title: RPC application in muography and specific developments

abstract:
  Muography is an imaging technique for large and dense structures as volcanoes
or nuclear reactors using atmospheric muons. We applied this technique to the
observation of the Puy de D\^ome, a volcano 2 km wide close to
Clermont-Ferrand, France. The detection is performed with a
1m$\times$1m$\times$1.80m telescope made of 4 layers of single gap glass-RPCs
operated in avalanche mode. The 1 cm$^2$ pad readout uses the Hardroc2 ASICs.
The three data taking campaigns over the last three years showed that a RPC
detector can be operated in-situ with good performances. Further developments
to decrease the gas and power consumption and to improve the position and
timing resolution of the detector are ongoing.


title:
Fine tuning consensus optimization for distributed radio interferometric
  calibration

abstract:
  We recently proposed the use of consensus optimization as a viable and
effective way to improve the quality of calibration of radio interferometric
data. We showed that it is possible to obtain far more accurate calibration
solutions and also to distribute the compute load across a network of computers
by using this technique. A crucial aspect in any consensus optimization problem
is the selection of the penalty parameter used in the alternating direction
method of multipliers (ADMM) iterations. This affects the convergence speed as
well as the accuracy. In this paper, we use the Hessian of the cost function
used in calibration to appropriately select this penalty. We extend our results
to a multi-directional calibration setting, where we propose to use a penalty
scaled by the squared intensity of each direction.


title:
Uniqueness and propagation of chaos for the Boltzmann equation with
  moderately soft potentials

abstract:
  We prove a strong/weak stability estimate for the 3D homogeneous Boltzmann
equation with moderately soft potentials ($\gamma\in(-1,0)$) using the
Wasserstein distance with quadratic cost. This in particular implies the
uniqueness in the class of all weak solutions, assuming only that the initial
condition has a finite entropy and a finite moment of sufficiently high order.
We also consider the Nanbu $N$-stochastic particle system which approximates
the weak solution. We use a probabilistic coupling method and give, under
suitable assumptions on the initial condition, a rate of convergence of the
empirical measure of the particle system to the solution of the Boltzmann
equation for this singular interaction.


title:
Deep Reinforcement Learning Radio Control and Signal Detection with
  KeRLym, a Gym RL Agent

abstract:
  This paper presents research in progress investigating the viability and
adaptation of reinforcement learning using deep neural network based function
approximation for the task of radio control and signal detection in the
wireless domain. We demonstrate a successful initial method for radio control
which allows naive learning of search without the need for expert features,
heuristics, or search strategies. We also introduce Kerlym, an open Keras based
reinforcement learning agent collection for OpenAI's Gym.


title:
A note on $\mathbb{Z}$ as a direct summand of nonstandard models of weak
  systems of arithmetic

abstract:
  There are nonstandard models of normal open induction ($NOI$) for which
$\mathbb{Z}$ is a direct summand of their additive group. We show that this is
impossible for nonstandard models of $IE_2$.


title: On large subsets of $F_q^n$ with no three-term arithmetic progression

abstract:
  In this note, we show that the method of Croot, Lev, and Pach can be used to
bound the size of a subset of $F_q^n$ with no three terms in arithmetic
progression by $c^n$ with $c < q$. For $q=3$, the problem of finding the
largest subset with no three terms in arithmetic progression is called the `cap
problem'. Previously the best known upper bound for the cap problem, due to
Bateman and Katz, was $O(3^n / n^{1+\epsilon})$.


title:
Suppressed magnetic circular dichroism and valley-selective
  magneto-absorption due to the effective mass anisotropy in bismuth

abstract:
  We have measured the far-infrared reflectivity and Kerr angle spectra on a
high-quality crystal of pure semimetallic bismuth as a function of magnetic
field, from which we extract the conductivity for left- and right handed
circular polarisations. The high spectral resolution allows us to separate the
intraband Landau level transitions for electrons and holes. The hole transition
exhibits 100% magnetic circular dichroism, it appears only for one polarisation
as expected for a circular cyclotron orbit. However the dichroism for electron
transitions is reduced to only $13\pm 1$%, which is quantitatively explained by
the large effective mass anisotropy of the electron pockets of the Fermi
surface. This observation is a signature of the mismatch between the metric
experienced by the photons and the electrons. It allows for a contactless
measurement of the effective mass anisotropy and provides a direction towards
valley polarised magneto-optical pumping with elliptically polarised light.


title: Eigenstate Gibbs Ensemble in Integrable Quantum Systems

abstract:
  The Eigenstate Thermalization Hypothesis implies that for a thermodynamically
large system in one of its eigenstates, the reduced density matrix describing
any finite subsystem is determined solely by a set of {\it relevant} conserved
quantities. In a generic system, only the energy plays that role and hence
eigenstates appear locally thermal. Integrable systems, on the other hand,
possess an extensive number of such conserved quantities and hence the reduced
density matrix requires specification of an infinite number of parameters
(Generalized Gibbs Ensemble). However, here we show by unbiased statistical
sampling of the individual eigenstates with a given finite energy density, that
the local description of an overwhelming majority of these states of even such
an integrable system is actually Gibbs-like, i.e. requires only the energy
density of the eigenstate. Rare eigenstates that cannot be represented by the
Gibbs ensemble can also be sampled efficiently by our method and their local
properties are then shown to be described by appropriately {\it truncated}
Generalized Gibbs Ensembles. We further show that the presence of these rare
eigenstates differentiates the model from the generic (non-integrable) case and
leads to the system being described by a Generalized Gibbs Ensemble at long
time under a unitary dynamics following a sudden quench, even when the initial
state is a Gibbs-like eigenstate of the pre-quench Hamiltonian.


title:
Global existence for a degenerate haptotaxis model of tumor invasion
  under the go-or-grow dichotomy hypothesis

abstract:
  We propose and study a strongly coupled PDE-ODE-ODE system modeling cancer
cell invasion through a tissue network under the go-or-grow hypothesis
asserting that cancer cells can either move or proliferate. Hence our setting
features two interacting cell populations with their mutual transitions and
involves tissue-dependent degenerate diffusion and haptotaxis for the moving
subpopulation. The proliferating cells and the tissue evolution are
characterized by way of ODEs for the respective densities. We prove the global
existence of weak solutions and illustrate the model behaviour by numerical
simulations in a two-dimensional setting.


title: Learning Combinatorial Functions from Pairwise Comparisons

abstract:
  A large body of work in machine learning has focused on the problem of
learning a close approximation to an underlying combinatorial function, given a
small set of labeled examples. However, for real-valued functions, cardinal
labels might not be accessible, or it may be difficult for an expert to
consistently assign real-valued labels over the entire set of examples. For
instance, it is notoriously hard for consumers to reliably assign values to
bundles of merchandise. Instead, it might be much easier for a consumer to
report which of two bundles she likes better. With this motivation in mind, we
consider an alternative learning model, wherein the algorithm must learn the
underlying function up to pairwise comparisons, from pairwise comparisons. In
this model, we present a series of novel algorithms that learn over a wide
variety of combinatorial function classes. These range from graph functions to
broad classes of valuation functions that are fundamentally important in
microeconomic theory, the analysis of social networks, and machine learning,
such as coverage, submodular, XOS, and subadditive functions, as well as
functions with sparse Fourier support.


title: On Noether's rationality problem for cyclic groups over $\mathbb{Q}$

abstract:
  Let $p$ be a prime number. Let $C_p$, the cyclic group of order $p$, permute
transitively a set of indeterminates $\{ x_1,\ldots ,x_p \}$. We prove that the
invariant field $\mathbb{Q}(x_1,\ldots ,x_p)^{C_p}$ is rational over
$\mathbb{Q}$ if and only if the $(p-1)$-th cyclotomic field
$\mathbb{Q}(\zeta_{p-1})$ has class number one.


title: End of a Dark Age?

abstract:
  We argue that dark matter and dark energy phenomena associated with galactic
rotation curves, X-ray cluster mass profiles, and type Ia supernova data can be
accounted for via small corrections to idealized general relativistic spacetime
geometries due to disordered locality. Accordingly, we fit THINGS rotation
curve data rivaling modified Newtonian dynamics, ROSAT/ASCA X-ray cluster mass
profile data rivaling metric-skew-tensor gravity, and SCP Union2.1 SN Ia data
rivaling $\Lambda$CDM without non-baryonic dark matter or a cosmological
constant. In the case of dark matter, we geometrically modify proper mass
interior to the Schwarzschild solution. In the case of dark energy, we modify
proper distance in Einstein-deSitter cosmology. Therefore, the phenomena of
dark matter and dark energy may be chimeras created by an errant belief that
spacetime is a differentiable manifold rather than a disordered graph.


title:
Spatial Organization of the Cytoskeleton enhances Cargo Delivery to
  Specific Target Areas on the Plasma Membrane of Spherical Cells

abstract:
  Intracellular transport is vital for the proper functioning and survival of a
cell. Cargo (proteins, vesicles, organelles, etc.) is transferred from its
place of creation to its target locations via molecular motor assisted
transport along cytoskeletal filaments. The transport efficiency is strongly
affected by the spatial organization of the cytoskeleton, which constitutes an
inhomogeneous, complex network. In cells with a centrosome microtubules grow
radially from the central microtubule organizing center towards the cell
periphery whereas actin filaments form a dense meshwork, the actin cortex,
underneath the cell membrane with a broad range of orientations. The emerging
ballistic motion along filaments is frequently interrupted due to constricting
intersection nodes or cycles of detachment and reattachment processes in the
crowded cytoplasm. In order to investigate the efficiency of search strategies
established by the cell's specific spatial organization of the cytoskeleton we
formulate a random velocity model with intermittent arrest states. With
extensive computer simulations we analyze the dependence of the mean first
passage times for narrow escape problems on the structural characteristics of
the cytoskeleton, the motor properties and the fraction of time spent in each
state. We find that an inhomogeneous architecture with a small width of the
actin cortex constitutes an efficient intracellular search strategy.


title:
Tunable scattering cancellation cloak with plasmonic ellipsoids in the
  visible

abstract:
  The scattering cancellation technique is a powerful tool to reduce the
scattered field from electrically small objects in a specific frequency window.
The technique relies on covering the object of interest with a shell that
scatters light into the far field of equal strength as the object, but $\pi$
out-of-phase. The resulting destructive interference prohibits its detection in
measurements that probe the scattered light. Whereas at radio or microwave
frequencies feasible designs have been proposed that allow to tune the
operational frequency upon request, similar capabilities have not yet been
explored in the visible. However, such ability is decisive to capitalize on the
technique in many envisioned applications. Here, we solve the problem and study
the use of small metallic nanoparticles with an ellipsoidal shape as the
material from which the shell is made to build an isotropic geometry. Changing
the aspect ratio of the ellipsoids allows to change the operational frequency.
The basic functionality is explored with two complementary analytical
approaches. Additionally, we present a powerful multiscattering algorithm that
can be used to perform full wave simulations of clusters of arbitrary
particles. We utilize this method to analyze the scattering of the presented
designs numerically. Hereby we provide useful guidelines for the fabrication of
this cloak with self-assembly methods by investigating the effects of disorder.


title:
Tradeoffs between Convergence Speed and Reconstruction Accuracy in
  Inverse Problems

abstract:
  Solving inverse problems with iterative algorithms is popular, especially for
large data. Due to time constraints, the number of possible iterations is
usually limited, potentially affecting the achievable accuracy. Given an error
one is willing to tolerate, an important question is whether it is possible to
modify the original iterations to obtain faster convergence to a minimizer
achieving the allowed error without increasing the computational cost of each
iteration considerably. Relying on recent recovery techniques developed for
settings in which the desired signal belongs to some low-dimensional set, we
show that using a coarse estimate of this set may lead to faster convergence at
the cost of an additional reconstruction error related to the accuracy of the
set approximation. Our theory ties to recent advances in sparse recovery,
compressed sensing, and deep learning. Particularly, it may provide a possible
explanation to the successful approximation of the l1-minimization solution by
neural networks with layers representing iterations, as practiced in the
learned iterative shrinkage-thresholding algorithm (LISTA).


title:
Noise-Resistant Quantum Teleportation, Ansibles, and the No-Projector
  Theorem

abstract:
  A method is presented for achieving entanglement-free teleportation of a
quantum state subject to any quantum noise. We apply this as a light-speed
noise-resistant communicator, but also treat the possibility of a quantum
ansible, a device for effectively superluminal communication and quantum
broadcasting. The results suggest a "no-projector theorem" analogous to the
no-cloning theorem. We then show how to build a pseudo-ansible for
connection-free light-speed communication.


title:
Two minimization problems on non-scattering solutions to
  mass-subcritical nonlinear Schr\"odinger equation

abstract:
  In this paper, we introduce two minimization problems on non-scattering
solutions to nonlinear Schr\"odinger equation. One gives us a sharp scattering
criterion, the other is concerned with minimal size of blowup profiles. We
first reformulate several previous results in terms of these two minimizations.
Then, the main result of the paper is existence of minimizers to the both
minimization problems for mass-subcritical nonlinear Schr\"odinger equations.
To consider the latter minimization, we consider the equation in a Fourier
transform of generalized Morrey space. It turns out that the minimizer to the
latter problem possesses a compactness property, which is so-called almost
periodicity modulo symmetry.


title:
Bulk effective theory in coupled wire construction from generalized
  Wilson line

abstract:
  We reconsider the coupled wire construction, which is a useful method of
obtaining two and three-dimensional topologically ordered states from an array
of one-dimensional CFTs, and show that there is the hidden structure in the
bulk of the constructed model. In order to uncover the structure hidden in the
gapped bulk, we introduce a generalized Wilson line and show the necessity of
introducing a new gauge field, which behaves like the Chern-Simons gauge field.
From these examination, it is possible to show that in this formulation the
bulk theory is the U(1) Chern-Simons gauge theory and the edge theory is the
chiral Luttinger theory. We explicitly demonstrate our method for the Laughlin
states and the chiral spin liquid state.


title: Einstein and Beyond: A Critical Perspective on General Relativity

abstract:
  An alternative approach to Einstein's theory of General Relativity (GR) is
reviewed, which is motivated by a range of serious theoretical issues
inflicting the theory, such as the cosmological constant problem, presence of
non-Machian solutions, problems related with the energy-stress tensor $T^{ik}$
and unphysical solutions.
  The new approach emanates from a critical analysis of these problems,
providing a novel insight that the matter fields, together with the ensuing
gravitational field, are already present inherently in the spacetime without
taking recourse to $T^{ik}$. Supported by numerous evidences, the new insight
revolutionizes our views on the representation of the source of gravitation and
establishes the spacetime itself as the source, which becomes crucial for
understanding the unresolved issues in a unified manner. This leads to a new
paradigm in GR by establishing equation $R^{ik}=0$ as the field equation of
gravitation plus inertia in the very presence of matter.


title:
Evaluation of Copper, Aluminum and Nickel Interatomic Potentials on
  Predicting the Elastic Properties

abstract:
  Choice of appropriate force field is one of the main concerns of any
atomistic simulation that needs to be seriously considered in order to yield
reliable results. Since, investigations on mechanical behavior of materials at
micro/nanoscale has been becoming much more widespread, it is necessary to
determine an adequate potential which accurately models the interaction of the
atoms for desired applications. In this framework, reliability of multiple
embedded atom method based interatomic potentials for predicting the elastic
properties was investigated. Assessments were carried out for different copper,
aluminum and nickel interatomic potentials at room temperature which is
considered as the most applicable case. Examined force fields for the three
species were taken from online repositories of National Institute of Standards
and Technology (NIST), as well as the Sandia National Laboratories, the LAMMPS
database. Using molecular dynamic simulations, the three independent elastic
constants, C11, C12 and C44 were found for Cu, Al and Ni cubic single crystals.
Voigt-Reuss-Hill approximation was then implemented to convert elastic
constants of the single crystals into isotropic polycrystalline elastic moduli
including Bulk, Shear and Young's modulus as well as Poisson's ratio.
Simulation results from massive molecular dynamic were compared with available
experimental data in the literature to justify the robustness of each potential
for each species. Eventually, accurate interatomic potentials have been
recommended for finding each of the elastic properties of the pure species.
Exactitude of the elastic properties was found to be sensitive to the choice of
the force fields. Those potentials were fitted for a specific compound may not
necessarily work accurately for all the existing pure species.


title:
Infinitely Many Weak Solutions for Fractional Dirichlet Problem with
  $p$-Laplacian

abstract:
  We focus on the study of $p$-Laplacian Dirichlet problem containing the left
and right fractional derivative operators. By using the genus properties in
critical point theory, we establish some new criteria to guarantee the
existence of infinitely many weak solutions for the considered problem.


title:
Pinwheels in the sky, with dust: 3D modeling of the Wolf-Rayet 98a
  environment

abstract:
  The Wolf-Rayet 98a (WR 98a) system is a prime target for interferometric
surveys, since its identification as a "rotating pinwheel nebulae", where
infrared images display a spiral dust lane revolving with a 1.4 year
periodicity. WR 98a hosts a WC9+OB star, and the presence of dust is puzzling
given the extreme luminosities of Wolf-Rayet stars. We present 3D hydrodynamic
models for WR 98a, where dust creation and redistribution are self-consistently
incorporated. Our grid-adaptive simulations resolve details in the wind
collision region at scales below one percent of the orbital separation (~4 AU),
while simulating up to 1300 AU. We cover several orbital periods under
conditions where the gas component alone behaves adiabatic, or is subject to
effective radiative cooling. In the adiabatic case, mixing between stellar
winds is effective in a well-defined spiral pattern, where optimal conditions
for dust creation are met. When radiative cooling is incorporated, the
interaction gets dominated by thermal instabilities along the wind collision
region, and dust concentrates in clumps and filaments in a volume-filling
fashion, so WR 98a must obey close to adiabatic evolutions to demonstrate the
rotating pinwheel structure. We mimic Keck, ALMA or future E-ELT observations
and confront photometric long-term monitoring. We predict an asymmetry in the
dust distribution between leading and trailing edge of the spiral, show that
ALMA and E-ELT would be able to detect fine-structure in the spiral indicative
of Kelvin-Helmholtz development, and confirm the variation in photometry due to
the orientation. Historic Keck images are reproduced, but their resolution is
insufficient to detect the details we predict.


title:
Extremals of Log Sobolev inequality on non-compact manifolds and Ricci
  soliton structures

abstract:
  In this paper we establish the existence of extremals for the Log Sobolev
functional on complete non-compact manifolds with Ricci curvature bounded from
below and strictly positive injectivity radius, under a condition near
infinity. When Ricci curvature is also bounded from above we get exponential
decay at infinity of the extremals. As a consequence of these analytical
results we establish, under the same assumptions, that non-trivial shrinking
Ricci solitons support a gradient Ricci soliton structure. On the way, we prove
two results of independent interest: the existence of a distance-like function
with uniformly controlled gradient and Hessian on complete non-compact
manifolds with bounded Ricci curvature and strictly positive injectivity radius
and a general growth estimate for the norm of the soliton vector field on
manifolds with bounded Ricci curvature.


title:
Leggett-Garg Correlation Functions from Non-Invasive Velocity
  Measurement Continuous in Time

abstract:
  In the Leggett-Garg approach to testing macrorealism, the two-time
correlation functions, which are normally obtained by sequential measurements
of a dichotomic variable Q, need to be measured in a non-invasive way in order
to exclude certain types of alternative classical explanation. Here, it is
shown, for a class of macrorealistic theories, that the correlation functions
are readily expressed in terms of a time integral of the velocity corresponding
to Q and that this expression can be determined from a single final-time
measurement of an auxiliary system in continual weak interaction with the
primary system. The protocol has the form of a "waiting detector" which clicks
only when Q changes sign. It shares features with both ideal negative
measurements and weak measurements and we argue that it is essentially
non-invasive, under certain reasonable assumptions. We show that the
non-invasiveness persists to a quantum model of the process.


title:
A comprehensive approach to dark matter studies: exploration of
  simplified top-philic models

abstract:
  Studies of dark matter lie at the interface of collider physics, astrophysics
and cosmology. Constraining models featuring dark matter candidates entails the
capability to provide accurate predictions for large sets of observables and
compare them to a wide spectrum of data. We present a framework which, starting
from a model lagrangian, allows one to consistently and systematically make
predictions, as well as to confront those predictions with a multitude of
experimental results. As an application, we consider a class of simplified dark
matter models where a scalar mediator couples only to the top quark and a
fermionic dark sector (i.e. the simplified top-philic dark matter model). We
study in detail the complementarity of relic density, direct/indirect detection
and collider searches in constraining the multi-dimensional model parameter
space, and efficiently identify regions where individual approaches to dark
matter detection provide the most stringent bounds. In the context of collider
studies of dark matter, we point out the complementarity of LHC searches in
probing different regions of the model parameter space with final states
involving top quarks, photons, jets and/or missing energy. Our study of dark
matter production at the LHC goes beyond the tree-level approximation and we
show examples of how higher-order corrections to dark matter production
processes can affect the interpretation of the experimental results.


title:
$H-$convergence result for nonlocal elliptic-type problems via Tartar's
  method

abstract:
  In this work we obtain a compactness result for the $H-$convergence of a
family of nonlocal and nonlinear monotone elliptic-type problems by means of
Tartar's method of oscillating test functions.


title:
A Note on the Area Requirement of Euclidean Greedy Embeddings of
  Christmas Cactus Graphs

abstract:
  An Euclidean greedy embedding of a graph is a straight-line embedding in the
plane, such that for every pair of vertices $s$ and $t$, the vertex $s$ has a
neighbor $v$ with smaller distance to $t$ than $s$. This drawing style is
motivated by greedy geometric routing in wireless sensor networks.
  A Christmas cactus is a connected graph in which every two simple cycles have
at most one vertex in common and in which every cutvertex is part of at most
two biconnected blocks. It has been proved that Christmas cactus graphs have an
Euclidean greedy embedding. This fact has played a crucial role in proving that
every 3-connected planar graph has an Euclidean greedy embedding. The proofs
construct greedy embeddings of Christmas cactuses of exponential size, and it
has been an open question whether exponential area is necessary in the worst
case for greedy embeddings of Christmas cactuses. We prove that this is indeed
the case.


title: Doppler-free spectroscopy on Cs D$_1$ line with a dual-frequency laser

abstract:
  We report on Doppler-free laser spectroscopy in a Cs vapor cell using a
dual-frequency laser system tuned on the Cs D$_1$ line. Using
counter-propagating beams with crossed linear polarizations, an original
sign-reversal of the usual saturated absorption dip and large increase in
Doppler-free atomic absorption is observed. This phenomenon is explained by
coherent population trapping (CPT) effects. The impact of laser intensity and
light polarization on absorption profiles is reported in both single-frequency
and dual-frequency regimes. In the latter, frequency stabilization of two diode
lasers was performed, yielding a beat-note fractional frequency stability at
the level of $3 \times 10^{-12}$ at 1 s averaging time. These performances are
about an order of magnitude better than those obtained using a conventional
single-frequency saturated absorption scheme.


title: Competing Sudakov Veto Algorithms

abstract:
  We present a way to analyze the distribution produced by a Monte Carlo
algorithm. We perform these analyses on several versions of the Sudakov veto
algorithm, adding a cutoff, a second variable and competition between emission
channels. The analysis allows us to prove that multiple, seemingly different
competition algorithms, including those that are currently implemented in most
parton showers, lead to the same result. Finally, we test their performance and
show that there are significantly faster alternatives to the commonly used
algorithms.


title: Anisotropic inflation in Gauss-Bonnet gravity

abstract:
  We study anisotropic inflation with Gauss-Bonnet correction in presence of a
massless vector field. In this scenario, exact anisotropic power-law inflation
is realized when the inflaton potential, gauge coupling function and the
Gauss-Bonnet coupling are exponential functions. We show that anisotropy
becomes proportional to two slow-roll parameters of the theory and hence gets
enhanced in presence of quadratic curvature corrections. The stability analysis
reveals that anisotropic power-law solutions remain stable over a substantially
large parameter region.


title:
Lepton flavor violating Higgs decay $h\rightarrow \mu\tau$ in the
  littlest Higgs Model with T-parity

abstract:
  Inspired by the recent CMS $h \to \mu\tau$ excess, we calculate the lepton
flavor violating Higgs decay $h \to \mu\tau$ in the littlest Higgs model with
T-parity (LHT). Under the constraints of $\ell_i \to \ell_j \gamma$, $Z \to
\ell_i \bar{\ell}_j$ and Higgs data, we find that the branching ratio of $h \to
\mu\tau$ can maximally reach $\mathcal O(10^{-4})$. We also investigate the
correlation between $h \to \mu\tau $, $\tau \to \mu \gamma$ and $Z \to
\mu\tau$, which can be used to test LHT model at future $e^+e^-$ colliders.


title: Compressed sensing and sparsity in photoacoustic tomography

abstract:
  Increasing the imaging speed is a central aim in photoacoustic tomography.
This issue is especially important in the case of sequential scanning
approaches as applied for most existing optical detection schemes. In this work
we address this issue using techniques of compressed sensing. We demonstrate,
that the number of measurements can significantly be reduced by allowing
general linear measurements instead of point-wise pressure values. A main
requirement in compressed sensing is the sparsity of the unknowns to be
recovered. For that purpose we develop the concept of sparsifying temporal
transforms for three-dimensional photoacoustic tomography. We establish a
two-stage algorithm that recovers the complete pressure Signals in a first step
and then applies a standard reconstruction algorithm such as back-projection.
This yields a novel reconstruction method with much lower complexity than
existing compressed sensing approaches for photoacoustic tomography.
Reconstruction results for simulated and for experimental data verify that the
proposed compressed sensing scheme allows to significantly reducing the number
of spatial measurements without reducing the spatial resolution.


title: Feature Extraction from Segmentations of Neuromuscular Junctions

abstract:
  Segmentations are often necessary for the analysis of image data. They are
used to identify different objects, for example cell nuclei, mitochondria, or
complete cells in microscopic images. There might be features in the data, that
cannot be detected by segmentation approaches directly, because they are not
characterized by their texture of boundaries, which are properties most
segmentation techniques rely on, but morphologically. In this report we will
introduce our algorithm for the extraction of suchlike morphological features
of segmented objects from segmentations of neuromuscular junctions and its
interface for informed parameter tuning.


title: Group classification of linear evolution equations

abstract:
  The group classification problem for the class of (1+1)-dimensional linear
$r$th order evolution equations is solved for arbitrary values of $r>2$. It is
shown that a related maximally gauged class of homogeneous linear evolution
equations is uniformly semi-normalized with respect to linear superposition of
solutions and hence the complete group classification can be obtained using the
algebraic method. We also compute exact solutions for equations from the class
under consideration using Lie reduction and its specific generalizations for
linear equations.


title: Complex Cobordism vs. Representing Formal Group Laws

abstract:
  We attempt to answer a question of D. C. Ravenel's: "Infinite loopspace
theorists, where are you?", or more prosaically: Can one start from the notion
of Ring Spectrum Representing [Formal Group Laws] (the functor) and arrive at
Complex Cobordism? Our answer is a tentative "sort-of".


title: Ultimate Statistical Physics: fluorescence of a single atom

abstract:
  We discuss the statistics of emission of photons by a single atom or ion
illuminated by a laser beam at the frequency of quasi-resonance between two
energy levels, a situation that corresponds to real experiments. We extend this
to the case of two laser beams resonant with the energy differences between two
excited levels and the ground state (three level atom in V-configuration). We
use a novel approach of this type of problem by considering Kolmogorov equation
for the probability distribution of the atomic state which takes into account
first the deterministic evolution of this state under the effect of the
incoming laser beam and the random emission of photons during the spontaneous
decay of the excited state(s) to the ground state. This approach yields
solvable equations in the two level atom case. For the three level atom case we
set the problem and define clearly its frame. The results obtained are valid
both in the opposite limits of rare and of frequent spontaneous decay, compared
to the period of the optical Rabi oscillations due to the interaction between
the resonant excitation and the atomic levels. Our theory gives access to
various statistical properties of the fluorescence light, including one showing
that its fluctuations in time are not invariants under time reversal. This
result puts in evidence the fundamentally irreversible character of quantum
measurements, represented here by the emission of photons of fluorescence.


title: Romans-mass-driven flows on the D2-brane

abstract:
  The addition of supersymmetric Chern-Simons terms to ${\cal N}=8$
super-Yang-Mills theory in three-dimensions is expected to make the latter flow
into infrared superconformal phases. We address this problem holographically by
studying the effect of the Romans mass on the D2-brane near-horizon geometry.
Working in a consistent, effective four-dimensional setting provided by $D=4$
${\cal N}=8$ supergravity with a dyonic $\textrm{ISO(7)}$ gauging, we verify
the existence of a rich web of supersymmetric domain walls triggered by the
Romans mass that interpolate between the (four-dimensional description of the)
D2-brane and various superconformal phases. We also construct domain walls for
which both endpoints are superconformal. While most of our results are
numerical, we provide analytic results for the $\textrm{SU}(3)\times
\textrm{U}(1)$-invariant flow into an ${\cal N}=2$ conformal phase recently
discovered.


title: Endomorphism algebras of 2-term silting complexes

abstract:
  We study possible values of the global dimension of endomorphism algebras of
2-term silting complexes. We show that for any algebra $A$ whose global
dimension $\mathop{\rm gl. dim}\nolimits A\leq 2$ and any 2-term silting
complex $\mathbf{P}$ in the bounded derived category ${D^b(A)}$ of $A$, the
global dimension of $\mathop{\rm End}\nolimits_{D^b(A)}(\mathbf{P})$ is at most
7. We also show that for each $n>2$, there is an algebra $A$ with $\mathop{\rm
gl. dim}\nolimits A=n$ such that ${D^b(A)}$ admits a 2-term silting complex
$\mathbf{P}$ with $\mathop{\rm gl. dim}\nolimits \mathop{\rm
End}\nolimits_{D^b(A)}(\mathbf{P})$ infinite.


title: The C*-algebra of SL(2,R)

abstract:
  The $C^*$-algebra of the group $SL(2,{\mathbb R})$ is characterized using the
operator valued Fourier transform. In particular, it is shown by explicit
computations, that the Fourier transform of this $C^*$-algebra fulfills the
norm controlled dual limit property.


title: Optimal Disruption of Complex Networks

abstract:
  The collection of all the strongly connected components in a directed graph,
among each cluster of which any node has a path to another node, is a typical
example of the intertwining structure and dynamics in complex networks, as its
relative size indicates network cohesion and it also composes of all the
feedback cycles in the network. Here we consider finding an optimal strategy
with minimal effort in removal arcs (for example, deactivation of directed
interactions) to fragment all the strongly connected components into tree
structure with no effect from feedback mechanism. We map the optimal network
disruption problem to the minimal feedback arc set problem, a
non-deterministically polynomial hard combinatorial optimization problem in
graph theory. We solve the problem with statistical physical methods from spin
glass theory, resulting in a simple numerical method to extract sub-optimal
disruption arc sets with significantly better results than a local heuristic
method and a simulated annealing method both in random and real networks. Our
results has various implications in controlling and manipulation of real
interacted systems.


title:
Short-time counting statistics of charge transfer in Coulomb-blockade
  systems

abstract:
  We study full counting statistics of electron tunneling in Coulomb-blockade
systems in the limit of short measuring-time intervals. This limit is
particularly suited to identify correlations among tunneling events, but only
when analyzing the charge-transfer statistics in terms of factorial cumulants
$C_{{\rm F}, m}(t)$ rather than ordinary ones commonly used in literature. In
the absence of correlations, the short-time behavior of the factorial cumulants
is given by $C_{{\rm F}, m}(t) \propto (-1)^{m-1}t^m$. A different sign and/or
a different power law of the time dependence indicates correlations. We
illustrate this for sequential and Andreev tunneling in a metallic
single-electron box.


title:
Labyrinthine water flow across multilayer graphene-based membranes:
  molecular dynamics versus continuum predictions

abstract:
  In this paper we investigate the hydrodynamic permeance of water through
graphene-based membranes, inspired by recent experimental findings on
graphene-oxide membranes. We consider the flow across multiple graphene layers
having nanoslits in a staggered alignment, with an inter-layer distance ranging
from sub- nanometer to a few nanometers. We compare results for the
permeability obtained by means of molecular dynamics simulations to continuum
predictions obtained by using the lattice Boltzmann calculations and
hydrodynamic modelization. This highlights that, in spite of extreme
confinement, the permeability across the graphene-based membrane is
quantitatively predicted on the basis of a continuum expression, taking
properly into account entrance and slippage effects of the confined water flow.
Our predictions refute the breakdown of hydrodynamics at small scales in these
membrane systems. They constitute a benchmark to which we compare published
experimental data.

categories: cond-mat.mes-hall cond-mat.soft physics.chem-ph physics.comp-ph physics.flu-dyn


title: Elliptic fibrations on K3 surfaces and Salem numbers of maximal degree

abstract:
  We study the maximal Salem degree of automorphisms of K3 surfaces via
elliptic fibrations. By generalizing \cite{EOY14}, we establish a
characterization of such maximum in terms of elliptic fibrations with infinite
automorphism groups. As an application, we show that any supersingular K3
surface in odd characteristic has an automorphism the entropy of which is the
natural logarithm of a Salem number of degree $22$.


title:
AMiBA: Cluster Sunyaev-Zel'dovich Effect Observations with the Expanded
  13-Element Array

abstract:
  The Yuan-Tseh Lee Array for Microwave Background Anisotropy (AMiBA) is a
co-planar interferometer array operating at a wavelength of 3mm to measure the
Sunyaev-Zeldovich effect (SZE) of galaxy clusters. In the first phase of
operation -- with a compact 7-element array with 0.6m antennas (AMiBA-7) -- we
observed six clusters at angular scales from 5\arcmin to 23\arcmin. Here, we
describe the expansion of AMiBA to a 13-element array with 1.2m antennas
(AMiBA-13), its subsequent commissioning, and our cluster SZE observing
program. The most important changes compared to AMiBA-7 are (1) array
re-configuration with baselines ranging from 1.4m to 4.8m covering angular
scales from 2\arcmin to 11.5\arcmin, (2) thirteen new lightweight
carbon-fiber-reinforced plastic (CFRP) 1.2m reflectors, and (3) additional
correlators and six new receivers. From the AMiBA-13 SZE observing program, we
present here maps of a subset of twelve clusters. In highlights, we combine
AMiBA-7 and AMiBA-13 observations of Abell 1689 and perform a joint fitting
assuming a generalized NFW pressure profile. Our cylindrically integrated
Compton-y values for this cluster are consistent with the BIMA/OVRA, SZA, and
Planck results. We report the first targeted SZE detection towards the
optically selected galaxy cluster RCS J1447+0828, and we demonstrate the
ability of AMiBA SZE data to serve as a proxy for the total cluster mass.
Finally, we show that our AMiBA-SZE derived cluster masses are consistent with
recent lensing mass measurements in the literature.


title: Three X-ray Flares Near Primary Eclipse of the RS CVn Binary XY UMa

abstract:
  We report on an archival X-ray observation of the eclipsing RS CVn binary XY
UMa ($\rm P_{orb}\approx$ 0.48d). In two $\emph{Chandra}$ ACIS observations
spanning 200 ks and almost five orbital periods, three flares occurred. We find
no evidence for eclipses in the X-ray flux. The flares took place around times
of primary eclipse, with one flare occurring shortly ($<0.125\rm P_{orb}$)
after a primary eclipse, and the other two happening shortly ($<0.05\rm
P_{orb}$) before a primary eclipse. Two flares occurred within roughly one
orbital period ($\Delta \phi\approx1.024\rm P_{orb}$) of each other. We analyze
the light curve and spectra of the system, and investigate coronal length
scales both during quiescence and during flares, as well as the timing of the
flares. We explore the possibility that the flares are orbit-induced by
introducing a small orbital eccentricity, which is quite challenging for this
close binary.


title: Development of SED Camera for Quasars in Early Universe (SQUEAN)

abstract:
  We describe the characteristics and performance of a camera system, Spectral
energy distribution Camera for Quasars in Early Universe (SQUEAN). It was
developed to measure SEDs of high redshift quasar candidates (z $\gtrsim$ 5)
and other targets, e.g., young stellar objects, supernovae, and gamma-ray
bursts, and to trace the time variability of SEDs of objects such as active
galactic nuclei (AGNs). SQUEAN consists of an on-axis focal plane camera
module, an auto-guiding system, and mechanical supporting structures. The
science camera module is composed of a focal reducer, a customizable filter
wheel, and a CCD camera on the focal plane. The filter wheel uses filter
cartridges that can house filters with different shapes and sizes, enabling the
filter wheel to hold twenty filters of 50 mm $\times$ 50 mm size, ten filters
of 86 mm $\times$ 86 mm size, or many other combinations. The initial filter
mask was applied to calibrate the filter wheel with high accuracy and we
verified that the filter position is repeatable at much less than one pixel
accuracy. We installed and tested 50 nm medium bandwidth filters of 600 --
1,050 nm and other filters at the commissioning observation in 2015 February.
We found that SQUEAN can reach limiting magnitudes of 23.3 - 25.3 AB mag at
5-$\sigma$ in a 1-hour total integration time. - 25.3 AB mag at 5-$\sigma$ in a
1-hour total integration time.


title:
Limiting Phase Trajectories: a new paradigm for the study of highly
  non-stationary processes in Nonlinear Physics

abstract:
  This Report discusses a recently developed concept of Limiting Phase
Trajectories (LPTs) providing a unified description of resonant energy
transport in a wide range of classical and quantum dynamical systems with
constant and time-varying parameters. It is shown that strongly modulated
non-stationary processes occurring in a nonlinear oscillator array under
certain initial conditions may characterize either maximum possible energy
exchange between the clusters of oscillators (effective particles) or maximum
energy transfer from an external source of energy to the system. The
trajectories corresponding to these processes are referred to as LPTs. The
development and the use of the LPT concept are motivated by the fact that
highly non-stationary resonance processes occurring in a broad variety of
finite-dimensional physical models are beyond the well-known paradigm of the
nonlinear normal modes (NNMs), fully justified only for stationary processes,
their stability and bifurcations, as well as for non-stationary processes
described approximately by some combinations of non-resonating normal modes.
Thus, the role of LPTs in understanding and description of non-stationary
energy transfer is similar to the role of NNMs for the stationary processes.
Several applications of the LPT concept to significant nonlinear problems and a
scenario of the transition from regular to chaotic behavior with the LPTs
implication are presented. In order to highlight the novelty and perspectives
of the developed approach, we place the LPT concept into the context of complex
dynamical phenomena related to energy transfer problems.


title: Constructing $G$-algebras

abstract:
  In this article we define $G$-algebras, that is, graded algebras on which a
reductive group $G$ acts as gradation preserving automorphisms. Starting from a
finite dimensional $G$-module $V$ and the polynomial ring $\mathbb{C}[V]$, it
is shown how one constructs a sequence of projective varieties $\mathbf{V}_k$
such that each point of $\mathbf{V}_k$ corresponds to a graded algebra with the
same decomposition up to degree $k$ as a $G$-module. After some general theory,
we apply this to the case that $V$ is the $n+1$-dimensional permutation
representation of $S_{n+1}$, the permutation group on $n+1$ letters.


title:
Towards protein-protein docking with significant structural changes
  using CABS-dock

abstract:
  The protein-protein interactions (PPIs) are crucial for understanding the
majority of cellular processes. PPIs play important role in gene transcription
regulation, cellular signaling, molecular basis of immune response and more.
Moreover, a disruption of hese mechanisms is frequently postulated as a
possible cause of diseases such as Alzheimer's or cancer. For many of
biologically relevant cases the structure of protein-protein complexes remain
unknown. Therefore computational techniques, including molecular docking, have
become a valuable part of drug discovery pipelines. Unfortunately, none of the
widely used protein-protein docking tools is free from serious limitations.
Typically, in docking simulations the protein flexibility is either completely
neglected or very limited. Additionally, some knowledge of the approximate
location and/or the shape of the active site is also required. Such limitations
arise mostly from the enormous number of degrees of freedom of protein-protein
systems. In this paper, an efficient computational method for protein-protein
docking is proposed and initially tested on a single docking case. The proposed
method is based on a two-step procedure. In the first step, CABS-dock web
server for protein-peptide docking is used to dock a peptide, which is the
appropriate protein fragment responsible for the protein-protein interaction,
to the other protein partner. During peptide docking, no knowledge about the
binding site, nor the peptide structure, is used and the peptide is allowed to
be fully flexible. In the second step, the docked peptide is used in the
structural adjustment of protein complex partners. The proposed method allowed
us to obtain a high accuracy model, therefore it provides a promising framework
for further advances.


title:
The slowly pulsating B-star 18 Peg: A testbed for upper main sequence
  stellar evolution

abstract:
  The predicted width of the upper main sequence in stellar evolution models
depends on the empirical calibration of the convective overshooting parameter.
Despite decades of discussions, its precise value is still unknown and further
observational constraints are required to gauge it. Based on a photometric and
preliminary asteroseismic analysis, we show that the mid B-type giant 18 Peg is
one of the most evolved members of the rare class of slowly pulsating B-stars
and, thus, bears tremendous potential to derive a tight lower limit for the
width of the upper main sequence. In addition, 18 Peg turns out to be part of a
single-lined spectroscopic binary system with an eccentric orbit that is
greater than 6 years. Further spectroscopic and photometric monitoring and a
sophisticated asteroseismic investigation are required to exploit the full
potential of this star as a benchmark object for stellar evolution theory.


title:
The Role of Inter-Controller Traffic for Placement of Distributed SDN
  Controllers

abstract:
  We consider a distributed Software Defined Networking (SDN) architecture
adopting a cluster of multiple controllers to improve network performance and
reliability. Besides the Openflow control traffic exchanged between controllers
and switches, we focus on the control traffic exchanged among the controllers
in the cluster, needed to run coordination and consensus algorithms to keep the
controllers synchronized. We estimate the effect of the inter-controller
communications on the reaction time perceived by the switches depending on the
data-ownership model adopted in the cluster. The model is accurately validated
in an operational Software Defined WAN (SDWAN). We advocate a careful placement
of the controllers, that should take into account both the above kinds of
control traffic. We evaluate, for some real ISP network topologies, the delay
tradeoffs for the controllers placement problem and we propose a novel
evolutionary algorithm to find the corresponding Pareto frontier. Our work
provides novel quantitative tools to optimize the planning and the design of
the network supporting the control plane of SDN networks, especially when the
network is very large and in-band control plane is adopted. We also show that
for operational distributed controllers (e.g. OpenDaylight and ONOS), the
location of the controller which acts as a leader in the consensus algorithm
has a strong impact on the reactivity perceived by switches.


title:
Flexible protein-peptide docking using CABS-dock with knowledge about
  the binding site

abstract:
  Despite considerable efforts, structural prediction of protein-peptide
complexes is still a very challenging task, mainly due to two reasons: high
flexibility of the peptides and transient character of their interactions with
proteins. Recently we have developed an automated web server CABS-dock
(http://biocomp.chem.uw.edu.pl/CABSdock), which conducts flexible
protein-peptide docking without any knowledge about the binding site. Our
method allows for full flexibility of the peptide, whereas the flexibility of
the receptor is restricted to near native conformations considering the main
chain, and full flexibility of the side chains. Performance of the CABS-dock
server was thoroughly tested on a benchmark of 171 test cases, both bound and
unbound. Evaluation of the obtained results showed overall good performance of
the method, especially that no information of the binding site was used. From
unsuccessful experiments we learned that the accuracy of docking might be
significantly improved, if only little information of the binding site was
considered. In fact, in real-life applications user typically has access to
some data indicating the location and/or structure of the binding site. In the
current work, we test and demonstrate the performance of the CABS-dock server
with two new features. The first one allows to utilize the knowledge about
receptor residue(s) constituting the binding site, and the second one allows to
enforce the desired secondary structure on the peptide structure. Based on the
given example, we observe significant improvement of the docking accuracy in
comparison to the default CABS-dock mode.


title:
Collective versus individual classicality for a pair of interacting
  qubits immersed in independent local environments

abstract:
  There is current interest in investigating which variables play an important
role in the physical processes with an open composite quan- tum system that
ranges from the foundational issues to the tasks of diverse applications in
quantum physics and technology. In this paper we contrast the local versus the
collective classical-like behavior of a pair of interacting qubits immersed in
the mutually independent thermal baths. The qubits can be locally subjected to
any of the standard, microscopically modelled, generalized amplitude damping
and phase damping channel, as well as to the recently introduced generalized
depolarizing channel. As a criterion for the classical-like behavior we use the
least entropy production, i.e. the total correlation in the system. The
classical-like collective behavior is found for short time intervals for
strongly interacting qubits. Only in a certain trivial case we observe the
simultaneous collective and individual-qubits classical- ity. Observation
(non-observation) of the collective (individual) classicality can reveal the
kind and strength of the qubits interaction or the ratio of the qubits'
energy-gaps, while manipulating the qubits interaction (by tuning the strength
and/or refocussing) can give rise to the desired kind of classicality.


title: Lamb shift of the Dirac cone of graphene

abstract:
  The fluctuations of the electromagnetic vacuum are one of the most powerful
manifestations of the quantum structure of nature. Their effect on the Dirac
electrons of graphene is known to induce some spectacular and purely quantistic
phenomena, like the Casimir and the Aharanov--Bohm effects. In this work we
demonstrate, by using a first principles approach, that the Dirac cone of
graphene is also affected by a sizable Lamb shift.We show that the microscopic
electronic currents flowing on the graphene plane couple efficiently with the
vacuum fluctuations causing a renormalization of the electronic levels (as
large as 4 meV) and of the velocities. This Lamb shift is one order of
magnitude larger than the value predicted for an isolated carbon atom.


title: Conformal symmetry breaking operators for differential forms on spheres

abstract:
  We give a complete classification of conformally covariant differential
operators between the spaces of $i$-forms on the sphere $S^n$ and $j$-forms on
the totally geodesic hypersphere $S^{n-1}$. Moreover, we find explicit
formul{\ae} for these new matrix-valued operators in the flat coordinates in
terms of basic operators in differential geometry and classical orthogonal
polynomials. We also establish matrix-valued factorization identities among all
possible combinations of conformally covariant differential operators. The main
machinery of the proof is the "F-method" based on the "algebraic Fourier
transform of Verma modules" (Kobayashi-Pevzner [Selecta Math. 2016]) and its
extension to matrix-valued case developed here. A short summary of the main
results was announced in [C. R. Acad. Sci. Paris, 2016].


title:
Uniqueness of the solution of the Gaudin's equations, which describe a
  one-dimensional system of point bosons with zero boundary conditions

abstract:
  We show that the system of Gaudin's equations for quasimomenta k_{j}, which
describes a one-dimensional system of spinless point bosons with zero boundary
conditions, has the unique real solution for each set of quantum numbers n_{j}.


title: Factorizations in bounded hereditary Noetherian prime rings

abstract:
  If $H$ is a monoid and $a=u_1 \cdots u_k \in H$ with atoms (irreducible
elements) $u_1, \ldots, u_k$, then $k$ is a length of $a$, the set of lengths
of $a$ is denoted by $\mathsf L(a)$, and $\mathcal L(H)=\{\,\mathsf L (a) \mid
a \in H \,\}$ is the system of sets of lengths of $H$. Let $R$ be a hereditary
Noetherian prime (HNP) ring. Then every element of the monoid of
non-zero-divisors $R^\bullet$ can be written as a product of atoms. We show
that, if $R$ is bounded and every stably free right $R$-ideal is free, then
there exists a transfer homomorphism from $R^{\bullet}$ to the monoid $B$ of
zero-sum sequences over a subset $G_{\textrm{max}}(R)$ of the ideal class group
$G(R)$. This implies that the systems of sets of lengths, together with further
arithmetical invariants, of the monoids $R^{\bullet}$ and $B$ coincide. It is
well-known that commutative Dedekind domains allow transfer homomorphisms to
monoids of zero-sum sequences, and the arithmetic of the latter has been the
object of much research. Our approach is based on the structure theory of
finitely generated projective modules over HNP rings, as established in the
recent monograph by Levy and Robson. We complement our results by giving an
example of a non-bounded HNP ring in which every stably free right $R$-ideal is
free but which does not allow a transfer homomorphism to a monoid of zero-sum
sequences over any subset of its ideal class group.


title: Optomechanics with two-phonon driving

abstract:
  We consider the physics of an optomechanical cavity subject to coherent
two-phonon driving, i.e. degenerate parametric amplification of the mechanical
mode. We show that in such a system, the cavity mode can effectively "inherit"
parametric driving from the mechanics, yielding phase-sensitive amplification
and squeezing of optical signals reflected from the cavity. We also demonstrate
how such a system can be used to perform single-quadrature detection of a
near-resonant narrow-band force applied to the mechanics with extremely low
added noise from the optics. The system also exhibits strong differences from a
conventional degenerate parametric amplifier: in particular, the cavity
spectral function can become negative, indicating a negative effective photon
temperature.


title: Langevin equations for landmark image registration with uncertainty

abstract:
  Registration of images parameterised by landmarks provides a useful method of
describing shape variations by computing the minimum-energy time-dependent
deformation field that flows one landmark set to the other. This is sometimes
known as the geodesic interpolating spline and can be solved via a Hamiltonian
boundary-value problem to give a diffeomorphic registration between images.
However, small changes in the positions of the landmarks can produce large
changes in the resulting diffeomorphism. We formulate a Langevin equation for
looking at small random perturbations of this registration. The Langevin
equation and three computationally convenient approximations are introduced and
used as prior distributions. A Bayesian framework is then used to compute a
posterior distribution for the registration, and also to formulate an average
of multiple sets of landmarks.


title: Towards negative index self-assembled metamaterials

abstract:
  We investigate the magnetic response of meta-atoms that can be fabricated by
a bottom-up technique. Usually such meta-atoms consist of a dielectric core
surrounded by a large number of solid metallic nanoparticles. In contrast to
those meta-atoms considered thus far, we study here for the first time hollow
metallic nanoparticles (shells). In doing so we solve one of the most pertinent
problems of current self-assembled metamaterials, namely implementing
meta-atoms with sufficiently large resonance strength and small absorption.
Both conditions have to be met for deep sub-wavelength meta-atoms to obtain
effectively homogeneous metamaterials which may be meaningfully described by
negative material parameters. Eventually we show that by using these findings
self-assembled negative index materials come in reach.


title: Universal Quantum Computing with Arbitrary Continuous-Variable Encoding

abstract:
  Implementing a qubit quantum computer in continuous-variable systems
conventionally requires the engineering of specific interactions according to
the encoding basis states. In this work, we present a unified formalism to
conduct universal quantum computation with a fixed set of operations but
arbitrary encoding. By storing a qubit in the parity of two or four qumodes,
all computing processes can be implemented by basis state preparations,
continuous-variable exponential-swap operations, and swap-tests. Our formalism
inherits the advantages that the quantum information is decoupled from
collective noise, and logical qubits with different encodings can be brought to
interact without decoding. We also propose a possible implementation of the
required operations by using interactions that are available in a variety of
continuous-variable systems. Our work separates the `hardware' problem of
engineering quantum-computing-universal interactions, from the `software'
problem of designing encodings for specific purposes. The development of
quantum computer architecture could hence be simplified.


title: Division by 2 on elliptic curves

abstract:
  We discuss a non-computational elementary approach to a well-known criterion
of divisibility by 2 in the group of rational points on an elliptic curve.


title:
Linear partial divided-difference equation satisfied by multivariate
  orthogonal polynomials on quadratic lattices

abstract:
  In this paper, a fourth-order partial divided-difference equation on
quadratic lattices with polynomial coefficients satisfied by bivariate Racah
polynomials is presented. From this equation we obtain explicitly the matrix
coefficients appearing in the three-term recurrence relations satisfied by any
bivariate orthogonal polynomial solution of the equation. In particular, we
provide explicit expressions for the matrices in the three-term recurrence
relations satisfied by the bivariate Racah polynomials introduced by Tratnik.
Moreover, we present the family of monic bivariate Racah polynomials defined
from the three-term recurrence relations they satisfy, and we solve the
connection problem between two different families of bivariate Racah
polynomials. These results are then applied to other families of bivariate
orthogonal polynomials, namely the bivariate Wilson, continuous dual Hahn and
continuous Hahn, the latter two through limiting processes. The fourth-order
partial divided-difference equations on quadratic lattices are shown to be of
hypergeometric type in the sense that the divided-difference derivatives of
solutions are themselves solution of the same type of divided-difference
equations.


title: On the principal eigenvectors of uniform hypergraphs

abstract:
  Let $\mathcal{A}(H)$ be the adjacency tensor of $r$-uniform hypergraph $H$.
If $H$ is connected, the unique positive eigenvector
$x=(x_1,x_2,\ldots,x_n)^{\mathrm{T}}$ with $||x||_r=1$ corresponding to
spectral radius $\rho(H)$ is called the principal eigenvector of $H$. The
maximum and minimum entries of $x$ are denoted by $x_{\max}$ and $x_{\min}$,
respectively. In this paper, we investigate the bounds of $x_{\max}$ and
$x_{\min}$ in the principal eigenvector of $H$. Meanwhile, we also obtain some
bounds of the ratio $x_i/x_j$ for $i$, $j\in [n]$ as well as the principal
ratio $\gamma(H)=x_{\max}/x_{\min}$ of $H$. As an application of these results
we finally give an estimate of the gap of spectral radii between $H$ and its
proper sub-hypergraph $H'$.


title:
Scale-Free Exponents of Resting State provide a Biomarker for Typical
  and Atypical Brain Activity

abstract:
  Scale-free networks (SFN) arise from simple growth processes, which can
encourage efficient, centralized and fault tolerant communication (1). Recently
its been shown that stable network hub structure is governed by a phase
transition at exponents (>2.0) causing a dramatic change in network structure
including a loss of global connectivity, an increasing minimum dominating node
set, and a shift towards increasing connectivity growth compared to node
growth. Is this SFN shift identifiable in atypical brain activity? The Pareto
Distribution (P(D)~D^-\b{eta}) on the hub Degree (D) is a signature of
scale-free networks. During resting-state, we assess Degree exponents across a
large range of neurotypical and atypical subjects. We use graph complexity
theory to provide a predictive theory of the brain network structure. Results.
We show that neurotypical resting-state fMRI brain activity possess scale-free
Pareto exponents (1.8 se .01) in a single individual scanned over 66 days as
well as in 60 different individuals (1.8 se .02). We also show that 60
individuals with Autistic Spectrum Disorder, and 60 individuals with
Schizophrenia have significantly higher (>2.0) scale-free exponents (2.4 se
.03, 2.3 se .04), indicating more fractionated and less controllable dynamics
in the brain networks revealed in resting state. Finally we show that the
exponent values vary with phenotypic measures of atypical disease severity
indicating that the global topology of the network itself can provide specific
diagnostic biomarkers for atypical brain activity.


title: Squares from any Quadrilateral

abstract:
  In 1998 A. Connes proposed an algebraic proof of Morley's trisector theorem.
He observed that the points of intersection of the trisectors are the fixed
points of pairwise products of rotations around vertices of the triangle with
angles two thirds of the corresponding angles of the triangle. This paper
enquires for similar results when the initial polygon is an arbitrary
quadrilateral. First we show that, when correctly gathered, fixed points of
products of rotations around vertices of the quadrilateral with angles (2n+1)/2
of the corresponding angles of the quadrilateral form essentially six
parallelograms for any integer n. Several congruence relations are exhibited
between these parallelograms. Then, we show that if the original quadrilateral
is itself a parallelogram, then for any integer n four of the resulting
parallelograms are squares. Hence we present a function which, when applied
twice, gives squares from any quadrilateral. The proofs use only algebraic
methods of undergraduate level.


title:
Global Analysis of the Source and Detector Nonstandard Interactions
  Using the Short Baseline Neutrino- and Antineutrino-Electron Scattering Data

abstract:
  We present a global analysis of the semileptonic and purely Leptonic
nonuniversal and flavor-changing nonstandard neutrino interactions in all the
known short-baseline neutrino- and antineutrino-electron scattering
experiments. The nonstandard effects at the source and at the detector can be
more transparent in these experiments because of the negligibly small ratio
between the baselines and the neutrino energies, which is not enough for the
neutrinos to oscillate, and thus can be sensitive to the new physics at the
both ends. We use data from two electron-neutrino electron scattering
experiments and six electron-antineutrino electron scattering experiments and
combine them to find the best fits on the nonstandard parameters using the
source-only, detector-only analyses, and then find the interplay between the
two cases. The bounds obtained in some cases are stronger and new, in some
cases comparable to the current ones, and in the other cases weaker. For
instance, the bound obtained from the interplay between the source and detector
nonstandard physics on the nonstandard parameter {\epsilon}_{ee}^{udL} at the
source is much stronger and is comparable with the indirect bound, but the
bounds on the parameters {\epsilon}_{{\mu}e}^{udL} and
{\epsilon}_{{\tau}e}^{udL} are weaker in this study in comparison with the
indirect bounds. We also find a global fit on the standard weak mixing angle
sin{\theta}_{W}=0.249+-0.020 with 2% improvement in its precision in comparison
with the previous studies.


title: A semi-classical recipe for wobbly limp noodles in partonic soup

abstract:
  We compute the average squared distance, $s^2(t)$, travelled by a
light-flavour off-mass-shell coloured parton in a strongly-coupled
$\mathcal{N}=4$ $SU(N_c)$ super-symmetric Yang Mills plasma using the
gauge/string duality. In fact, we derive a closed integral expression for
$s^2(t;a)$ in $AdS_3$-Schwarzschild, which interpolates between a heavy quark
when $a = 0$ and a light quark when $a = 1$, that we evaluate analytically for
small virtualities - labelled $s_\text{small}^2(t;a)$. For arbitrary
virtualities, we show that for asymptotically early times the motion is
ballistic, $\left.s^2(t;a)\right|_{t\ll\beta}\sim t^2$, while at asymptotically
late times the motion is diffusive, $\left. s^2(t;a) \right|_{t\gg\beta} =
s_\text{small}^2(t;a) \sim 2D(a) t$, from which we are able to extract the
diffusion coefficient $D(a)$. Motivated by the apparent universality of the
late time behaviour, we compute $s_{\text{small}}^2(t;a,d)$ and $D(a,d)$ for an
arbitrary $AdS_d$-Schwarzschild geometry. From $D(a,d)$ we then compute for the
first time the dynamic, time-dependent transverse momentum squared per unit
path length picked up by a high momentum light quark in a strongly-coupled
plasma, the transport coefficient $\hat{q}(t)$, which is critically important
for phenomenology in heavy ion collisions.


title:
Spectroscopy of Kerr black holes with Earth- and space-based
  interferometers

abstract:
  We estimate the potential of present and future interferometric
gravitational-wave detectors to test the Kerr nature of black holes through
"gravitational spectroscopy," i.e. the measurement of multiple quasinormal mode
frequencies from the remnant of a black hole merger. Using population synthesis
models of the formation and evolution of stellar-mass black hole binaries, we
find that Voyager-class interferometers will be necessary to perform these
tests. Gravitational spectroscopy in the local Universe may become routine with
the Einstein Telescope, but a 40-km facility like Cosmic Explorer is necessary
to go beyond $z\sim 3$. In contrast, eLISA-like detectors should carry out a
few - or even hundreds - of these tests every year, depending on uncertainties
in massive black hole formation models. Many space-based spectroscopical
measurements will occur at high redshift, testing the strong gravity dynamics
of Kerr black holes in domains where cosmological corrections to general
relativity (if they occur in nature) must be significant.


title: GAVIP: A Platform for Gaia Data Analysis

abstract:
  Gaia is a major European Space Agency (ESA) astrophysics mission designed to
map and analyse 10$^9$ stars, ultimately generating more than 1 PetaByte of
data products. As Gaia data becomes publicly available and reaches a wider
audience, there is an increasing need to facilitate the further use of Gaia
products without needing to download large datasets. The Gaia Added Value
Interface Platform (GAVIP) is designed to address this challenge by providing
an innovative platform within which scientists can submit and deploy code,
packaged as "Added Value Interfaces" (AVIs), which will be executed close to
the data. Deployed AVIs and associated outputs may also be made available to
other GAVIP platform users, thus providing a mechanism for scientific
experiment reproducibility. This paper describes the capabilities and features
of GAVIP.


title:
Generalized Network Psychometrics: Combining Network and Latent Variable
  Models

abstract:
  We introduce the network model as a formal psychometric model,
conceptualizing the covariance between psychometric indicators as resulting
from pairwise interactions between observable variables in a network structure.
This contrasts with standard psychometric models, in which the covariance
between test items arises from the influence of one or more common latent
variables. Here, we present two generalizations of the network model that
encompass latent variable structures, establishing network modeling as parts of
the more general framework of Structural Equation Modeling (SEM). In the first
generalization, we model the covariance structure of latent variables as a
network. We term this framework Latent Network Modeling (LNM) and show that,
with LNM, a unique structure of conditional independence relationships between
latent variables can be obtained in an explorative manner. In the second
generalization, the residual variance-covariance structure of indicators is
modeled as a network. We term this generalization Residual Network Modeling
(RNM) and show that, within this framework, identifiable models can be obtained
in which local independence is structurally violated. These generalizations
allow for a general modeling framework that can be used to fit, and compare,
SEM models, network models, and the RNM and LNM generalizations. This
methodology has been implemented in the free-to-use software package lvnet,
which contains confirmatory model testing as well as two exploratory search
algorithms: stepwise search algorithms for low-dimensional datasets and
penalized maximum likelihood estimation for larger datasets. We show in
simulation studies that these search algorithms performs adequately in
identifying the structure of the relevant residual or latent networks. We
further demonstrate the utility of these generalizations in an empirical
example on a personality inventory dataset.


title: Universal isolation in the AdS landscape

abstract:
  We study the universal conditions for quantum non-perturbative stability
against bubble nucleation for pertubatively stable AdS vacua based on positive
energy theorems. We also compare our analysis with the pre-existing ones in the
literature carried out within the thin-wall approximation. The aforementioned
criterion is then tested in two explicit examples describing massive type IIA
string theory compactified on $S^3$ and $S^3\,\times\,S^3$, respectively. The
AdS landscape of both classes of compactifications is known to consist of a set
of isolated points. The main result is that all critical points respecting the
Breitenlohner-Freedaman (BF) bound also turn out be stable at a
non-perturbative level. Finally, we speculate on the possible universal
features that may be extracted from the above specific examples.


title:
Concavity of Perelman's $\mathcal{W}$-functional over the space of
  K\"ahler potentials

abstract:
  In this short note we observe that the concavity of Perelman's
$\mathcal{W}$-functional over a neighborhood of a K\"ahler-Ricci soliton inside
the space of K\"ahler potentials is a direct consequence of author's solution
of the variational stability problem for K\"ahler-Ricci solitons.
Independently, we provide a rather simple proof of this fact based on some
elementary formulas obtained in our previous work.


title: Polymer additives in fluid turbulence and distributed chaos

abstract:
  The fluids and polymers have different fundamental symmetries. Namely, the
Lagrangian relabeling symmetry of fluids is absent for polymers (while the
translational and rotational symmetries are still present). This fact results
in spontaneous breaking of the relabeling symmetry in fluid turbulence even at
a tiny polymer addition. Since helicity conservation in inviscid fluid motions
is a consequence of the relabeling symmetry (due to the Noether's theorem)
violation of this conservation by the polymer additives results in the strong
effects in the distributed chaos. The distributed chaos in turbulence with the
spontaneously broken relabeling symmetry is characterized by stretched
exponential spectra $\propto \exp(-k/k_{\beta})^{\beta}$ with $\beta =2/5$. The
spectral range of this distributed chaos is extended in direction of the small
wavenumbers and $k_{\beta}$ becomes much larger in comparison with the pure
fluid (Newtonian) case. This results in substantial suppression of small-scale
turbulence and large-scale mixing enhancement. Good agreement with results of
direct numerical simulations (DNS) and experimental data has been established
for a channel flow (DNS), for Rayleigh-Taylor turbulent convection (DNS) and
for Rayleigh-Benard turbulent convection (experiment).


title: Hecke operators on half-integral weight Siegel Eisenstein series

abstract:
  We construct a basis for the space of half-integral weight Siegel Eisenstein
series of level 4N where N is odd and square-free. Then we restrict our
attention to those Eisenstein series generated from elements of $\Gamma_0(4)$,
commenting on why this restriction is necessary for our methods. We directly
apply to these forms all Hecke operators attached to odd primes, and we realize
the images explicitly as linear combinations of Siegel Eisenstein series. Using
this information, we diagonalize the subspace of Eisenstein series generated
from elements of $\Gamma_0(4)$, obtaining a multiplicity-one result.


title: Internal Guidance for Satallax

abstract:
  We propose a new internal guidance method for automated theorem provers based
on the given-clause algorithm. Our method influences the choice of unprocessed
clauses using positive and negative examples from previous proofs. To this end,
we present an efficient scheme for Naive Bayesian classification by
generalising label occurrences to types with monoid structure. This makes it
possible to extend existing fast classifiers, which consider only positive
examples, with negative ones. We implement the method in the higher-order logic
prover Satallax, where we modify the delay with which propositions are
processed. We evaluated our method on a simply-typed higher-order logic version
of the Flyspeck project, where it solves 26% more problems than Satallax
without internal guidance.


title:
Probing vacuum birefringence using x-ray free electron and optical
  high-intensity lasers

abstract:
  Vacuum birefringence is one of the most striking predictions of strong field
quantum electrodynamics: Probe photons traversing a strong field region can
indirectly sense the applied "pump" electromagnetic field via quantum
fluctuations of virtual charged particles which couple to both pump and probe
fields. This coupling is sensitive to the field alignment and can effectively
result in two different indices of refraction for the probe photon polarization
modes giving rise to a birefringence phenomenon. In this article we perform a
dedicated theoretical analysis of the proposed discovery experiment of vacuum
birefringence at a x-ray free electron laser/optical high-intensity laser
facility. Describing both pump and probe laser pulses realistically in terms of
their macroscopic electromagnetic fields, we go beyond previous analyses by
accounting for various effects not considered before in this context. Our study
facilitates stringent quantitative predictions and optimizations of the signal
in an actual experiment.


title:
The Latin American Giant Observatory: a successful collaboration in
  Latin America based on Cosmic Rays and computer science domains

abstract:
  In this work the strategy of the Latin American Giant Observatory (LAGO) to
build a Latin American collaboration is presented. Installing Cosmic Rays
detectors settled all around the Continent, from Mexico to the Antarctica, this
collaboration is forming a community that embraces both high energy physicist
and computer scientists. This is so because the data that are measured must be
analytical processed and due to the fact that \textit{a priori} and \textit{a
posteriori} simulations representing the effects of the radiation must be
performed. To perform the calculi, customized codes have been implemented by
the collaboration. With regard to the huge amount of data emerging from this
network of sensors and from the computational simulations performed in a
diversity of computing architectures and e-infrastructures, an effort is being
carried out to catalog and preserve a vast amount of data produced by the
water-Cherenkov Detector network and the complete LAGO simulation workflow that
characterize each site. Metadata, Permanent Identifiers and the facilities from
the LAGO Data Repository are described in this work jointly with the simulation
codes used. These initiatives allow researchers to produce and find data and to
directly use them in a code running by means of a Science Gateway that provides
access to different clusters, Grid and Cloud infrastructures worldwide.


title: On the Fundamental Importance of Gauss-Newton in Motion Optimization

abstract:
  Hessian information speeds convergence substantially in motion optimization.
The better the Hessian approximation the better the convergence. But how good
is a given approximation theoretically? How much are we losing? This paper
addresses that question and proves that for a particularly popular and
empirically strong approximation known as the Gauss-Newton approximation, we
actually lose very little--for a large class of highly expressive objective
terms, the true Hessian actually limits to the Gauss-Newton Hessian quickly as
the trajectory's time discretization becomes small. This result both motivates
it's use and offers insight into computationally efficient design. For
instance, traditional representations of kinetic energy exploit the generalized
inertia matrix whose derivatives are usually difficult to compute. We introduce
here a novel reformulation of rigid body kinetic energy designed explicitly for
fast and accurate curvature calculation. Our theorem proves that the
Gauss-Newton Hessian under this formulation efficiently captures the kinetic
energy curvature, but requires only as much computation as a single evaluation
of the traditional representation. Additionally, we introduce a technique that
exploits these ideas implicitly using Cholesky decompositions for some cases
when similar objective terms reformulations exist but may be difficult to find.
Our experiments validate these findings and demonstrate their use on a
real-world motion optimization system for high-dof motion generation.


title:
Chaos in generically coupled phase oscillator networks with nonpairwise
  interactions

abstract:
  The Kuramoto-Sakaguchi system of coupled phase oscillators, where interaction
between oscillators is determined by a single harmonic of phase differences of
pairs of oscillators, has very simple emergent dynamics in the case of
identical oscillators that are globally coupled: there is a variational
structure that means the only attractors are full synchrony (in-phase) or splay
phase (rotating wave/full asynchrony) oscillations and the bifurcation between
these states is highly degenerate. Here we show that nonpairwise coupling -
including three and four-way interactions of the oscillator phases - that
appears generically at the next order in normal-form based calculations, can
give rise to complex emergent dynamics in symmetric phase oscillator networks.
In particular, we show that chaos can appear in the smallest possible dimension
of four coupled phase oscillators for a range of parameter values.


title: Minimal Conditions for Implications of Gronwall-Bellman Type

abstract:
  Gronwall-Bellman type inequalities entail the following implication: if a
sufficiently integrable function satisfies a certain homogeneous linear
integral inequality, then it is nonpositive. We present a minimal (necessary
and sufficient) condition on the Borel measure underlying the integrals for
this implication to hold. The condition is also a necessary prerequisite for
any nontrivial bound on solutions to inhomogeneous linear integral inequalities
of Gronwall-Bellman type.


title: k2-means for fast and accurate large scale clustering

abstract:
  We propose k^2-means, a new clustering method which efficiently copes with
large numbers of clusters and achieves low energy solutions. k^2-means builds
upon the standard k-means (Lloyd's algorithm) and combines a new strategy to
accelerate the convergence with a new low time complexity divisive
initialization. The accelerated convergence is achieved through only looking at
k_n nearest clusters and using triangle inequality bounds in the assignment
step while the divisive initialization employs an optimal 2-clustering along a
direction. The worst-case time complexity per iteration of our k^2-means is
O(nk_nd+k^2d), where d is the dimension of the n data points and k is the
number of clusters and usually n << k << k_n. Compared to k-means' O(nkd)
complexity, our k^2-means complexity is significantly lower, at the expense of
slightly increasing the memory complexity by O(nk_n+k^2). In our extensive
experiments k^2-means is order(s) of magnitude faster than standard methods in
computing accurate clusterings on several standard datasets and settings with
hundreds of clusters and high dimensional data. Moreover, the proposed divisive
initialization generally leads to clustering energies comparable to those
achieved with the standard k-means++ initialization, while being significantly
faster.


title: Planetary Nebulae in the Small Magellanic Cloud

abstract:
  We analyse the planetary nebulae (PNe) population of the Small Magellanic
Cloud (SMC), based on evolutionary models of stars with metallicities in the
range $10^{-3} \leq Z \leq 4\times 10^{-3}$ and mass $0.9 M\odot < M <
8M\odot$, evolved through the asymptotic giant branch (AGB) phase. The models
used account for dust formation in the circumstellar envelope. To characterise
the PNe sample of the SMC, we compare the observed abundances of the various
species with the final chemical composition of the AGB models: this study
allows us to identify the progenitors of the PNe observed, in terms of mass and
chemical composition. According to our interpretation, most of the PNe descend
from low-mass ($M < 2 M\odot$) stars, which become carbon rich, after
experiencing repeated third dredge-up episodes, during the AGB phase. A
fraction of the PNe showing the signature of advanced CNO processing are
interpreted as the progeny of massive AGB stars, with mass above $\sim 6
M\odot$, undergoing strong hot bottom burning. The differences with the
chemical composition of the PNe population of the Large Magellanic Cloud (LMC)
is explained on the basis of the diverse star formation history and
age-metallicity relation of the two galaxies. The implications of the present
study for some still highly debated points regarding the AGB evolution are also
commented.


title:
An Efficient Density Matrix Renormalization Group Algorithm for Chains
  with Periodic Boundary Condition

abstract:
  The Density Matrix Renormalization Group (DMRG) is a state-of-the-art
numerical technique for a one dimensional quantum many-body system; but
calculating accurate results for a system with Periodic Boundary Condition
(PBC) from the conventional DMRG has been a challenging job from the inception
of DMRG. The recent development of the Matrix Product State (MPS) algorithm
gives a new approach to find accurate results for the one dimensional PBC
system. The most efficient implementation of the MPS algorithm can scale as
O($p \times m^3$), where $p$ can vary from 4 to $m^2$. In this paper, we
propose a new DMRG algorithm, which is very similar to the conventional DMRG
and gives comparable accuracy to that of MPS. The computation effort of the new
algorithm goes as O($m^3$) and the conventional DMRG code can be easily
modified for the new algorithm.


title:
The further chameleon groups of Richard Thompson and Graham Higman:
  Automorphisms via dynamics for the Higman groups $G_{n,r}$

abstract:
  We describe, through the use of Rubin's theorem, the automorphism groups of
the Higman-Thompson groups $G_{n,r}$ as groups of specific homeomorphisms of
Cantor spaces $\mathfrak{C}_{n,r}$. This continues a thread of research begun
by Brin, and extended later by Brin and Guzm\'an: to characterise the
automorphism groups of the `Chameleon groups of Richard Thompson,' as Brin
referred to them in 1996. The work here completes the first stage of that
twenty-year-old program, containing (amongst other things) a characterisation
of the automorphism group of $V$, which was the `last chameleon.' The
homeomorphisms which arise fit naturally into the framework of Grigorchuk,
Nekrashevich, and Suschanskii's rational group $\mathscr{R}$: they are exactly
those homeomorphisms which are induced by bi-sychronizing transducers, which we
define in the paper. This result appears to offer insight into the nature of
Brin and Guzman's exotic automorphisms, while also uncovering connections with
the theory of reset words for automata (arising in the Road Colouring Problem)
and with the theory of automorphism groups of the full shift.


title: Highly flexible protein-peptide docking using CABS-dock

abstract:
  Protein-peptide molecular docking is a difficult modeling problem. It is even
more challenging when significant conformational changes that may occur during
the binding process need to be predicted. In this chapter, we demonstrate the
capabilities and features of the CABS-dock server for flexible protein-peptide
docking. CABS-dock allows highly efficient modeling of full peptide flexibility
and significant flexibility of a protein receptor. During CABS-dock docking,
the peptide folding and binding process is explicitly simulated and no
information about the peptide binding site or its structure, is used. This
chapter presents a successful CABS-dock use for docking a potentially
therapeutic peptide to a protein target. Moreover, simulation contact maps, a
new CABS-dock feature, are described and applied to the docking test case.
Finally, a tutorial for running CABS-dock from the command line or command line
scripts is provided. The CABS-dock web server is available from
http://biocomp.chem.uw.edu.pl/CABSdock/


title:
Synthesizing the preferred inputs for neurons in neural networks via
  deep generator networks

abstract:
  Deep neural networks (DNNs) have demonstrated state-of-the-art results on
many pattern recognition tasks, especially vision classification problems.
Understanding the inner workings of such computational brains is both
fascinating basic science that is interesting in its own right - similar to why
we study the human brain - and will enable researchers to further improve DNNs.
One path to understanding how a neural network functions internally is to study
what each of its neurons has learned to detect. One such method is called
activation maximization (AM), which synthesizes an input (e.g. an image) that
highly activates a neuron. Here we dramatically improve the qualitative state
of the art of activation maximization by harnessing a powerful, learned prior:
a deep generator network (DGN). The algorithm (1) generates qualitatively
state-of-the-art synthetic images that look almost real, (2) reveals the
features learned by each neuron in an interpretable way, (3) generalizes well
to new datasets and somewhat well to different network architectures without
requiring the prior to be relearned, and (4) can be considered as a
high-quality generative method (in this case, by generating novel, creative,
interesting, recognizable images).


title:
Search for dark matter and supersymmetry with a compressed mass spectrum
  in the vector boson fusion topology in proton-proton collisions at sqrt(s) =
  8 TeV

abstract:
  A first search for pair production of dark matter candidates through vector
boson fusion in proton-proton collisions at sqrt(s) = 8 TeV is performed with
the CMS detector. The vector boson fusion topology enhances missing transverse
momentum, providing a way to probe supersymmetry also in the case of a
compressed mass spectrum. The data sample corresponds to an integrated
luminosity of 18.5 inverse femtobarns recorded by the CMS experiment. The
observed dijet mass spectrum is consistent with the standard model expectation.
In an effective field theory, dark matter masses are explored as a function of
contact interaction strength. The most stringent limit on bottom squark
production with mass below 315 GeV is also reported, assuming a 5 GeV mass
difference with respect to the lightest neutralino.


title:
Rapid mapping of digital integrated circuit logic gates via
  multi-spectral backside imaging

abstract:
  Modern semiconductor integrated circuits are increasingly fabricated at
untrusted third party foundries. There now exist myriad security threats of
malicious tampering at the hardware level and hence a clear and pressing need
for new tools that enable rapid, robust and low-cost validation of circuit
layouts. Optical backside imaging offers an attractive platform, but its
limited resolution and throughput cannot cope with the nanoscale sizes of
modern circuitry and the need to image over a large area. We propose and
demonstrate a multi-spectral imaging approach to overcome these obstacles by
identifying key circuit elements on the basis of their spectral response. This
obviates the need to directly image the nanoscale components that define them,
thereby relaxing resolution and spatial sampling requirements by 1 and 2 - 4
orders of magnitude respectively. Our results directly address critical
security needs in the integrated circuit supply chain and highlight the
potential of spectroscopic techniques to address fundamental resolution
obstacles caused by the need to image ever shrinking feature sizes in
semiconductor integrated circuits.


title:
Joint Caching, Routing, and Channel Assignment for Collaborative
  Small-Cell Cellular Networks

abstract:
  We consider joint caching, routing, and channel assignment for video delivery
over coordinated small-cell cellular systems of the future Internet. We
formulate the problem of maximizing the throughput of the system as a linear
program in which the number of variables is very large. To address channel
interference, our formulation incorporates the conflict graph that arises when
wireless links interfere with each other due to simultaneous transmission. We
utilize the column generation method to solve the problem by breaking it into a
restricted master subproblem that involves a select subset of variables and a
collection of pricing subproblems that select the new variable to be introduced
into the restricted master problem, if that leads to a better objective
function value. To control the complexity of the column generation optimization
further, due to the exponential number of independent sets that arise from the
conflict graph, we introduce an approximation algorithm that computes a
solution that is within $\epsilon$ to optimality, at much lower complexity. Our
framework demonstrates considerable gains in average transmission rate at which
the video data can be delivered to the users, over the state-of-the-art
Femtocaching system, of up to 46%. These operational gains in system
performance map to analogous gains in video application quality, thereby
enhancing the user experience considerably.


title:
Revisiting the one leptoquark solution to the $R(D^{(\ast)})$ anomalies
  and its phenomenological implications

abstract:
  It has been shown recently that the anomalies observed in $\bar B\to
D^{(\ast)}\tau\bar\nu_\tau$ and $\bar B\to \bar K\ell^+\ell^-$ decays could be
resolved with just one scalar leptoquark. Fitting to the current data on
$R(D^{(\ast)})$ along with acceptable $q^2$ distributions in $\bar B\to
D^{(\ast)}\tau\bar\nu_\tau$ decays, four best-fit solutions for the operator
coefficients have been found. In this paper, we explore the possibilities of
how to discriminate these four solutions. Firstly, we find that two of them are
already excluded by the decay $B_c^-\to \tau^-\bar\nu_\tau$, because the
predicted decay widths have already overshot the total width $\Gamma_{B_c}$. It
is then found that the remaining two solutions result in two effective
Hamiltonians governing $b\to c \tau \bar\nu_{\tau}$ transition, which differ by
a sign and enhance the absolute value of the coefficient of $\bar c_L\gamma_\mu
b_L\,\bar \tau_L\gamma^\mu{\nu_\tau}_L$ operator by about $12\%$. However, they
give nearly the same predictions as in the SM for the $D^\ast$ and $\tau$
longitudinal polarizations as well as the lepton forward-backward asymmetries
in $\bar B\to D^{(\ast)}\tau\bar\nu_\tau$ decays. For the other observables
like $\mathcal B(B_c^-\to \tau^-\bar\nu_\tau)$, $\mathcal B(B_c^- \to
\gamma\tau^-\bar\nu_\tau)$, $R_{D^{(\ast)}}(q^2)$, ${\rm d}\mathcal B(\bar B\to
D^{(\ast)}\tau\bar\nu_\tau)/{\rm d}q^2$ and $\mathcal B(\bar B\to
X_c\tau\bar\nu_\tau)$, on the other hand, the two solutions give sizable
enhancements relative to the SM predictions. With measurement of $B_c^-\to
\tau^-\bar\nu_\tau$ at LHCb and refined measurements of observables in $\bar
B\to D^{(\ast)}\tau\bar\nu_\tau$ at both LHCb and Belle-II, such a specific NP
scenario could be further deciphered.


title:
Renormalization group analysis of graphene with a supercritical Coulomb
  impurity

abstract:
  We develop a field-theoretic approach to massless Dirac fermions in a
supercritical Coulomb potential. By introducing an Aharonov--Bohm solenoid at
the potential center, the critical Coulomb charge can be made arbitrarily small
for one partial-wave sector, where a perturbative renormalization group
analysis becomes possible. We show that a scattering amplitude for reflection
of particle at the potential center exhibits the renormalization group limit
cycle, i.e., log-periodic revolutions as a function of the scattering energy,
revealing the emergence of discrete scale invariance. This outcome is further
incorporated in computing the induced charge and current densities, which turn
out to have power-law tails with coefficients log-periodic with respect to the
distance from the potential center. Our findings are consistent with the
previous prediction obtained by directly solving the Dirac equation and can in
principle be realized by graphene experiments with charged impurities.


title: Synthetic Dimensions for Cold Atoms from Shaking a Harmonic Trap

abstract:
  We introduce a simple scheme to implement synthetic dimensions in ultracold
atomic gases, which only requires two basic and ubiquitous ingredients: the
harmonic trap, which confines the atoms, combined with a periodic shaking. In
our approach, standard harmonic oscillator eigenstates are reinterpreted as
lattice sites along a synthetic dimension, while the coupling between these
lattice sites is controlled by the applied time-modulation. The phase of this
modulation enters as a complex hopping phase, leading straightforwardly to an
artificial magnetic field upon adding a second dimension. We show that this
artificial gauge field has important consequences, such as the counterintuitive
reduction of average energy under resonant driving, or the realisation of
quantum Hall physics. Our approach offers significant advantages over previous
implementations of synthetic dimensions, providing an intriguing route towards
higher-dimensional topological physics and strongly-correlated states.