title: An Extension of Godunov SPH II: Application to Elastic Dynamics

abstract:
  Godunov Smoothed Particle Hydrodynamics (Godunov SPH) method is a
computational fluid dynamics method that utilizes a Riemann solver and achieves
the second-order accuracy in space. In this paper, we extend the Godunov SPH
method to elastic dynamics by incorporating deviatoric stress tensor that
represents the stress for shear deformation or anisotropic compression.
Analogously to the formulation of the original Godunov SPH method, we formulate
the equation of motion, the equation of energy, and the time evolution equation
of deviatoric stress tensor so that the resulting discretized system achieves
the second-order accuracy in space. The standard SPH method tends to suffer
from the tensile instability that results in unphysical clustering of particles
especially in tension-dominated region. We find that the tensile instability
can be suppressed by selecting appropriate interpolation for density
distribution in the equation of motion for the Godunov SPH method even in the
case of elastic dynamics. Several test calculations for elastic dynamics are
performed, and the accuracy and versatility of the present method are shown.


title:
Mapping between the classical and pseudoclassical models of a
  relativistic spinning particle in external bosonic and fermionic fields. II

abstract:
  The exact solution of a system of bilinear identities derived in the first
part of our work [Nucl.Phys.A 938 (2015) 59] for the case of real Grassmann-odd
tensor aggregate of the type $(S,V_{\mu},\!\,^{\ast}T_{\mu \nu},A_{\mu}, P)$ is
obtained. The consistency of the solution with a corresponding system of
bilinear identities including both the tensor variables and their derivatives
$(\dot{S},\dot{V}_{\mu},\!\,^{\ast}\dot{T}_{\mu\nu},\dot{A}_{\mu},\dot{P})$ is
considered. The alternative approach in solving of the algebraic system based
on introducing complex tensor quantities is discussed. This solution is used in
constructing the mapping of the interaction terms of spinning particle with a
background (Majorana) fermion field $\Psi^{i}_{{\rm
M}\hspace{0.02cm}\alpha}(x)$. A way of the extension of the obtained results
for the case of the Dirac spinors $(\psi_{{\rm
D}\hspace{0.03cm}\alpha},\theta_{{\rm D}\hspace{0.03cm}\alpha})$ and a
background Dirac field $\Psi^{i}_{{\rm D}\hspace{0.03cm}\alpha}(x)$, is
suggested. It is shown that for the construction of one-to-one correspondence
between the most general spinors and the tensor variables, we need a four-fold
increase of the number of the tensor ones. A connection with the higher-order
derivative Lagrangians for a point particle and in particular, with the
Lagrangian suggested by A.M. Polyakov, is proposed.


title: 2D Visual Place Recognition for Domestic Service Robots at Night

abstract:
  Domestic service robots such as lawn mowing and vacuum cleaning robots are
the most numerous consumer robots in existence today. While early versions
employed random exploration, recent systems fielded by most of the major
manufacturers have utilized range-based and visual sensors and user-placed
beacons to enable robots to map and localize. However, active range and visual
sensing solutions have the disadvantages of being intrusive, expensive, or only
providing a 1D scan of the environment, while the requirement for beacon
placement imposes other practical limitations. In this paper we present a
passive and potentially cheap vision-based solution to 2D localization at night
that combines easily obtainable day-time maps with low resolution
contrast-normalized image matching algorithms, image sequence-based matching in
two-dimensions, place match interpolation and recent advances in conventional
low light camera technology. In a range of experiments over a domestic lawn and
in a lounge room, we demonstrate that the proposed approach enables 2D
localization at night, and analyse the effect on performance of varying
odometry noise levels, place match interpolation and sequence matching length.
Finally we benchmark the new low light camera technology and show how it can
enable robust place recognition even in an environment lit only by a moonless
sky, raising the tantalizing possibility of being able to apply all
conventional vision algorithms, even in the darkest of nights.


title:
Occupation times of intervals until last passage times for spectrally
  negative Levy processes

abstract:
  In this paper, we derive the joint Laplace transforms of occupation times
until its last passage times as well as its positions. Motivated by Baurdoux
[2], the last times before an independent exponential variable are studied. By
applying dual arguments, explicit formulas are derived in terms of new
analytical identities from Loeffen et al. [12].


title: Efficient quantum circuits for Toeplitz and Hankel matrices

abstract:
  Toeplitz and Hankel matrices have been a subject of intense interest in a
wide range of science and engineering related applications. In this paper, we
show that quantum circuits can efficiently implement sparse or Fourier-sparse
Toeplitz and Hankel matrices. This provides an essential ingredient for solving
many physical problems with Toeplitz or Hankel symmetry in the quantum setting
with deterministic queries.


title:
Roe C*-algebra for groupoids and generalized Lichnerowicz Vanishing
  theorem for foliated manifolds

abstract:
  We introduce the concept of Roe C*-algebra for a locally compact groupoid
whose unit space is in general not compact, and that is equipped with an
appropriate coarse structure and Haar system. Using Connes' tangent groupoid
method, we introduce an analytic index for an elliptic differential operator on
a Lie groupoid equipped with additional metric structure, which takes values in
the K-theory of the Roe C*-algebra. We apply our theory to derive a
Lichnerowicz type vanishing result for foliations on open manifolds.


title:
Probing chiral superconductivity in Sr$_{2}$RuO$_{4}$ underneath the
  surface by point contact measurements

abstract:
  Sr$_{2}$RuO$_{4}$ (SRO) is the prime candidate for chiral $p$-wave
superconductor with critical temperature $T_{c}(SRO)\sim$1.5 K. Chiral domains
with opposite chiralities $p_{x}\pm ip_{y}$ were proposed, but yet to be
confirmed. We measure the field dependence of the point contact (PC) resistance
between a tungsten tip and the SRO-Ru eutectic crystal, where micrometer-sized
Ru inclusions are embedded in SRO with atomic sharp interface. Ruthenium is an
$s$-wave superconductor with $T_{c}(Ru)\sim$0.5 K, flux pinned near the Ru
inclusions can suppress its superconductivity as reflected from the PC
resistance and spectra. This flux pinning effect is originated from SRO
\textit{underneath} the surface and is very strong. To fully remove it, one has
to thermal cycle the sample above $T_{c}(SRO)$. This resembles the thermal
demagnetization for a ferromagnet, where ferromagnetic domains are randomized
above its Curie temperature. Another way is by applying alternating fields with
decreasing amplitude, resembling field demagnetization for the ferromagnet. The
observed hysteresis in magnetoresistance can be explained by domain dynamics,
providing support for the existence of chiral domains. The origin of strong
pinning \textit{underneath} the surface is also discussed.


title:
A Positivity Criterion for the Wave Equation and Global Existence of
  Large Solutions

abstract:
  In dimensions one to three, the fundamental solution to the free wave
equation is positive. Therefore, there exists a simple positivity criterion for
solutions. We use this to obtain large global solutions to two well-studied
energy-supercritical semilinear wave equations, as well as some new results in
the subcritical and critical cases.


title: Decay of correlations for billiards with flat points II: cusps effect

abstract:
  In this paper we continue to study billiards with flat points, by
constructing a spec family of dispersing billiards with cusps. All boundaries
of the table have positive curvature except that the curvature vanishes at the
vertex of a cusp, i.e. there is a pair of boundaries intersection at the flat
point tangentially. We study the mixing rates of this one-parameter family of
billiards with parameter $\beta\in (2,\infty)$, and show that the correlation
functions of the collision map decay polynomially with order
$\cO(n^{-\frac{1}{\beta-1}})$ as $n\to\infty$. In particular, this solves an
open question raised by Chernov and Markarian \cite{CM05}.


title: Harmonic maps of punctured surfaces to the hyperbolic plane

abstract:
  In this paper, we construct polynomial growth harmonic maps from
once-punctured Riemann surfaces of any finite genus to any even-sided, regular,
ideal polygon in the hyperbolic plane. We also establish their uniqueness
within a class of maps which differ by exponentially decaying variations.
Previously, harmonic maps from once-punctured spheres to the hyperbolic plane
have been parameterized by holomorphic quadratic differentials on the complex
plane. Our harmonic maps, mapping a genus g>1 domain to a k-sided polygon,
correspond to meromorphic quadratic differentials having one pole of order
(k+2) and (4g+k-2) zeros (counting multiplicity). In this way, we can associate
to these maps a holomorphic quadratic differential on the punctured Riemann
surface domain. As an example, we specialize our theorems to obtain a harmonic
map from a punctured square torus to an ideal square, and deduce the five
possibilities for the divisor of its Hopf differential.


title: Deeply-Fused Nets

abstract:
  In this paper, we present a novel deep learning approach, deeply-fused nets.
The central idea of our approach is deep fusion, i.e., combine the intermediate
representations of base networks, where the fused output serves as the input of
the remaining part of each base network, and perform such combinations deeply
over several intermediate representations. The resulting deeply fused net
enjoys several benefits. First, it is able to learn multi-scale representations
as it enjoys the benefits of more base networks, which could form the same
fused network, other than the initial group of base networks. Second, in our
suggested fused net formed by one deep and one shallow base networks, the flows
of the information from the earlier intermediate layer of the deep base network
to the output and from the input to the later intermediate layer of the deep
base network are both improved. Last, the deep and shallow base networks are
jointly learnt and can benefit from each other. More interestingly, the
essential depth of a fused net composed from a deep base network and a shallow
base network is reduced because the fused net could be composed from a less
deep base network, and thus training the fused net is less difficult than
training the initial deep base network. Empirical results demonstrate that our
approach achieves superior performance over two closely-related methods, ResNet
and Highway, and competitive performance compared to the state-of-the-arts.


title: Deep Structured Energy Based Models for Anomaly Detection

abstract:
  In this paper, we attack the anomaly detection problem by directly modeling
the data distribution with deep architectures. We propose deep structured
energy based models (DSEBMs), where the energy function is the output of a
deterministic deep neural network with structure. We develop novel model
architectures to integrate EBMs with different types of data such as static
data, sequential data, and spatial data, and apply appropriate model
architectures to adapt to the data structure. Our training algorithm is built
upon the recent development of score matching \cite{sm}, which connects an EBM
with a regularized autoencoder, eliminating the need for complicated sampling
method. Statistically sound decision criterion can be derived for anomaly
detection purpose from the perspective of the energy landscape of the data
distribution. We investigate two decision criteria for performing anomaly
detection: the energy score and the reconstruction error. Extensive empirical
studies on benchmark tasks demonstrate that our proposed model consistently
matches or outperforms all the competing methods.


title: Atmospheric nitrogen evolution on Earth and Venus

abstract:
  Nitrogen is the most common element in Earth's atmosphere and also appears to
be present in significant amounts in the mantle. However, its long-term cycling
between these two reservoirs remains poorly understood. Here a range of biotic
and abiotic mechanisms are evaluated that could have caused nitrogen exchange
between Earth's surface and interior over time. In the Archean, biological
nitrogen fixation was likely strongly limited by nutrient and/or electron
acceptor constraints. Abiotic fixation of dinitrogen becomes efficient in
strongly reducing atmospheres, but only once temperatures exceed around 1000 K.
Hence if atmospheric N2 levels really were as low as they are today 3.0 - 3.5
Ga, the bulk of Earth's mantle nitrogen must have been emplaced in the Hadean,
most likely at a time when the surface was molten. The elevated atmospheric N
content on Venus compared to Earth can be explained abiotically by a water loss
redox pump mechanism, where oxygen liberated from H2O photolysis and subsequent
H loss to space oxidises the mantle, causing enhanced outgassing of nitrogen.
This mechanism has implications for understanding the partitioning of other
Venusian volatiles and atmospheric evolution on exoplanets.


title:
Reshaped Wirtinger Flow and Incremental Algorithm for Solving Quadratic
  System of Equations

abstract:
  We study the phase retrieval problem, which solves quadratic system of
equations, i.e., recovers a vector $\boldsymbol{x}\in \mathbb{R}^n$ from its
magnitude measurements $y_i=|\langle \boldsymbol{a}_i, \boldsymbol{x}\rangle|,
i=1,..., m$. We develop a gradient-like algorithm (referred to as RWF
representing reshaped Wirtinger flow) by minimizing a nonconvex nonsmooth loss
function. In comparison with existing nonconvex Wirtinger flow (WF) algorithm
\cite{candes2015phase}, although the loss function becomes nonsmooth, it
involves only the second power of variable and hence reduces the complexity. We
show that for random Gaussian measurements, RWF enjoys geometric convergence to
a global optimal point as long as the number $m$ of measurements is on the
order of $n$, the dimension of the unknown $\boldsymbol{x}$. This improves the
sample complexity of WF, and achieves the same sample complexity as truncated
Wirtinger flow (TWF) \cite{chen2015solving}, but without truncation in gradient
loop. Furthermore, RWF costs less computationally than WF, and runs faster
numerically than both WF and TWF. We further develop the incremental
(stochastic) reshaped Wirtinger flow (IRWF) and show that IRWF converges
linearly to the true signal. We further establish performance guarantee of an
existing Kaczmarz method for the phase retrieval problem based on its
connection to IRWF. We also empirically demonstrate that IRWF outperforms
existing ITWF algorithm (stochastic version of TWF) as well as other batch
algorithms.


title: Neutrino dynamics below the electroweak crossover

abstract:
  We estimate the thermal masses and damping rates of active (m < eV) and
sterile (M ~ GeV) neutrinos with thermal momenta k ~ 3T at temperatures below
the electroweak crossover (5 GeV < T < 160 GeV). These quantities fix the
equilibration or "washout" rates of Standard Model lepton number densities.
Sterile neutrinos interact via direct scatterings mediated by Yukawa couplings,
and via their overlap with active neutrinos. Including all leading-order
reactions we find that the washout rate generally exceeds the Hubble rate for 5
GeV < T < 30 GeV. Therefore it is challenging to generate a large lepton
asymmetry facilitating dark matter computations operating at T < 5 GeV, whereas
the generation of a baryon asymmetry at T > 130 GeV remains an option. Our
differential rates are tabulated in a form suitable for studies of specific
scenarios with given neutrino Yukawa matrices.


title:
Order and Chaos in the One-Dimensional $\phi^4$ Model : N-Dependence and
  the Second Law of Thermodynamics

abstract:
  We revisit the equilibrium one-dimensional $\phi^4$ model from the dynamical
systems point of view. We find an infinite number of periodic orbits which are
computationally stable. At the same time some of the orbits are found to
exhibit positive Lyapunov exponents! The periodic orbits confine every particle
in a periodic chain to trace out either the same or a mirror-image trajectory
in its two-dimensional phase space. These "computationally stable" sets of
pairs of single-particle orbits are either symmetric or antisymmetric to the
very last computational bit. In such a periodic chain the odd-numbered and
even-numbered particles' coordinates and momenta are either identical or differ
only in sign. "Positive Lyapunov exponents" can and do result if an
infinitesimal perturbation breaking a perfect two-dimensional antisymmetry is
introduced so that the motion expands into a four-dimensional phase space. In
that extended space a positive exponent results.
  We formulate a standard initial condition for the investigation of the
microcanonical chaotic number dependence of the model. We speculate on the
uniqueness of the model's chaotic sea and on the connection of such collections
of deterministic and time-reversible states to the Second Law of
Thermodynamics.


title: Yum-me: A Personalized Nutrient-based Meal Recommender System

abstract:
  Nutrient-based meal recommendations have the potential to help individuals
prevent or manage conditions such as diabetes and obesity. However, learning
people's food preferences and making recommendations that simultaneously appeal
to their palate and satisfy nutritional expectations are challenging. Existing
approaches either only learn high-level preferences or require a prolonged
learning period. We propose Yum-me, a personalized nutrient-based meal
recommender system designed to meet individuals' nutritional expectations,
dietary restrictions, and fine-grained food preferences. Yum-me enables a
simple and accurate food preference profiling procedure via a visual quiz-based
user interface, and projects the learned profile into the domain of
nutritionally appropriate food options to find ones that will appeal to the
user. We present the design and implementation of Yum-me, and further describe
and evaluate two innovative contributions. The first contriution is an open
source state-of-the-art food image analysis model, named FoodDist. We
demonstrate FoodDist's superior performance through careful benchmarking and
discuss its applicability across a wide array of dietary applications. The
second contribution is a novel online learning framework that learns food
preference from item-wise and pairwise image comparisons. We evaluate the
framework in a field study of 227 anonymous users and demonstrate that it
outperforms other baselines by a significant margin. We further conducted an
end-to-end validation of the feasibility and effectiveness of Yum-me through a
60-person user study, in which Yum-me improves the recommendation acceptance
rate by 42.63%.


title: Data Programming: Creating Large Training Sets, Quickly

abstract:
  Large labeled training sets are the critical building blocks of supervised
learning methods and are key enablers of deep learning techniques. For some
applications, creating labeled training sets is the most time-consuming and
expensive part of applying machine learning. We therefore propose a paradigm
for the programmatic creation of training sets called data programming in which
users express weak supervision strategies or domain heuristics as labeling
functions, which are programs that label subsets of the data, but that are
noisy and may conflict. We show that by explicitly representing this training
set labeling process as a generative model, we can "denoise" the generated
training set, and establish theoretically that we can recover the parameters of
these generative models in a handful of settings. We then show how to modify a
discriminative loss function to make it noise-aware, and demonstrate our method
over a range of discriminative models including logistic regression and LSTMs.
Experimentally, on the 2014 TAC-KBP Slot Filling challenge, we show that data
programming would have led to a new winning score, and also show that applying
data programming to an LSTM model leads to a TAC-KBP score almost 6 F1 points
over a state-of-the-art LSTM baseline (and into second place in the
competition). Additionally, in initial user studies we observed that data
programming may be an easier way for non-experts to create machine learning
models when training data is limited or unavailable.


title:
Neutrino Mass Ordering in Future Neutrinoless Double Beta Decay
  Experiments

abstract:
  Motivated by recent intensive experimental efforts on searching for
neutrinoless double beta decays, we present a detailed quantitative analysis on
the prospect of resolving neutrino mass ordering in the next generation
$^{76}$Ge-type experiments.


title: Adversarial Training Methods for Semi-Supervised Text Classification

abstract:
  Adversarial training provides a means of regularizing supervised learning
algorithms while virtual adversarial training is able to extend supervised
learning algorithms to the semi-supervised setting. However, both methods
require making small perturbations to numerous entries of the input vector,
which is inappropriate for sparse high-dimensional inputs such as one-hot word
representations. We extend adversarial and virtual adversarial training to the
text domain by applying perturbations to the word embeddings in a recurrent
neural network rather than to the original input itself. The proposed method
achieves state of the art results on multiple benchmark semi-supervised and
purely supervised tasks. We provide visualizations and analysis showing that
the learned word embeddings have improved in quality and that while training,
the model is less prone to overfitting. Code is available at
https://github.com/tensorflow/models/tree/master/research/adversarial_text.


title: A presentation of PGL(2,Q)

abstract:
  We give a conjectural presentation of the infinitely generated group PGL(2,Q)
with an infinite list of relators.


title:
Lattice Complements and the Subadditivity of Syzygies of Simplicial
  Forests

abstract:
  We prove the subadditivity property for the maximal degrees of the syzygies
of facet ideals simplicial forests. For such an ideal $I$, if the $i$-th Betti
number is nonzero and $i=a+b$, we show that there are monomials in the lcm
lattice of $I$ that are complements in part of the lattice, each supporting a
nonvanishing $a$-th and $b$-th Betti numbers. The subadditivity formula follows
from this observation.


title: Small Representations of Big Kidney Exchange Graphs

abstract:
  Kidney exchanges are organized markets where patients swap willing but
incompatible donors. In the last decade, kidney exchanges grew from small and
regional to large and national---and soon, international. This growth results
in more lives saved, but exacerbates the empirical hardness of the
$\mathcal{NP}$-complete problem of optimally matching patients to donors.
State-of-the-art matching engines use integer programming techniques to clear
fielded kidney exchanges, but these methods must be tailored to specific models
and objective functions, and may fail to scale to larger exchanges. In this
paper, we observe that if the kidney exchange compatibility graph can be
encoded by a constant number of patient and donor attributes, the clearing
problem is solvable in polynomial time. We give necessary and sufficient
conditions for losslessly shrinking the representation of an arbitrary
compatibility graph. Then, using real compatibility graphs from the UNOS
nationwide kidney exchange, we show how many attributes are needed to encode
real compatibility graphs. The experiments show that, indeed, small numbers of
attributes suffice.


title:
Cooperative Tx/Rx Caching in Interference Channels: A Storage-Latency
  Tradeoff Study

abstract:
  This paper studies the storage-latency tradeoff in the $3\times3$ wireless
interference network with caches equipped at all transmitters and receivers.
The tradeoff is characterized by the so-called fractional delivery time (FDT)
at given normalized transmitter and receiver cache sizes. We first propose a
generic cooperative transmitter/receiver caching strategy with adjustable file
splitting ratios. Based on this caching strategy, we then design the delivery
phase carefully to turn the considered interference channel opportunistically
into broadcast channel, multicast channel, X channel, or a hybrid form of these
channels. After that, we obtain an achievable upper bound of the minimum FDT by
solving a linear programming problem of the file splitting ratios. The
achievable FDT is a convex and piece-wise linear decreasing function of the
cache sizes. Receiver local caching gain, coded multicasting gain, and
transmitter cooperation gain (interference alignment and interference
neutralization) are leveraged in different cache size regions.


title: Convergence analysis of the Generalized Empirical Interpolation Method

abstract:
  Let $F$ be a compact set of a Banach space $\mathcal{X}$. This paper analyses
the "Generalized Empirical Interpolation Method" (GEIM) which, given a function
$f\in F$, builds an interpolant $\mathcal{J}_n[f]$ in an $n$-dimensional
subspace $X_n \subset \mathcal{X}$ with the knowledge of $n$ outputs
$(\sigma_i(f))_{i=1}^n$, where $\sigma_i\in \mathcal{X}'$ and $\mathcal{X}'$ is
the dual space of $\mathcal{X}$. The space $X_n$ is built with a greedy
algorithm that is adapted to $F$ in the sense that it is generated by elements
of $F$ itself. The algorithm also selects the linear functionals
$(\sigma_i)_{i=1}^n$ from a dictionary $\Sigma\subset \mathcal{X}'$. In this
paper, we study the interpolation error $\max_{f\in F} \Vert
f-\mathcal{J}_n[f]\Vert_{\mathcal{X}}$ by comparing it with the best possible
performance on an $n$-dimensional space, i.e., the Kolmogorov $n$-width of $F$
in $\mathcal{X}$, $d_n(F,\mathcal{X})$. For polynomial or exponential decay
rates of $d_n(F,\mathcal{X})$, we prove that the interpolation error has the
same behavior modulo the norm of the interpolation operator. Sharper results
are obtained in the case where $\mathcal X$ is a Hilbert space.


title:
A maximum-caliber approach to predicting perturbed folding kinetics due
  to mutations

abstract:
  We present a maximum-caliber method for inferring transition rates of a
Markov State Model (MSM) with perturbed equilibrium populations, given
estimates of state populations and rates for an unperturbed MSM. It is similar
in spirit to previous approaches but given the inclusion of prior information
it is more robust and simple to implement. We examine its performance in simple
biased diffusion models of kinetics, and then apply the method to predicting
changes in folding rates for several highly non-trivial protein folding systems
for which non-native interactions play a significant role, including (1)
tryptophan variants of GB1 hairpin, (2) salt-bridge mutations of Fs peptide
helix, and (3) MSMs built from ultra-long folding trajectories of FiP35 and GTT
variants of WW domain. In all cases, the method correctly predicts changes in
folding rates, suggesting the wide applicability of maximum-caliber approaches
to efficiently predict how mutations perturb protein conformational dynamics.


title: Isolating Mice and Elephant in Data Centers

abstract:
  Data centers traffic is composed by numerous latency-sensitive "mice" flows,
which is consisted of only several packets, and a few throughput-sensitive
"elephant" flows, which occupy more than 80% of overall load. Generally, the
short-lived "mice" flows induce transient congestion and the long-lived
"elephant" flows cause persistent congestion. The network congestion is a major
performance inhibitor. Conventionally, the hop-by-hop and end-to-end flow
control mechanisms are employed to relief transient and persistent congestion,
respectively. However, in face of the mixture of elephants and mice, we find
the hybrid congestion control scheme including hop-by-hop and end-to-end flow
control mechanisms suffers from serious performance impairments. As a step
further, our in-depth analysis reveals that the hybrid scheme performs poor at
latency of mice and throughput of elephant. Motivated by this understanding, we
argue for isolating mice and elephants in different queues, such that the
hop-by-hop and end-to-end flow control mechanisms are independently imposed to
short-lived and long-lived flows, respectively. Our solution is
readily-deployable and compatible with current commodity network devices and
can leverage various congestion control mechanisms. Extensive simulations show
that our proposal of isolation can simultaneously improve the latency of mice
by at least 30% and the link utilization to almost 100%.


title:
On model architecture for a children's speech recognition interactive
  dialog system

abstract:
  This report presents a general model of the architecture of information
systems for the speech recognition of children. It presents a model of the
speech data stream and how it works. The result of these studies and presented
veins architectural model shows that research needs to be focused on
acoustic-phonetic modeling in order to improve the quality of children's speech
recognition and the sustainability of the systems to noise and changes in
transmission environment. Another important aspect is the development of more
accurate algorithms for modeling of spontaneous child speech.


title: Recursive SDN for Carrier Networks

abstract:
  Control planes for global carrier networks should be programmable (so that
new functionality can be easily introduced) and scalable (so they can handle
the numerical scale and geographic scope of these networks). Neither
traditional control planes nor new SDN-based control planes meet both of these
goals. In this paper, we propose a framework for recursive routing computations
that combines the best of SDN (programmability) and traditional networks
(scalability through hierarchy) to achieve these two desired properties.
Through simulation on graphs of up to 10,000 nodes, we evaluate our design's
ability to support a variety of routing and traffic engineering solutions,
while incorporating a fast failure recovery mechanism.


title: Design and development a children's speech database

abstract:
  The report presents the process of planning, designing and the development of
a database of spoken children's speech whose native language is Bulgarian. The
proposed model is designed for children between the age of 4 and 6 without
speech disorders, and reflects their specific capabilities. At this age most
children cannot read, there is no sustained concentration, they are emotional,
etc. The aim is to unite all the media information accompanying the recording
and processing of spoken speech, thereby to facilitate the work of researchers
in the field of speech recognition. This database will be used for the
development of systems for children's speech recognition, children's speech
synthesis systems, games which allow voice control, etc. As a result of the
proposed model a prototype system for speech recognition is presented.


title: Learning Multiagent Communication with Backpropagation

abstract:
  Many tasks in AI require the collaboration of multiple agents. Typically, the
communication protocol between agents is manually specified and not altered
during training. In this paper we explore a simple neural model, called
CommNet, that uses continuous communication for fully cooperative tasks. The
model consists of multiple agents and the communication between them is learned
alongside their policy. We apply this model to a diverse set of tasks,
demonstrating the ability of the agents to learn to communicate amongst
themselves, yielding improved performance over non-communicative agents and
baselines. In some cases, it is possible to interpret the language devised by
the agents, revealing simple but effective strategies for solving the task at
hand.


title: Legendrian lens space surgeries

abstract:
  We show that every tight contact structure on any of the lens spaces
$L(ns^2-s+1,s^2)$ with $n\geq 2$, $s\geq 1$, can be obtained by a single
Legendrian surgery along a suitable Legendrian realisation of the negative
torus knot $T(s,-(sn-1))$ in the tight or an overtwisted contact structure on
the 3-sphere.


title: One-loop Chiral Perturbation Theory with two fermion representations

abstract:
  We develop Chiral Perturbation Theory for chirally broken theories with
fermions in two different representations of the gauge group. Any such theory
has a non-anomalous singlet $U(1)_A$ symmetry, yielding an additional
Nambu-Goldstone boson when spontaneously broken. We calculate the
next-to-leading order corrections for the pseudoscalar masses and decay
constants, which include the singlet Nambu-Goldstone boson, as well as for the
two condensates. The results can be generalized to more than two
representations.


title:
Observing random walks of atoms in buffer gas through resonant light
  absorption

abstract:
  Using resonant light absorption, random walk motions of rubidium atoms in
nitrogen buffer gas are observed directly. The transmitted light intensity
through atomic vapor is measured and its spectrum is obtained, down to orders
of magnitude below the shot noise level to detect fluctuations caused by atomic
motions. To understand the measured spectra, the spectrum for atoms performing
random walks in a gaussian light beam is computed and its analytical form is
obtained. The spectrum has $1/f^2$ ($f$: frequency) behavior at higher
frequencies, crossing over to a different, but well defined behavior at lower
frequencies. The properties of this theoretical spectrum agree excellently with
the measured spectrum. This understanding also enables us to obtain the
diffusion constant, the photon cross section of atoms in buffer gas and the
atomic number density, from a single spectral measurement. We further discuss
other possible applications of our experimental method and analysis.


title:
Improving energy efficiency and classification accuracy of neuromorphic
  chips by learning binary synaptic crossbars

abstract:
  Deep Neural Networks (DNN) have achieved human level performance in many
image analytics tasks but DNNs are mostly deployed to GPU platforms that
consume a considerable amount of power. Brain-inspired spiking neuromorphic
chips consume low power and can be highly parallelized. However, for deploying
DNNs to energy efficient neuromorphic chips the incompatibility between
continuous neurons and synaptic weights of traditional DNNs, discrete spiking
neurons and synapses of neuromorphic chips has to be overcome. Previous work
has achieved this by training a network to learn continuous probabilities and
deployment to a neuromorphic architecture by random sampling these
probabilities. An ensemble of sampled networks is needed to approximate the
performance of the trained network.
  In the work presented in this paper, we have extended previous research by
directly learning binary synaptic crossbars. Results on MNIST show that better
performance can be achieved with a small network in one time step (92.7%
maximum observed accuracy vs 95.98% accuracy in our work). Top results on a
larger network are similar to previously published results (99.42% maximum
observed accuracy vs 99.45% accuracy in our work). More importantly, in our
work a smaller ensemble is needed to achieve similar or better accuracy than
previous work, which translates into significantly decreased energy consumption
for both networks. Results of our work are stable since they do not require
random sampling.


title: Stellar rotation effects in polarimetric microlensing

abstract:
  It is well known that the polarization signal in microlensing events of hot
stars is larger than that of main-sequence stars. Most hot stars rapidly rotate
around their stellar axes. The stellar rotation makes ellipticity and
gravity-darkening effects which break the spherical symmetry of the source
shape and the circular symmetry of the source surface brightness respectively.
Hence, it causes a net polarization signal for the source star. This
polarization signal should be considered in polarimetry microlensing of fast
rotating stars. For moderate rotating stars, lensing can magnify or even
characterize small polarization signals due to the stellar rotation through
polarimetry observations. The gravity-darkening effect due to a rotating source
star makes asymmetric perturbations in polarimetry and photometry microlensing
curves whose maximum happens when the lens trajectory crosses the projected
position of the rotation pole on the sky plane. The stellar ellipticity makes a
time shift (i) in the position of the second peak of the polarimetry curves in
transit microlensing events and (ii) in the peak position of the polarimetry
curves with respect to the photometry peak position in bypass microlensing
events. By measuring this time shift via polarimetry observations of
microlensing events, we can evaluate the ellipticity of the projected source
surface on the sky plane. Given the characterizations of the FOcal Reducer and
low dispersion Spectrograph (FORS2) polarimeter at Very Large Telescope (VLT)
telescope, the probability of observing this time shift is so small. The more
accurate polarimeters of the next generation may likely measure these time
shifts and evaluate the ellipticity of microlensing source stars.


title: Carrying a Torch for Dust in Binary Star Systems

abstract:
  Young stars are frequently observed to host circumstellar disks, within which
their attendant planetary systems are formed. Scattered light imaging of these
proto-planetary disks reveals a rich variety of structures including spirals,
gaps and clumps. Self-consistent modelling of both imaging and multi-wavelength
photometry enables the best interpretation of the location and size
distribution of disks' dust. Epsilon Sagittarii is an unusual star system. It
is a binary system with a B9.5III primary that is also believed to host a
debris disk in an unstable configuration. Recent polarimetric measurements of
the system with the High Precision Polarimetric Instrument (HIPPI) revealed an
unexpectedly high fractional linear polarisation, one greater than the
fractional infrared excess of the system. Here we develop a spectral energy
distribution model for the system and use this as a basis for radiative
transfer modelling of its polarisation with the RADMC-3D software package. The
measured polarisation can be reproduced for grain sizes around 2.0 microns.


title: Character theory approach to Sato-Tate groups

abstract:
  In this article, we propose to use the character theory of compact Lie groups
and their orthogonality relations for the study of Frobenius distribution and
Sato-Tate groups. The results show the advantages of this new approach in
several aspects. With samples of Frobenius ranging in size much smaller than
the moment statistic approach, we obtain very good approximation to the
expected values of these orthogonality relations, which give useful information
about the underlying Sato-Tate groups and strong evidence of the correctness of
the generalized Sato-Tate conjecture. In fact, $2^{10}$ to $2^{12}$ points
provide satisfactory convergence. Even for $g = 2$, the classical approach
using moment statistics requires about $2^{30}$ sample points to obtain such
information.


title:
What are the observable effects of the physical properties of a quantum
  system?

abstract:
  In recent work (Nii et al., arXiv:1603.06291; Iinuma et al., Phys. Rev. A 93,
032104 (2016)(arXiv:1510.03958)) we have studied the relation between
experimental outcomes and the physical properties represented by Hilbert space
operators of a quantum system. We find that the values of physical properties
are determined by the combination of initial and final conditions, which means
that eigenstates and eigenvalues should not be misinterpreted as an exclusive
set of possible realities. Here, we discuss the practical implications of these
results and point out the importance of quantitative relations for a proper
understanding of physical effects.


title: A precise and general notion of manifold

abstract:
  We give a completely formalized definition of a notion of " general manifold
". It turns out that " gluing data " form an equivalence-partially ordered set
(e-pos), which is a special instance of an ordered groupoid. We state and prove
reconstruction theorems, allowing to reconstruct general manifolds and their
mor-phisms from such gluing data. To describe morphisms between manifolds, the
notion of natural relations between groupoids is introduced, which emphasizes
the close analogy with natural transformations of general category theory.


title: Solving discrete logarithms on a 170-bit MNT curve by pairing reduction

abstract:
  Pairing based cryptography is in a dangerous position following the
breakthroughs on discrete logarithms computations in finite fields of small
characteristic. Remaining instances are built over finite fields of large
characteristic and their security relies on the fact that the embedding field
of the underlying curve is relatively large. How large is debatable. The aim of
our work is to sustain the claim that the combination of degree 3 embedding and
too small finite fields obviously does not provide enough security. As a
computational example, we solve the DLP on a 170-bit MNT curve, by exploiting
the pairing embedding to a 508-bit, degree-3 extension of the base field.


title:
NESTT: A Nonconvex Primal-Dual Splitting Method for Distributed and
  Stochastic Optimization

abstract:
  We study a stochastic and distributed algorithm for nonconvex problems whose
objective consists of a sum of $N$ nonconvex $L_i/N$-smooth functions, plus a
nonsmooth regularizer. The proposed NonconvEx primal-dual SpliTTing (NESTT)
algorithm splits the problem into $N$ subproblems, and utilizes an augmented
Lagrangian based primal-dual scheme to solve it in a distributed and stochastic
manner. With a special non-uniform sampling, a version of NESTT achieves
$\epsilon$-stationary solution using
$\mathcal{O}((\sum_{i=1}^N\sqrt{L_i/N})^2/\epsilon)$ gradient evaluations,
which can be up to $\mathcal{O}(N)$ times better than the (proximal) gradient
descent methods. It also achieves Q-linear convergence rate for nonconvex
$\ell_1$ penalized quadratic problems with polyhedral constraints. Further, we
reveal a fundamental connection between primal-dual based methods and a few
primal only methods such as IAG/SAG/SAGA.


title:
Freezeout conditions in proton-proton collisions at the top RHIC and LHC
  energies

abstract:
  The freezeout conditions in proton-proton collisions at
$\sqrt{s_{\textrm{NN}}}= 200$, $900$ and $7000$ GeV have been extracted by fits
to the mean hadron yields at mid-rapidity within the framework of the
statistical model of an ideal gas of hadrons and resonances in the grand
canonical ensemble. The variation of the extracted freezeout thermal parameters
and the goodness of the fits with $\sqrt{s_{\textrm{NN}}}$ are discussed. We
find the extracted temperature and baryon chemical potential of the freezeout
surface to be similar in p+p and heavy ion collisions. On the other hand, the
thermal behaviour of the strange hadrons is qualitatively different in p+p as
compared to A+A. We find an additional parameter accounting for non-equilibrium
strangeness production is essential for describing the p+p data. This is in
contrast to A+A where the non-equilibrium framework could be successfully
replaced by a sequential and complete equilibrium model with an early freezeout
of the strange hadrons.


title: Computing cardinalities of Q-curve reductions over finite fields

abstract:
  We present a specialized point-counting algorithm for a class of elliptic
curves over F\_{p^2} that includes reductions of quadratic Q-curves modulo
inert primes and, more generally, any elliptic curve over F\_{p^2} with a
low-degree isogeny to its Galois conjugate curve. These curves have interesting
cryptographic applications. Our algorithm is a variant of the
Schoof--Elkies--Atkin (SEA) algorithm, but with a new, lower-degree
endomorphism in place of Frobenius. While it has the same asymptotic asymptotic
complexity as SEA, our algorithm is much faster in practice.


title:
A virtual instrument to standardise the calibration of atomic force
  microscope cantilevers

abstract:
  Atomic force microscope (AFM) users often calibrate the spring constants of
cantilevers using functionality built into individual instruments. This is
performed without reference to a global standard, which hinders robust
comparison of force measurements reported by different laboratories. In this
article, we describe a virtual instrument (an internet-based initiative)
whereby users from all laboratories can instantly and quantitatively compare
their calibration measurements to those of others - standardising AFM force
measurements - and simultaneously enabling non-invasive calibration of AFM
cantilevers of any geometry. This global calibration initiative requires no
additional instrumentation or data processing on the part of the user. It
utilises a single website where users upload currently available data. A
proof-of-principle demonstration of this initiative is presented using measured
data from five independent laboratories across three countries, which also
allows for an assessment of current calibration.


title: Visualizing the large-$Z$ scaling of the kinetic energy density of atoms

abstract:
  The scaling of neutral atoms to large $Z$, combining periodicity with a
gradual trend to homogeneity, is a fundamental probe of density functional
theory, one that has driven recent advances in understanding both the kinetic
and exchange-correlation energies. Although research focus is normally upon the
scaling of energies, insights can also be gained from energy densities. We
visualize the scaling of the positive-definite kinetic energy density (KED) in
closed-shell atoms, in comparison to invariant quantities based upon the
gradient and Laplacian of the density. We notice a striking fit of the KED
within the core of any atom to a gradient expansion using both the gradient and
the Laplacian, appearing as an asymptotic limit around which the KED
oscillates. The gradient expansion is qualitatively different from that derived
from first principles for a slowly-varying electron gas and is correlated with
a nonzero Pauli contribution to the KED near the nucleus. We propose and
explore orbital-free meta-GGA models for the kinetic energy to describe these
features, with some success, but the effects of quantum oscillations in the
inner shells of atoms makes a complete parametrization difficult. We discuss
implications for improved orbital-free description of molecular properties.


title:
Approximate methods for the generation of dark matter halo catalogs in
  the age of precision cosmology

abstract:
  Precision cosmology has recently triggered new attention on the topic of
approximate methods for the clustering of matter on large scales, whose
foundations date back to the period from late '60s to early '90s. Indeed,
although the prospect of reaching sub-percent accuracy in the measurement of
clustering poses a challenge even to full N-body simulations, an accurate
estimation of the covariance matrix of clustering statistics, not to mention
the sampling of parameter space, requires usage of a large number (hundreds in
the most favourable cases) of simulated (mock) galaxy catalogs. Combination of
few N-body simulations with a large number of realizations performed with
approximate methods gives the most promising approach to solve these problems
with a reasonable amount of resources. In this paper I review this topic,
starting from the foundations of the methods, then going through the pioneering
efforts of the '90s, and finally presenting the latest extensions and a few
codes that are now being used in present-generation surveys and thoroughly
tested to assess their performance in the context of future surveys.


title: Deciding Maxmin Reachability in Half-Blind Stochastic Games

abstract:
  Two-player, turn-based, stochastic games with reachability conditions are
considered, where the maximizer has no information (he is blind) and is
restricted to deterministic strategies whereas the minimizer is perfectly
informed. We ask the question of whether the game has maxmin 1, in other words
we ask whether for all $\epsilon>0$ there exists a deterministic strategy for
the (blind) maximizer such that against all the strategies of the minimizer, it
is possible to reach the set of final states with probability larger than
$1-\epsilon$. This problem is undecidable in general, but we define a class of
games, called leaktight half-blind games where the problem becomes decidable.
We also show that mixed strategies in general are stronger for both players and
that optimal strategies for the minimizer might require infinite-memory.


title: 0.75 atoms improve the clock signal of 10,000 atoms

abstract:
  Since the pioneering work of Ramsey, atom interferometers are employed for
precision metrology, in particular to measure time and to realize the second.
In a classical interferometer, an ensemble of atoms is prepared in one of the
two input states, whereas the second one is left empty. In this case, the
vacuum noise restricts the precision of the interferometer to the standard
quantum limit (SQL). Here, we propose and experimentally demonstrate a novel
clock configuration that surpasses the SQL by squeezing the vacuum in the empty
input state. We create a squeezed vacuum state containing an average of 0.75
atoms to improve the clock sensitivity of 10,000 atoms by 2.05 dB. The SQL
poses a significant limitation for today's microwave fountain clocks, which
serve as the main time reference. We evaluate the major technical limitations
and challenges for devising a next generation of fountain clocks based on
atomic squeezed vacuum.


title: A compactness theorem for surfaces with Bounded Integral Curvature

abstract:
  We prove a compactness theorem for metrics with Bounded Integral Curvature on
a fixed closed surface $\Sigma$. As a corollary, we obtain a compactification
of the space of Riemannian metrics with conical singularities, where an
accumulation of singularities is allowed.


title: Inkjet-printed vertically emitting solid-state organic lasers

abstract:
  In this paper, we show that Inkjet Printing can be successfully applied to
external-cavity vertically-emitting thin-film organic lasers, and can be used
to generate a diffraction-limited output beam with an output energy as high as
33.6 uJ with a slope efficiency S of 34%. Laser emission shows to be
continuously tunable from 570 to 670 nm using an intracavity polymer-based
Fabry-Perot etalon. High-optical quality films with several um thicknesses are
realized thanks to ink-jet printing. We introduce a new optical material where
EMD6415 commercial ink constitutes the optical host matrix and exhibits a
refractive index of 1.5 and an absorption coefficient of 0.66 cm-1 at 550-680
nm. Standard laser dyes like Pyromethene 597 and Rhodamine 640 are incorporated
in solution to the EMD6415 ink. Such large size " printed pixels " of 50 mm 2
present uniform and flat surfaces, with roughness measured as low as 1.5 nm in
different locations of a 50um x 50um AFM scan. Finally, as the gain capsules
fabricated by Inkjet printing are simple and do not incorporate any tuning or
cavity element, they are simple to make, have a negligible fabrication cost and
can be used as fully disposable items. This works opens the way towards the
fabrication of really low-cost tunable visible lasers with an affordable
technology that has the potential to be widely disseminated.


title: K{\"u}lshammer ideals of algebras of quaternion type

abstract:
  For a symmetric algebra A over a field K of characteristic p > 0
K{\"u}lshammer constructed a descending sequence of ideals of the centre of A.
If K is perfect this sequence was shown to be an invariant under derived
equivalence and for algebraically closed K under stable equivalence of Morita
type. Erdmann classified algebras of tame representation type which may be
blocks of group algebras, and Holm classified Erdmann's list up to derived
equivalence. In both classifications certain parameters occur in the
classification, and it was unclear if different parameters lead to different
algebras. Erdmann's algebras fall into three classes, namely of dihedral,
semidihedral and of quaternion type. In previous joint work with Holm we used
K{\"u}lshammer ideals to distinguish classes with respect to these parameters
in case of algebras of dihedral and semidihedral type. In the present paper we
determine the K{\"u}lshammer ideals for algebras of quaternion type and
distinguish again algebras with respect to certain parameters.


title: On the radicals of exponential Lie groups

abstract:
  Let $G$ be a connected exponential Lie group and $R$ be the solvable radical
of $G$. We describe a condition on $G/R$ under which one can then conclude that
$R$ is an exponential Lie group. The condition holds in particular when $G$ is
a complex Lie group and this yields a stronger version of a result of Moskowitz
and Sacksteder \cite{MS} on the center of a complex exponential Lie group being
connected. Along the way we prove a criterion for elements from certain subsets
of a solvable Lie group to be exponential, which would be of independent
interest.


title:
Classification of solutions to general Toda systems with singular
  sources

abstract:
  We classify all the solutions to the elliptic Toda system associated to a
general simple Lie algebra with singular sources at the origin and with finite
energy. The solution space is shown to be parametrized by a subgroup of the
corresponding complex Lie group. We also show the quantization result for the
finite integrals. This work generalizes the previous works in [Lin, Wei, Ye]
and [Nie] for Toda systems of types $A$ and $B, C$. However, a more
Lie-theoretic method is needed here for the general case, and the method relies
heavily on the structure theories of the local solutions and of the
$W$-invariants for the Toda system. This work will have applications to
nonabelian Chern-Simons-Higgs gauge theory and to the mean field equations of
Toda type.


title: Challenges in Mobile Multi-Device Ecosystems

abstract:
  Coordinated multi-display environments from the desktop, second-screen to
gigapixel display walls are increasingly common. Personal and intimate mobile
and wearable devices such as head-mounted displays, smartwatches, smartphones
and tablets are rarely part of such multi-device ecosystems. With this paper,
we contribute to a better understanding about factors that impede the creation
and use of such mobile multi-device ecosystems. We base our findings on
literature research and an expert survey. Specifically, we present grounded
challenges relevant for the design, development and use of mobile multi-device
environments.


title:
Designing Distributed Fixed-Time Consensus Protocols for Linear
  Multi-Agent Systems Over Directed Graphs

abstract:
  This technical note addresses the distributed fixed-time consensus protocol
design problem for multi-agent systems with general linear dynamics over
directed communication graphs. By using motion planning approaches, a class of
distributed fixed-time consensus algorithms are developed, which rely only on
the sampling information at some sampling instants. For linear multi-agent
systems, the proposed algorithms solve the fixed-time consensus problem for any
directed graph containing a directed spanning tree. In particular, the settling
time can be off-line pre-assigned according to task requirements. Compared with
the existing results for multi-agent systems, to our best knowledge, it is the
first-time to solve fixed-time consensus problems for general linear
multi-agent systems over directed graphs having a directed spanning tree.
Extensions to the fixed-time formation flying are further studied for multiple
satellites described by Hill equations.


title: Subdivisions of oriented cycles in digraphs with large chromatic number

abstract:
  An oriented cycle is an orientation of a undirected cycle. We first show that
for any oriented cycle $C$, there are digraphs containing no subdivision of $C$
(as a subdigraph) and arbitrarily large chromatic number. In contrast, we show
that for any $C$ a cycle with two blocks, every strongly connected digraph with
sufficiently large chromatic number contains a subdivision of $C$. We prove a
similar result for the antidirected cycle on four vertices (in which two
vertices have out-degree $2$ and two vertices have in-degree $2$).


title: C-FLAT: Control-FLow ATtestation for Embedded Systems Software

abstract:
  Remote attestation is a crucial security service particularly relevant to
increasingly popular IoT (and other embedded) devices. It allows a trusted
party (verifier) to learn the state of a remote, and potentially
malware-infected, device (prover). Most existing approaches are static in
nature and only check whether benign software is initially loaded on the
prover. However, they are vulnerable to run-time attacks that hijack the
application's control or data flow, e.g., via return-oriented programming or
data-oriented exploits. As a concrete step towards more comprehensive run-time
remote attestation, we present the design and implementation of Control- FLow
ATtestation (C-FLAT) that enables remote attestation of an application's
control-flow path, without requiring the source code. We describe a full
prototype implementation of C-FLAT on Raspberry Pi using its ARM TrustZone
hardware security extensions. We evaluate C-FLAT's performance using a
real-world embedded (cyber-physical) application, and demonstrate its efficacy
against control-flow hijacking attacks.


title:
Vacuum ultraviolet photolysis of hydrogenated amorphous carbons. III.
  Diffusion of photo-produced H2 as a function of temperature

abstract:
  Hydrogenated amorphous carbon (a-C:H) has been proposed as one of the
carbonaceous solids detected in the interstellar medium. Energetic processing
of the a-C:H particles leads to the dissociation of the C-H bonds and the
formation of hydrogen molecules and small hydrocarbons. Photo-produced H2
molecules in the bulk of the dust particles can diffuse out to the gas phase
and contribute to the total H2 abundance. We have simulated this process in the
laboratory with plasma-produced a-C:H and a-C:D analogs under astrophysically
relevant conditions to investigate the dependence of the diffusion as a
function of temperature. Plasma-produced a-C:H analogs were UV-irradiated using
a microwave-discharged hydrogen flow lamp. Molecules diffusing to the gas-phase
were detected by a quadrupole mass spectrometer, providing a measurement of the
outgoing H2 or D2 flux. By comparing the experimental measurements with the
expected flux from a one-dimensional diffusion model, a diffusion coefficient D
could be derived for experiments carried out at different temperatures.
Dependance on the diffusion coefficient D with the temperature followed an
Arrhenius-type equation. The activation energy for the diffusion process was
estimated (ED(H2)=1660+-110 K, ED(D2)=2090+-90 K), as well as the
pre-exponential factor (D0(H2)=0.0007+0.0013-0.0004 cm2 s-1,
D0(D2)=0.0045+0.005-0.0023 cm2 s-1) The strong decrease of the diffusion
coefficient at low dust particle temperatures exponentially increases the
diffusion times in astrophysical environments. Therefore, transient dust
heating by cosmic rays needs to be invoked for the release of the photo-
produced H2 molecules in cold PDR regions, where destruction of the aliphatic
component in hydrogenated amorphous carbons most probably takes place.


title:
On square-free values of large polynomials over the rational function
  field

abstract:
  We investigate the density of square-free values of polynomials with large
coefficients over the rational function field $\mathbb{F}_q[t]$. Some
interesting questions answered as special cases of our results include the
density of square-free polynomials in short intervals, and an asymptotic for
the number of representations of a large polynomial $N$ as a sum of a small
$k$-th power and a square-free polynomial.


title:
Integrating Distributional Lexical Contrast into Word Embeddings for
  Antonym-Synonym Distinction

abstract:
  We propose a novel vector representation that integrates lexical contrast
into distributional vectors and strengthens the most salient features for
determining degrees of word similarity. The improved vectors significantly
outperform standard models and distinguish antonyms from synonyms with an
average precision of 0.66-0.76 across word classes (adjectives, nouns, verbs).
Moreover, we integrate the lexical contrast vectors into the objective function
of a skip-gram model. The novel embedding outperforms state-of-the-art models
on predicting word similarities in SimLex-999, and on distinguishing antonyms
from synonyms.


title: iStar 2.0 Language Guide

abstract:
  The i* modeling language was introduced to fill the gap in the spectrum of
conceptual modeling languages, focusing on the intentional (why?), social
(who?), and strategic (how? how else?) dimensions. i* has been applied in many
areas, e.g., healthcare, security analysis, eCommerce. Although i* has seen
much academic application, the diversity of extensions and variations can make
it difficult for novices to learn and use it in a consistent way. This document
introduces the iStar 2.0 core language, evolving the basic concepts of i* into
a consistent and clear set of core concepts, upon which to build future work
and to base goal-oriented teaching materials. This document was built from a
set of discussions and input from various members of the i* community. It is
our intention to revisit, update and expand the document after collecting
examples and concrete experiences with iStar 2.0.


title: Holographic fluctuations and the principle of minimal complexity

abstract:
  We discuss, from a quantum information perspective, recent proposals of
Maldacena, Ryu, Takayanagi, van Raamsdonk, Swingle, and Susskind that spacetime
is an emergent property of the quantum entanglement of an associated boundary
quantum system. We review the idea that the informational principle of minimal
complexity determines a dual holographic bulk spacetime from a minimal quantum
circuit U preparing a given boundary state from a trivial reference state. We
describe how this idea may be extended to determine the relationship between
the fluctuations of the bulk holographic geometry and the fluctuations of the
boundary low-energy subspace. In this way we obtain, for every quantum system,
an Einstein-like equation of motion for what might be interpreted as a bulk
gravity theory dual to the boundary system.


title: Epimorphic subgroups of algebraic groups

abstract:
  In this note, we show that the epimorphic subgroups of an algebraic group are
exactly the pull-backs of the epimorphic subgroups of its affinization. We also
obtain epimorphicity criteria for subgroups of affine algebraic groups, which
generalize a result of Bien and Borel. Moreover, we extend the affinization
theorem for algebraic groups to homogeneous spaces.


title:
Recursion Operators and Tri-Hamiltonian Structure of the First Heavenly
  Equation of Pleba\'nski

abstract:
  We present first heavenly equation of Pleba\'nski in a two-component
evolutionary form and obtain Lagrangian and Hamiltonian representations of this
system. We study all point symmetries of the two-component system and, using
the inverse Noether theorem in the Hamiltonian form, obtain all the integrals
of motion corresponding to each variational (Noether) symmetry. We derive two
linearly independent recursion operators for symmetries of this system related
by a discrete symmetry of both the two-component system and its symmetry
condition. Acting by these operators on the first Hamiltonian operator $J_0$ we
obtain second and third Hamiltonian operators. However, we were not able to
find Hamiltonian densities corresponding to the latter two operators.
Therefore, we construct two recursion operators, which are either even or odd,
respectively, under the above-mentioned discrete symmetry. Acting with them on
$J_0$, we generate another two Hamiltonian operators $J_+$ and $J_-$ and find
the corresponding Hamiltonian densities, thus obtaining second and third
Hamiltonian representations for the first heavenly equation in a two-component
form. Using P. Olver's theory of the functional multi-vectors, we check that
the linear combination of $J_0$, $J_+$ and $J_-$ with arbitrary constant
coefficients satisfies Jacobi identities. Since their skew symmetry is obvious,
these three operators are compatible Hamiltonian operators and hence we obtain
a tri-Hamiltonian representation of the first heavenly equation. Our
well-founded conjecture applied here is that P. Olver's method works fine for
nonlocal operators and our proof of the Jacobi identities and bi-Hamiltonian
structures crucially depends on the validity of this conjecture.


title:
Modeling the relativistic runaway electron avalanche and the feedback
  mechanism with GEANT4

abstract:
  This paper presents the first study that uses the GEometry ANd Tracking 4
(GEANT4) toolkit to do quantitative comparisons with other modelling results
related to the production of Terrestrial Gamma-ray Flashes (TGFs) and
high-energy particle emission from thunderstorms. We will study the
Relativistic Runaway Electron Avalanche (RREA) and the relativistic feedback
process, as well as the production of bremsstrahlung photons from Runaway
Electrons (REs). The Monte Carlo (MC) simulations take into account the effects
of electron ionisation, electron by electron (M{\o}ller) and electron by
positron (Bhabha) scattering as well as the bremsstrahlung process and
pair-production, in the $250$ eV$-100$ GeV energy range. Our results indicate
that the multiplication of electrons during the development of RREAs and under
the influence of feedback, are consistent with previous estimates. This is
important to validate GEANT4 as a tool to model RREAs and feedback in
homogeneous electric fields. We also determine the ratio of bremsstrahlung
photons to energetic electrons $N_\gamma/N_e$. We then show that the ratio has
a dependence on the electric field which can be expressed by the avalanche time
$\tau(E)$ and the bremsstrahlung coefficient $\alpha(\varepsilon)$. In
addition, we present comparisons of GEANT4 simulations performed with a
"standard" and a "low-energy" physics list both validated in the $1$ keV$-100$
GeV energy range. This comparison shows that the choice of physics list used in
GEANT4 simulations has a significant effect on the results.


title:
An efficient cooling of the quantized vibration by a four-level
  configuration

abstract:
  Cooling vibrational degrees of freedom down to ground states is essential to
observation of quantum properties of systems with mechanical vibration. We
propose two cooling schemes employing four internal levels of the systems,
which achieve the ground-state cooling in an efficient fashion by completely
deleting the carrier and first-order blue-sideband transitions. The schemes,
based on the quantum interference and Stark-shift gates, are robust to
fluctuation of laser intensity and frequency. The feasibility of the schemes is
justified using current laboratory technology. In practice, our proposal
readily applies to an nano-diamond nitrogen-vacancy center levitated in an
optic trap or attached to a cantilever.


title: A new presentation for the inner Tutte group of a matroid

abstract:
  The inner Tutte group of a matroid is a finitely generated abelian group
introduced as an algebraic counterpart of Tutte's homotopy theory of matroids.
The aim of this work is to provide a new presentation for this group with a set
of generators that is smaller than those previously known.


title: Generalized Mirror Descents in Congestion Games

abstract:
  Different types of dynamics have been studied in repeated game play, and one
of them which has received much attention recently consists of those based on
"no-regret" algorithms from the area of machine learning. It is known that
dynamics based on generic no-regret algorithms may not converge to Nash
equilibria in general, but to a larger set of outcomes, namely coarse
correlated equilibria. Moreover, convergence results based on generic no-regret
algorithms typically use a weaker notion of convergence: the convergence of the
average plays instead of the actual plays. Some work has been done showing that
when using a specific no-regret algorithm, the well-known multiplicative
updates algorithm, convergence of actual plays to equilibria can be shown and
better quality of outcomes in terms of the price of anarchy can be reached for
atomic congestion games and load balancing games. Are there more cases of
natural no-regret dynamics that perform well in suitable classes of games in
terms of convergence and quality of outcomes that the dynamics converge to?
  We answer this question positively in the bulletin-board model by showing
that when employing the mirror-descent algorithm, a well-known generic
no-regret algorithm, the actual plays converge quickly to equilibria in
nonatomic congestion games. Furthermore, the bandit model considers a probably
more realistic and prevalent setting with only partial information, in which at
each time step each player only knows the cost of her own currently played
strategy, but not any costs of unplayed strategies. For the class of atomic
congestion games, we propose a family of bandit algorithms based on the
mirror-descent algorithms previously presented, and show that when each player
individually adopts such a bandit algorithm, their joint (mixed) strategy
profile quickly converges with implications.


title:
Isochronous centers of polynomial Hamiltonian systems and a conjecture
  of Jarque and Villadelprat

abstract:
  We study the conjecture of Jarque and Villadelprat stating that every center
of a planar polynomial Hamiltonian system of even degree is nonisochronous.
This conjecture is proved for quadratic and quartic systems. Using the
correction of a vector field to characterize isochronicity and explicit
computations of this quantity for polynomial vector fields, wa are able to
describe a very large class of nonisochronous Hamiltonian system of even degree
of degree arbitrary large.


title:
Optical and mechanical mode tuning in an optomechanical crystal with
  light-induced thermal effects

abstract:
  We report on the modification of the optical and mechanical properties of a
silicon 1D optomechanical crystal cavity due to thermo-optic effects in a high
phonon/photon population regime. The cavity heats up due to light absorption in
a way that shifts the optical modes towards longer wavelengths and the
mechanical modes to lower frequencies. By combining the experimental optical
results with finite-difference time-domain simulations we establish a direct
relation between the observed wavelength drift and the actual effective
temperature increase of the cavity. By assuming that the Young's modulus
decreases accordingly to the temperature increase, we find a good agreement
between the mechanical mode drift predicted using a finite element method and
the experimental one.


title: Valley filtering and electronic optics using polycrystalline graphene

abstract:
  In this Letter, both the manipulation of valley-polarized currents and the
optical-like behaviors of Dirac fermions are theoretically explored in
polycrystalline graphene. When strain is applied, the misorientation between
two graphene domains separated by a grain boundary can result in a mismatch of
their electronic structures. Such a discrepancy manifests itself in a strong
breaking of the inversion symmetry, leading to perfect valley polarization in a
wide range of transmission directions. In addition, these graphene domains act
as different media for electron waves, offering the possibility to modulate and
obtain negative refraction indexes.


title:
Global analysis of isospin dependent microscopic nucleon-nucleus optical
  potential in Dirac Bruckner Hartree-Fock approach

abstract:
  The Microscopic Otical Model Potential is evaluated within a relativistic
scheme which provides a natural and consistent relation between the spin-orbit
part and the central part of the potential. The Dirac-Brueckner-Hartree-Fock
(DBHF) approach provides such a microscopic relativistic scheme, which is based
on a realistic nucleon-nucleon interaction and reproduce the saturation
properties of symmetric nuclear matter without any adjustable parameter. Its
solution using the projection technique within the subtracted T-matrix (STM)
representation provides a reliable extension to asymmetric nuclear matter,
which is important to describe the features of the isospin asymmetric nuclei.
Therefore, the present work aims to perform a global analysis of the
isospin-dependent nucleon-nucleus MOP based on the DBHF calculation in
symmetric and asymmetric nuclear matter. The DBHF is used to evaluate the
relativistic structure of the nucleon self-energies in nuclear matter at
various densities and asymmetries. The Schr\"odinger equivalent potentials of
finite nuclei are derived from these Dirac components by a local density
approximation (LDA). The nucleon-nucleus scattering calculations are carried
out for a broad spectrum $n$ and $p$ scattering experiments below 200 MeV with
targets ranging from $^{12}$C to $^{208}$Pb.


title: Neural Universal Discrete Denoiser

abstract:
  We present a new framework of applying deep neural networks (DNN) to devise a
universal discrete denoiser. Unlike other approaches that utilize supervised
learning for denoising, we do not require any additional training data. In such
setting, while the ground-truth label, i.e., the clean data, is not available,
we devise "pseudo-labels" and a novel objective function such that DNN can be
trained in a same way as supervised learning to become a discrete denoiser. We
experimentally show that our resulting algorithm, dubbed as Neural DUDE,
significantly outperforms the previous state-of-the-art in several applications
with a systematic rule of choosing the hyperparameter, which is an attractive
feature in practice.


title:
Determining protoplanetary disk gas masses from CO isotopologues line
  observations

abstract:
  Despite intensive studies of protoplanetary disks, there is still no reliable
way to determine their total mass and their surface density distribution,
quantities that are crucial for describing both the structure and the evolution
of disks up to the formation of planets. The goal of this work is to use less
abundant CO isotopologues, whose detection is routine for ALMA, to infer the
gas mass of disks. Isotope-selective effects need to be taken into account in
the analysis, because they can significantly modify CO isotopologues line
intensities. CO isotope-selective photodissociation has been implemented in the
physical-chemical code DALI and 800 disk models have been run for a range of
disk and stellar parameters. Dust and gas temperature structures have been
computed self-consistently, together with a chemical calculation of the main
species. Both disk structure and stellar parameters have been investigated.
Total fluxes have been ray-traced for different CO isotopologues and for
various transitions for different inclinations. A combination of 13CO and C18O
total intensities allows inference of the total disk mass, although with
non-negligible uncertainties. These can be overcome by employing spatially
resolved observations, i.e. the disk's radial extent and inclination.
Comparison with parametric models shows differences at the factor of a few
level, especially for extremely low and high disk masses. Finally, total line
intensities for different CO isotopologue and for various low-J transitions are
provided and are fitted to simple formulae. The effects of a lower gas-phase
carbon abundance and different gas/dust ratios are investigated as well, and
comparison with other tracers is made. Disk masses can be determined within a
factor of a few by comparing CO isotopologue lines observations with the
simulated line fluxes, modulo the uncertainties in the volatile elemental
abundances.


title:
The Oxygen Features in Type Ia Supernovae and the Implications for the
  Nature of Thermonuclear Explosions

abstract:
  The absorption feature O I 7773 is an important spectral indicator for type
Ia supernovae (SNe~Ia) that can be used to trace the unburned material at outer
layers of the exploding white dwarf. In this work, we use a large sample of
SNe~Ia to examine this absorption at early phases (i.e., -13 days <t <-7 days),
and make comparisons with the absorption features of Si~II 6355 and Ca~II
near-infrared (NIR) triplet. We show that for a subgroup of spectroscopically
normal SNe with normal photospheric velocities (i.e., v_si < 12,500 km s^{-1}
at optical maximum), the line strength of high velocity feature (HVF) of O~I is
inversely correlated with that of Si~II (or Ca~II), and this feature also shows
a negative correlation with the luminosity of SNe Ia. This finding, together
with other features we find for the O~I HVF, reveal that for this subgroup of
SNe~Ia explosive oxygen burning occurs at the outermost layer of supernova and
difference in burning there could lead to the observed diversity, which are in
remarkable agreement with the popular delayed-detonation model of Chandrasekhar
mass WD.


title: Discs in misaligned binary systems

abstract:
  We perform SPH simulations to study precession and changes in alignment
between the circumprimary disc and the binary orbit in misaligned binary
systems. We find that the precession process can be described by the rigid-disc
approximation, where the disc is considered as a rigid body interacting with
the binary companion only gravitationally. Precession also causes change in
alignment between the rotational axis of the disc and the spin axis of the
primary star. This type of alignment is of great important for explaining the
origin of spin-orbit misaligned planetary systems. However, we find that the
rigid-disc approximation fails to describe changes in alignment between the
disc and the binary orbit. This is because the alignment process is a
consequence of interactions that involve the fluidity of the disc, such as the
tidal interaction and the encounter interaction. Furthermore, simulation
results show that there are not only alignment processes, which bring the
components towards alignment, but also anti-alignment processes, which tend to
misalign the components. The alignment process dominates in systems with
misalignment angle near 90 degrees, while the anti-alignment process dominates
in systems with the misalignment angle near 0 or 180 degrees. This means that
highly misaligned systems will become more aligned but slightly misaligned
systems will become more misaligned.


title:
Spectroscopy and Dynamics of a Two-Dimensional Electron Gas on top of
  Ultrathin Helium Films on Cu(111)

abstract:
  Electrons in image-potential states on the surface of bulk helium represent a
unique model system of a two-dimensional electron gas. Here, we investigate
their properties in the extreme case of reduced film thickness: a monolayer of
helium physisorbed on a single-crystalline (111)-oriented Cu surface. For this
purpose we have utilized a customized setup for time-resolved two-photon
photoemission (2PPE) at very low temperatures under ultra-high vacuum
conditions. We demonstrate that the highly polarizable metal substrate
increases the binding energy of the first (n = 1) image-potential state by more
than two orders of magnitude as compared to the surface of liquid helium. An
electron in this state is still strongly decoupled from the metal surface due
to the large negative electron affinity of helium and we find that even one
monolayer of helium increases its lifetime by one order of magnitude compared
to the bare Cu(111) surface.


title: Fast Algorithms for Robust PCA via Gradient Descent

abstract:
  We consider the problem of Robust PCA in the fully and partially observed
settings. Without corruptions, this is the well-known matrix completion
problem. From a statistical standpoint this problem has been recently
well-studied, and conditions on when recovery is possible (how many
observations do we need, how many corruptions can we tolerate) via
polynomial-time algorithms is by now understood. This paper presents and
analyzes a non-convex optimization approach that greatly reduces the
computational complexity of the above problems, compared to the best available
algorithms. In particular, in the fully observed case, with $r$ denoting rank
and $d$ dimension, we reduce the complexity from
$\mathcal{O}(r^2d^2\log(1/\varepsilon))$ to
$\mathcal{O}(rd^2\log(1/\varepsilon))$ -- a big savings when the rank is big.
For the partially observed case, we show the complexity of our algorithm is no
more than $\mathcal{O}(r^4d \log d \log(1/\varepsilon))$. Not only is this the
best-known run-time for a provable algorithm under partial observation, but in
the setting where $r$ is small compared to $d$, it also allows for
near-linear-in-$d$ run-time that can be exploited in the fully-observed case as
well, by simply running our algorithm on a subset of the observations.

categories: cs.IT cs.LG math.IT math.ST stat.ML stat.TH


title: Geometry-aware stationary subspace analysis

abstract:
  In many real-world applications data exhibits non-stationarity, i.e., its
distribution changes over time. One approach to handling non-stationarity is to
remove or minimize it before attempting to analyze the data. In the context of
brain computer interface (BCI) data analysis this may be done by means of
stationary subspace analysis (SSA). The classic SSA method finds a matrix that
projects the data onto a stationary subspace by optimizing a cost function
based on a matrix divergence. In this work we present an alternative method for
SSA based on a symmetrized version of this matrix divergence. We show that this
frames the problem in terms of distances between symmetric positive definite
(SPD) matrices, suggesting a geometric interpretation of the problem. Stemming
from this geometric viewpoint, we introduce and analyze a method which utilizes
the geometry of the SPD matrix manifold and the invariance properties of its
metrics. Most notably we show that these invariances alleviate the need to
whiten the input matrices, a common step in many SSA methods which often
introduces errors. We demonstrate the usefulness of our technique in
experiments on both synthesized and real-world data.


title:
A proposed direct measurement of cross section at Gamow window for key
  reaction $^{19}$F($p$,$\alpha$)$^{16}$O in Asymptotic Giant Branch stars with
  a planned accelerator in CJPL

abstract:
  In 2014, the National Natural Science Foundation of China (NSFC) approved the
Jinping Underground Nuclear Astrophysics laboratory (JUNA) project, which aims
at direct cross-section measurements of four key stellar nuclear reactions
right down to the Gamow windows. In order to solve the observed fluorine
overabundances in Asymptotic Giant Branch (AGB) stars, measuring the key
$^{19}$F($p$,$\alpha$)$^{16}$O reaction at effective burning energies (i.e., at
Gamow window) is established as one of the scientific research sub-projects.
The present paper describes this sub-project in details, including motivation,
status, experimental setup, yield and background estimation, aboveground test,
as well as other relevant reactions.


title: Flexible signal denoising via flexible empirical Bayes shrinkage

abstract:
  Signal denoising---also known as non-parametric regression---is often
performed through shrinkage estimation in a transformed (e.g., wavelet) domain;
shrinkage in the transformed domain corresponds to smoothing in the original
domain. A key question in such applications is how much to shrink, or,
equivalently, how much to smooth. Empirical Bayes shrinkage methods provide an
attractive solution to this problem; they use the data to estimate a
distribution of underlying "effects", hence automatically select an appropriate
amount of shrinkage. However, most existing implementations of Empirical Bayes
shrinkage are less flexible than they could be--both in their assumptions on
the underlying distribution of effects, and in their ability to handle
heterskedasticity---which limits their signal denoising applications. Here we
address this by taking a particularly flexible, stable and computationally
convenient Empirical Bayes shrinkage method, and we apply it to several signal
denoising problems. These applications include smoothing of Poisson data and
heteroskedastic Gaussian data. We show through empirical comparisons that the
results are competitive with other methods, including both simple thresholding
rules and purpose-built Empirical Bayes procedures. Our methods are implemented
in the R package smashr, "SMoothing by Adaptive SHrinkage in R," available at
https://www.github.com/stephenslab/smashr


title: A singular limit for an age structured mutation problem

abstract:
  The spread of a particular trait in a cell population often is modelled by an
appropriate system of ordinary differential equations describing how the sizes
of subpopulations of the cells with the same genome change in time. On the
other hand, it is recognized that cells have their own vital dynamics and
mutations, leading to changes in their genome, mostly occurring during the cell
division at the end of its life cycle. In this context, the process is
described by a system of McKendrick type equations which resembles a network
transport problem. In this paper we show that, under an appropriate scaling of
the latter, these two descriptions are asymptotically equivalent.


title:
Designing a single-molecule biophysics tool for characterizing DNA
  damage for techniques that kill infectious pathogens through DNA damage
  effects

abstract:
  Antibiotics such as the quinolones and fluoroquinolones kill bacterial
pathogens ultimately through DNA damage. They target the essential type IIA
topoisomerases in bacteria by stabilising the normally transient double strand
break state which is created to modify the supercoiling state of the DNA. Here
we discuss the development of these antibiotics and their method of action.
Existing methods for DNA damage visualisation, such as the comet assay and
immunofluorescence imaging can often only be analysed qualitatively and this
analysis is subjective. We describe a putative single-molecule fluorescence
technique for quantifying DNA damage via the total fluorescence intensity of a
DNA origami tile fully saturated with an intercalating dye, along with the
optical requirements for how to implement these into a light microscopy imaging
system capable of single-molecule millisecond timescale imaging. This system
promises significant improvements in reproducibility of the quantification of
DNA damage over traditional techniques.


title:
Tensor polarization dependent fragmentation functions and e+e-\to V \pi
  X at high energies

abstract:
  We present the systematic results for three dimensional fragmentation
functions of spin one hadrons defined via quark-quark correlator. There are
totally 72 such fragmentation functions, among them 18 are twist-2, 36 are
twist-3 and 18 are twist-4. We also present the relationships between the
twist-3 parts and those defined via quark-gluon-quark correlator obtained from
the QCD equation of motion. We show that two particle semi-inclusive hadron
production process $e^+e^-\to V\pi X$ at high energies is one of the best
places to study the three-dimensional tensor polarization dependent
fragmentation functions. We present the general kinematic analysis of this
process and show that the cross section should be expressed in terms of 81
independent structure functions. After that we present parton model results for
the hadronic tensor, the structure functions, the azimuthal and spin
asymmetries in terms of these gauge invariant fragmentation functions at the
leading order pQCD up to twist-3.


title:
A proof of Mader's conjecture on large clique subdivisions in $C_4$-free
  graphs

abstract:
  Given any integers $s,t\geq 2$, we show there exists some $c=c(s,t)>0$ such
that any $K_{s,t}$-free graph with average degree $d$ contains a subdivision of
a clique with at least $cd^{\frac{1}{2}\frac{s}{s-1}}$ vertices. In particular,
when $s=2$ this resolves in a strong sense the conjecture of Mader in 1999 that
every $C_4$-free graph has a subdivision of a clique with order linear in the
average degree of the original graph. In general, the widely conjectured
asymptotic behaviour of the extremal density of $K_{s,t}$-free graphs suggests
our result is tight up to the constant $c(s,t)$.


title: Force spectroscopy in studying infection

abstract:
  Biophysical force spectroscopy tools - for example optical tweezers, magnetic
tweezers, atomic force microscopy, - have been used to study elastic,
mechanical, conformational and dynamic properties of single biological
specimens from single proteins to whole cells to reveal information not
accessible by ensemble average methods such as X-ray crystallography, mass
spectroscopy, gel electrophoresis and so on. Here we review the application of
these tools on a range of infection-related questions from antibody-inhibited
protein processivity to virus-cell adhesion. In each case we focus on how the
instrumental design tailored to the biological system in question translates
into the functionality suitable for that particular study. The unique insights
that force spectroscopy has gained to complement knowledge learned through
population averaging techniques in interrogating biomolecular details prove to
be instrumental in therapeutic innovations such as those in structure-based
drug design.


title:
Single-molecule observation of DNA replication repair pathways in E.
  coli

abstract:
  The method of action of many antibiotics is to interfere with DNA replication
- quinolones trap DNA gyrase and topoisomerase proteins onto DNA while
metronidazole causes single and double stranded breaks in DNA. To understand
how bacteria respond to these drugs, it is important to understand the repair
processes utilised when DNA replication is blocked. We have used tandem lac
operators inserted into the chromosome bound by fluorescently labelled lac
repressors as a model protein block to replication in E. coli. We have used
dual-colour, alternating-laser, single-molecule narrowfield microscopy to
quantify the amount of operator at the block and simultaneously image
fluorescently labelled DNA polymerase. We anticipate use of this system as a
quantitative platform to study replication stalling and repair proteins.


title:
Effect of further-neighbor interactions on the magnetization behaviors
  of the Ising model on a triangular lattice

abstract:
  In this work, we study the magnetization behaviors of the classical Ising
model on the triangular lattice using Monte Carlo simulations, and pay
particular attention to the effect of further-neighbor interactions. Several
fascinating spin states are identified to be stabilized in certain magnetic
field regions, respectively, resulting in the magnetization plateaus at 2/3,
5/7, 7/9 and 5/6 of the saturation magnetization MS, in addition to the well
known plateaus at 0, 1/3 and 1/2 of MS. The stabilization of these interesting
orders can be understood as the consequence of the competition between Zeeman
energy and exchange energy.


title:
A discretisation method with the $H_{\rm div}$ inner product for
  electric field integral equations

abstract:
  A discretisation method with the $H_{\rm div}$ inner product for the electric
field integral equation~(EFIE) is proposed. The EFIE with the conventional
Galerkin discretisation shows bad accuracy for problems with a small frequency,
a problem known as the low-frequency breakdown. The discretisation method
proposed in this paper utilises the $H_{\rm div}$ scalar product with a scalar
coefficient for the Galerkin discretisation and overcomes the low-frequency
problem with an appropriately chosen coefficient. As regards the
preconditioning, we find that a naive use of the widely-used Calderon
preconditioning is not efficient for reducing the computational time with the
new discretisation. We therefore propose a new preconditioning which can
accelerate the computation successfully. The efficiency of the proposed
discretisation and preconditioning is verified through some numerical examples.


title:
Using Fluorescence Recovery After Photobleaching (FRAP) to study
  dynamics of the Structural Maintenance of Chromosome (SMC) complex in vivo

abstract:
  The SMC complex, MukBEF, is important for chromosome organization and
segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct
spots (or 'foci') in the cell, where it is thought to carry out most of its
chromosome associated activities. This chapter outlines the technique of
Fluorescence Recovery After Photobleaching (FRAP) as a method to study the
properties of YFP-tagged MukB in fluorescent foci. This method can provide
important insight into the dynamics of MukB on DNA and be used to study its
biochemical properties in vivo.


title:
Single molecule narrowfield microscopy of protein-DNA binding dynamics
  in glucose signal transduction of live yeast cells

abstract:
  Single-molecule narrowfield microscopy is a versatile tool to investigate a
diverse range of protein dynamics in live cells and has been extensively used
in bacteria. Here, we describe how these methods can be extended to larger
eukaryotic, yeast cells, which contain sub-cellular compartments. We describe
how to obtain single-molecule microscopy data but also how to analyse these
data to track and obtain the stoichiometry of molecular complexes diffusing in
the cell. We chose glucose mediated signal transduction of live yeast cells as
the system to demonstrate these single-molecule techniques as transcriptional
regulation is fundamentally a single molecule problem - a single repressor
protein binding a single binding site in the genome can dramatically alter
behaviour at the whole cell and population level.


title: Additive posets, CW-complexes, and graphs

abstract:
  We introduce and study additive posets. We show that the top homology group
(with coefficients in Z/2Z) of a finite dimensional CW-complex carries a
structure of an additive poset invariant under subdivisions. Applications to
CW-complexes and graphs are discussed.


title:
Computer assisted proof of Shil'nikov homoclinics: with application to
  the Lorenz-84 model

abstract:
  We present a methodology for computer assisted proofs of Shil'nikov
homoclinic intersections. It is based on geometric bounds on the invariant
manifolds using rate conditions, and on propagating the bounds by an interval
arithmetic integrator. Our method ensures uniqueness of the parameter for which
the homoclinic takes place. We apply the method for the Lorenz-84 atmospheric
circulation model, obtaining a sharp bound for the parameter, and also for
where the homoclinic intersection of the stable/unstable manifolds takes place.


title: The chemical composition of Galactic ring nebulae around massive stars

abstract:
  We present deep spectra of ring nebulae associated with Wolf-Rayet (WR) and
O-type stars: NGC 6888, G2.4+1.4, RCW 58, S 308, NGC 7635 and RCW 52. The data
have been taken with the 10m Gran Telescopio Canarias and the 6.5m Clay
Telescope. We extract spectra of several apertures in some of the objects. We
derive C$^{++}$ and O$^{++}$ abundances from faint recombination lines in NGC
6888 and NGC 7635, permitting to derive their C/H and C/O ratios and estimate
the abundance discrepancy factor (ADF) of O$^{++}$. The ADFs are larger than
the typical ones of normal HII regions but similar to those found in the
ionised gas of star-forming dwarf galaxies. We find that chemical abundances
are rather homogeneous in the nebulae where we have spectra of several
apertures: NGC 6888, NGC 7635 and G2.4+1.4. We obtain very high values of
electron temperature in a peripheral zone of NGC 6888, finding that shock
excitation can reproduce its spectral properties. We find that all the objects
associated with WR stars show N enrichment. Some of them also show He
enrichment and O deficiency as well as a lower Ne/O than expected, this may
indicate the strong action of the ON and NeNa cycles. We have compared the
chemical composition of NGC 6888, G2.4+1.4, RCW 58 and S 308 with the
nucleosynthesis predicted by stellar evolution models of massive stars. We find
that non-rotational models of stars of initial masses between 25 and 40 solar
masses seem to reproduce the observed abundance ratios of most of the nebulae.


title: Distributed optimal control of a nonstandard nonlocal phase field system

abstract:
  We investigate a distributed optimal control problem for a nonlocal phase
field model of viscous Cahn-Hilliard type. The model constitutes a nonlocal
version of a model for two-species phase segregation on an atomic lattice under
the presence of diffusion that has been studied in a series of papers by P.
Podio-Guidugli and the present authors. The model consists of a highly
nonlinear parabolic equation coupled to an ordinary differential equation. The
latter equation contains both nonlocal and singular terms that render the
analysis difficult. Standard arguments of optimal control theory do not apply
directly, although the control constraints and the cost functional are of
standard type. We show that the problem admits a solution, and we derive the
first-order necessary conditions of optimality.


title: On intersective polynomials with non-solvable Galois group

abstract:
  We present new theoretical results on the existence of intersective
polynomials with certain prescribed Galois groups, namely the projective and
affine linear groups $PGL_2(\ell)$ and $AGL_2(\ell)$ as well as the affine
symplectic groups $AGSp_4(\ell):=(\mathbb{F}_\ell)^4 \rtimes GSp_4(\ell)$. For
further families of affine groups, existence results are proven conditional on
the existence on certain tamely ramified Galois extensions. We also compute
explicit families of intersective polynomials for certain non-solvable groups.