork- lie in this parameter space and show that there is a
tight relation between Concentration and M20 for normal galaxies. M20 can be
used to classify galaxies into earlier and later types (e.g., to separate
spirals from irregulars). Several criteria using these parameters exist to
select systems with a disturbed morphology, i.e., those that appear to be
undergoing a tidal interaction. We examine the applicability of these criteria
to Spitzer near-infrared imaging. We find that four relations, based on the
parameters A&S, G&M20, GM, and C&M20, respectively, select outliers in the
morphological parameter space, but each selects different subsets of galaxies.
Two criteria (GM > 0.6, G > -0.115 x M20 + 0.384) seem most appropriate to
identify possible mergers and the merger fraction in near-infrared surveys. We
find no strong relation between lopsidedness and most of these morphological
parameters, except for a weak dependence of lopsidedness on Concentration and
M20.Comment: 22 pages, 19 figures, 7 tables. Full catalogs available on request.
  Accepted by Ap
Non-Bunch-Davies Initial State Reconciles Chaotic Models with BICEP and
  Planck

The BICEP2 experiment has announced a signal for primordial gravity waves
with tensor-to-scalar ratio $r=0.2^{+0.07}_{-0.05}$ [arXiv:1403.3985]. There
are two ways to reconcile this result with the latest Planck experiment
[arXiv:1303.5082]. One is by assuming that there is a considerable tilt of $r$,
$\mathcal{T}_r$, with a positive sign, $\mathcal{T}_r=d\ln r/d\ln k\gtrsim
0.57^{+0.29}_{-0.27}$ corresponding to a blue tilt for the tensor modes of
order $n_T\simeq0.53 ^{+0.29}_{-0.27}$, assuming the Planck experiment best-fit
value for tilt of scalar power spectrum $n_S$. The other possibility is to
assume that there is a negative running in the scalar spectral index,
$dn_S/d\ln k\simeq -0.02$ which pushes up the upper bound on $r$ from $0.11$ up
to $0.26$ in the Planck analysis assuming the existence of a tensor spectrum.
Simple slow-roll models fail to provide such large values for $\mathcal{T}_r$
or negative runnings in $n_S$ [arXiv:1403.3985]. In this note we show that a
non-Bunch-Davies initial state for perturbations can provide a match between
large field chaotic models (like $m^2\phi^2$) with the latest Planck result
[arXiv:1306.4914] and BICEP2 results by accommodating either the blue tilt of
$r$ or the negative large running of $n_S$.Comment: v1:5 pages, double column; v2: 6 pages, double column, the option of
  negative running of scalar spectral index and some references were added; v3:
  Matched the PLB versio
Symmetry breaking caused by large R-charge

We discuss the gauge symmetry breaking via the Hosotani mechanism by using
exact results on supersymmetric gauge theories based on the localization
method. We use the theories on S^2 x S^1 Euclidean space, and study how the
effective potential for the Wilson line phase varies by running an imaginary
chemical potential. In order to break the symmetry, we find that large R-charge
is necessary. With such large R-charge, we study the phase structure of the
theory. In addition, we observed that a finite size effect on our curved space
when we take R-charge is not so large.Comment: 20 pages, 7 figures. Typos corrected, Comments on the limit adde
The Heisenberg Matrix Formulation of Quantum Field Theory

Heisenberg's matrix formulation of quantum mechanics can be generalized to relativistic systems by evolving in light-front time tau = t+z/c. The spectrum and wavefunctions of bound states, such as hadrons in quantum chromodynamics, can be obtained from matrix diagonalization of the light-front Hamiltonian on a finite dimensional light-front Fock basis defined using periodic boundary conditions in the light-front space coordinates. This method, discretized light-cone quantization (DLCQ), preserves the frame-independence of the front form even at finite resolution and particle number. Light-front quantization can also be used in the Hamiltonian form to construct an event generator for high energy physics reactions at the amplitude level. The light-front partition function, summed over exponentially-weighted light-front energies, has simple boost properties which may be useful for studies in heavy ion collisions. I also review recent work which shows that the structure functions measured in deep inelastic lepton scattering are affected by final-state rescattering, thus modifying their connection to light-front probability distributions. In particular, the shadowing of nuclear structure functions is due to destructive interference effects from leading-twist diffraction of the virtual photon, physics not included in the nuclear light-front wavefunctions
Topology and Phase Transitions II. Theorem on a necessary relation

In this second paper, we prove a necessity Theorem about the topological
origin of phase transitions. We consider physical systems described by smooth
microscopic interaction potentials V_N(q), among N degrees of freedom, and the
associated family of configuration space submanifolds {M_v}_{v \in R}, with
M_v={q \in R^N | V_N(q) \leq v}. On the basis of an analytic relationship
between a suitably weighed sum of the Morse indexes of the manifolds {M_ v}_{v
\in R} and thermodynamic entropy, the Theorem states that any possible unbound
growth with N of one of the following derivatives of the configurational
entropy S^{(-)}(v)=(1/N) \log \int_{M_v} d^Nq, that is of |\partial^k
S^{(-)}(v)/\partial v^k|, for k=3,4, can be entailed only by the weighed sum of
Morse indexes.
  Since the unbound growth with N of one of these derivatives corresponds to
the occurrence of a first or of a second order phase transition, and since the
variation of the Morse indexes of a manifold is in one-to-one correspondence
with a change of its topology, the Main Theorem of the present paper states
that a phase transition necessarily stems from a topological transition in
configuration space. The proof of the Theorem given in the present paper cannot
be done without Main Theorem of paper I.Comment: 21 pages. This second paper follows up paper I archived in
  math-ph/0505057. Added minor changes: Title, Abstract, Introductio
Upper large deviations for the maximal flow in first passage percolation

We consider the standard first passage percolation in $\mathbb{Z}^{d}$ for
$d\geq 2$ and we denote by $\phi_{n^{d-1},h(n)}$ the maximal flow through the
cylinder $]0,n]^{d-1} \times ]0,h(n)]$ from its bottom to its top. Kesten
proved a law of large numbers for the maximal flow in dimension three: under
some assumptions, $\phi_{n^{d-1},h(n)} / n^{d-1}$ converges towards a constant
$\nu$. We look now at the probability that $\phi_{n^{d-1},h(n)} / n^{d-1}$ is
greater than $\nu + \epsilon$ for some $\epsilon >0$, and we show under some
assumptions that this probability decays exponentially fast with the volume of
the cylinder. Moreover, we prove a large deviations principle for the sequence
$(\phi_{n^{d-1},h(n)} / n^{d-1}, n\in \mathbb{N})$.Comment: 27 pages, 4 figures; small changes of notation
Rapidity Asymmetry in High-energy $d+A$ Collisions

In contrast to the recent prediction of high $p_T$ hadron suppression within
the parton saturation model, it is shown that multiple parton scattering
suffered by the projectile will enhance high $p_T$ hadron spectra in $d+A$
collisions relative to a superposition of binary $p+p$ collisions at RHIC. A
stronger enhancement in the forward rapidity region of the projectile is also
predicted, resulting in a unique rapidity asymmetry of the hadron spectra at
high $p_T$. The shape of the rapidity asymmetry should be reversed for low
$p_T$ hadrons that are dominated by soft and coherent interactions which
suppress hadron spectra in the projectile rapidity region. The phenomenon at
the LHC energies is shown to be qualitatively different because of parton
shadowing.Comment: 13 pages in RevTex, 5 figures. The numerical data files of the
  figures can be downloaded from
  http://www-hpc.lbl.gov/datacode_files/hadrons.ht
Gluing of completely positive maps

Gluings of completely positive maps (CPMs) are defined and investigated. As a
brief description of this concept consider a pair of `evolution machines', each
with the ability to evolve the internal state of a `particle' inserted into its
input. Each of these machines is characterized by a channel describing the
operation the internal state has experienced when the particle is returned at
the output. Suppose a particle is put in a superposition between the input of
the first and the second machine. Here it is shown that the total evolution
caused by a pair of such devices is not uniquely determined by the channels of
the two machines. Such `global' channels describing the machine pair are
examples of gluings of the two single machine channels. Under the limiting
assumption that all involved Hilbert spaces are finite-dimensional, an
expression which generates all subspace preserving gluings of a given pair of
CPMs, is derived. The nature of the non-uniqueness of gluings and its relation
to a proposed definition of subspace locality, is discussed.Comment: References added, A proposition adde
Students’ preferences in undergraduate mathematics assessment

Existing research into students' preferences for assessment methods has been developed from a restricted sample: in particular, the voice of students in the ‘hard-pure sciences’ has rarely been heard. We conducted a mixed method study to explore mathematics students' preferences of assessment methods. In contrast to the message from the general assessment literature, we found that mathematics students differentially prefer traditional assessment methods such as closed book examination; they perceive them to be fairer than innovative methods and they perceive traditional methods to be the best discriminators of mathematical ability. We also found that although students prefer to be assessed by traditional methods they are also concerned by the mix of methods they encounter during their degree, suggesting that more account needs to be taken about the students' views of this mix. We discuss the impact of the results on the way general findings about assessment preference should be interpreted
Bayesian field theoretic reconstruction of bond potential and bond
  mobility in single molecule force spectroscopy

Quantifying the forces between and within macromolecules is a necessary first
step in understanding the mechanics of molecular structure, protein folding,
and enzyme function and performance. In such macromolecular settings, dynamic
single-molecule force spectroscopy (DFS) has been used to distort bonds. The
resulting responses, in the form of rupture forces, work applied, and
trajectories of displacements, have been used to reconstruct bond potentials.
Such approaches often rely on simple parameterizations of one-dimensional bond
potentials, assumptions on equilibrium starting states, and/or large amounts of
trajectory data. Parametric approaches typically fail at inferring
complex-shaped bond potentials with multiple minima, while piecewise estimation
may not guarantee smooth results with the appropriate behavior at large
distances. Existing techniques, particularly those based on work theorems, also
do not address spatial variations in the diffusivity that may arise from
spatially inhomogeneous coupling to other degrees of freedom in the
macromolecule, thereby presenting an incomplete picture of the overall bond
dynamics. To solve these challenges, we have developed a comprehensive
empirical Bayesian approach that incorporates data and regularization terms
directly into a path integral. All experiemental and statistical parameters in
our method are estimated empirically directly from the data. Upon testing our
method on simulated data, our regularized approach requires fewer data and
allows simultaneous inference of both complex bond potentials and diffusivity
profiles.Comment: In review - Python source code available on github. Abridged abstract
  on arXi
MOA-2007-BLG-197: Exploring the brown dwarf desert

We present the analysis of MOA-2007-BLG-197Lb, the first brown dwarf
companion to a Sun-like star detected through gravitational microlensing. The
event was alerted and followed-up photometrically by a network of telescopes
from the PLANET, MOA, and uFUN collaborations, and observed at high angular
resolution using the NaCo instrument at the VLT. From the modelling of the
microlensing light curve, we derived the binary lens separation in Einstein
radius units (s~1.13) and a mass ratio of (4.732+/-0.020)x10^{-2}. Annual
parallax, lens orbital motion and finite source effects were included in the
models. To recover the lens system's physical parameters, we combined the
resulting light curve best-fit parameters with (J,H,Ks) magnitudes obtained
with VLT NaCo and calibrated using IRSF and 2MASS data. We derived a lens total
mass of 0.86+/-0.04 Msun and a lens distance of 4.2+/-0.3 kpc. We find that the
companion of MOA-2007-BLG-197L is a brown dwarf of 41+/-2 Mjup observed at a
projected separation of 4.3+/-0.1 AU, and orbits a 0.82+/-0.04 Msun G-K dwarf
star. We study the statistical properties of this population of brown dwarfs
detected by microlensing, transit, radial velocity, and direct imaging (most of
these objects orbit solar-type stars), and we performed a two-dimensional,
non-parametric probability density distribution fit to the data, which draws a
structured brown dwarf landscape. We confirm the existence of a region that is
strongly depleted in objects at short periods and intermediate masses (P<30 d,
M~30-60 Mjup), but also find an accumulation of objects around P~500 d and M~20
Mjup, as well as another depletion region at long orbital periods (P>500 d) and
high masses (M>50 Mjup). While these data provide important clues on mechanisms
of brown dwarfs formation, more data are needed to establish their relative
importance, in particular as a function of host star mass.Comment: 16 pages, 12 figure
Finite $\epsilon_2$-corrections to the $\mathcal{N}=2$ SYM prepotential

We derive the first $\epsilon_2$-correction to the instanton partition
functions of $\mathcal{N}=2$ Super Yang-Mills (SYM) in four dimensions in the
Nekrasov-Shatashvili limit $\epsilon_2\rightarrow 0$. In the latter we recall
the emergence of the famous Thermodynamic Bethe Ansatz-like equation which has
been found by Mayer expansion techniques. Here we combine efficiently these to
field theory arguments. In a nutshell, we find natural and resolutive the
introduction of a new operator $\nabla$ that distinguishes the singularities
within and outside the integration contour of the partition function.Comment: 13 pages, 1 figur