title: On symplectic capacities of toric domains

abstract:
  A toric domain is a subset of $(\mathbb{C}^n,\omega_{\text{std}})$ which is
invariant under the standard rotation action of $\mathbb{T}^n$ on
$\mathbb{C}^n$. For a toric domain $U$ from a certain large class for which
this action is not free, we find a corresponding toric domain $V$ where the
standard action is free, and for which $c(U)=c(V)$ for any symplectic capacity
$c$. Michael Hutchings gives a combinatorial formula for calculating his
embedded contact homology symplectic capacities for certain toric
four-manifolds on which the $\mathbb{T}^2$-action is free. Our theorem allows
one to extend this formula to a class of toric domains where the action is not
free. We apply our theorem to compute ECH capacities for certain intersections
of ellipsoids, and find that these capacities give sharp obstructions to
symplectically embedding these ellipsoid intersections into balls.


title: Non-linear dependences in finance

abstract:
  The thesis is composed of three parts. Part I introduces the mathematical and
statistical tools that are relevant for the study of dependences, as well as
statistical tests of Goodness-of-fit for empirical probability distributions. I
propose two extensions of usual tests when dependence is present in the sample
data and when observations have a fat-tailed distribution. The financial
content of the thesis starts in Part II. I present there my studies regarding
the "cross-sectional" dependences among the time series of daily stock returns,
i.e. the instantaneous forces that link several stocks together and make them
behave somewhat collectively rather than purely independently. A calibration of
a new factor model is presented here, together with a comparison to
measurements on real data. Finally, Part III investigates the temporal
dependences of single time series, using the same tools and measures of
correlation. I propose two contributions to the study of the origin and
description of "volatility clustering": one is a generalization of the
ARCH-like feedback construction where the returns are self-exciting, and the
other one is a more original description of self-dependences in terms of
copulas. The latter can be formulated model-free and is not specific to
financial time series. In fact, I also show here how concepts like recurrences,
records, aftershocks and waiting times, that characterize the dynamics in a
time series can be written in the unifying framework of the copula.


title:
Parametric Hierarchical Matrix Approach for the Wideband Optical
  Response of Large-Scale Molecular Aggregates

abstract:
  Fast and efficient calculations of optical responses using electromagnetic
models require computational acceleration and compression techniques. A
hierarchical matrix approach is adopted for this purpose. In order to model
large-scale molecular structures these methods should be applied over wide
frequency spectra. Here we introduce a novel parametric hierarchical matrix
method that allows one for a rapid construction of a wideband system
representation and enables an efficient wideband solution. We apply the
developed method to the modeling of the optical response of bacteriochorophyll
tubular aggregates as found in green photosynthetic bacteria. We show that the
parametric method can provide one with the frequency and time-domain solutions
for structures of the size of 100, 000 molecules, which is comparable to the
size of the whole antenna complex in a bacterium. The absorption spectrum is
calculated and the significance of electrodynamic retardation effects for
relatively large structures, i.e. with respect to the wavelength of light, is
briefly studied.


title:
A Calibration Algorithm for Microelectromechanical Systems
  Accelerometers in Inertial Navigation Sensors

abstract:
  In the present work we develop an algorithm for calibrating MEMS sensors,
which accounts for the nonorthogonality of the accelerometers' axis, as well as
for the constant bias and scaling errors. We derive an explicit formula for
computing the calibrated acceleration, given data from the sensors. We also
study the error, that is caused by the nonorthogonality of the axis.


title:
Mean-Field Models for Heterogeneous Networks of Two-Dimensional
  Integrate and Fire Models

abstract:
  We analytically derive mean-field models for all-to-all coupled networks of
heterogeneous, adapting, two-dimensional integrate and fire neurons. The class
of models we consider includes the Izhikevich, adaptive exponential, and
quartic integrate and fire models. The heterogeneity in the parameters leads to
different moment closure assumptions that can be made in the derivation of the
mean-field model from the population density equation for the large network.
Three different moment closure assumptions lead to three different mean-field
systems. These systems can be used for distinct purposes such as bifurcation
analysis of the large networks, prediction of steady state firing rate
distributions, parameter estimation for actual neurons, and faster exploration
of the parameter space. We use the mean-field systems to analyze adaptation
induced bursting under realistic sources of heterogeneity in multiple
parameters. Our analysis demonstrates that the presence of heterogeneity causes
the Hopf bifurcation associated with the emergence of bursting to change from
sub-critical to super-critical. This is confirmed with numerical simulations of
the full network for biologically reasonable parameter values. This change
decreases the plausibility of adaptation being the cause of bursting in
hippocampal area CA3, an area with a sizable population of heavily coupled,
strongly adapting neurons.


title:
The MOG Weak Field approximation II. Observational test of Chandra X-ray
  Clusters

abstract:
  We apply the weak field approximation limit of the covariant
Scalar-Tensor-Vector Gravity (STVG) theory, so-called MOdified gravity (MOG),
to the dynamics of clusters of galaxies by using only baryonic matter. The MOG
effective gravitational potential in the weak field approximation is composed
of an attractive Newtonian term and a repulsive Yukawa term with two parameters
$\alpha$ and $\mu$. The numerical values of these parameters have been obtained
by fitting the predicted rotation curves of galaxies to observational data,
yielding the best fit result: $\alpha = 8.89 \pm 0.34$ and $\mu= 0.042\pm
0.004$ kpc$^{-1}$~\cite{rah13}. We extend the observational test of this theory
to clusters of galaxies, using data for the ionized gas and the temperature
profile of nearby clusters obtained by the Chandra X-ray telescope. Using the
MOG virial theorem for clusters, we compare the mass profiles of clusters from
observation and theory for eleven clusters. The theoretical mass profiles for
the inner parts of clusters exceed the observational data. However, the
observational data for the inner parts of clusters (i.e., $r<0.1 r_{500}$) is
scattered, but at distances larger than $\sim 300$ kpc, the observed and
predicted mass profiles converge. Our results indicate that MOG as a theory of
modified gravity is compatible with the observational data from the the solar
system to Mega parsec scales without invoking dark matter.


title:
A filter-flow perspective of hematogenous metastasis offers a
  non-genetic paradigm for personalized cancer therapy

abstract:
  Research into mechanisms of hematogenous metastasis has largely become
genetic in focus, attempting to understand the molecular basis of `seed-soil'
relationships. Preceeding this biological mechanism is the physical process of
dissemination of circulating tumour cells (CTCs). We utilize a `filter-flow'
paradigm to show that assumptions about CTC dynamics strongly affect metastatic
efficiency: without data on CTC dynamics, any attempt to predict metastatic
spread in individual patients is impossible.


title:
Investigation of atomic and electronic structures of MgOFeSe studied by
  the first-principles calculations

abstract:
  In order to assist the search of new superconductors in iron selenide
materials by intercalation, we calculate the crystal and electronic structures
of MgOFeSe using the first-principles density functional theory. MgOFeSe is
isotructural to the parent compound of iron pnictide superconductor LaOFeAs. In
LaOFeAs, the anion O$^{2-}$ is located at the center of each LaO tetrahedra.
But for MgOFeSe, we find that the crystal structure with the cation Mg$^{2+}$
as the tetrahedral center in the MgO layer is energetically more stable. The
low energy band structures around the Fermi surfaces of MgOFeSe are contributed
mainly by Fe 3$d$ orbitals. The ground state of MgOFeSe is collinearly
antiferromagnetically ordered. The height of Se atoms above the Fe-Fe layer is
about 1.38 \AA, which is close to the height of As from the Fe-Fe layer in the
iron pnictide superconductors with optimal superconducting transition
temperatures.


title: Study of a model equation in detonation theory

abstract:
  Here we analyze properties of an equation that we previously proposed to
model the dynamics of unstable detonation waves [A. R. Kasimov, L. M. Faria,
and R. R. Rosales. Model for shock wave chaos. Physical Review Letters,
110(10):104104, 2013]. The equation is \[
u_{t}+\frac{1}{2}\left(u^{2}-uu\left(0_{-},t\right)\right)_{x}=f\left(x,u\left(0_{-},t\right)\right),\quad
x\le0,\quad t>0. \] It describes a detonation shock at $x=0$ with the reaction
zone in $x<0$. We investigate the nature of the steady-state solutions of this
nonlocal hyperbolic balance law, the linear stability of these solutions, and
the nonlinear dynamics. We establish the existence of instability followed by a
cascade of period-doubling bifurcations leading to chaos.


title:
Energy estimates for a class of semilinear elliptic equations on half
  Euclidean balls

abstract:
  For a class of semi-linear elliptic equations with critical Sobolev exponents
and boundary conditions, we prove point-wise estimates for blowup solutions and
energy estimates. A special case of this class of equations is a locally
defined prescribing scalar curvature and mean curvature type equation.


title: Symbolic Powers of Monomial Ideals

abstract:
  We investigate symbolic and regular powers of monomial ideals. For a
square-free monomial ideal $I$ in $k[x_0, \ldots, x_n]$ we show
$I^{t(m+e-1)-e+r)}$ is a subset of $M^{(t-1)(e-1)+r-1}(I^{(m)})^t$ for all
positive integers $m$, $t$ and $r$, where $e$ is the big-height of $I$ and $M =
(x_0, \ldots, x_n)$. This captures two conjectures ($r=1$ and $r=e$): one of
Harbourne-Huneke and one of Bocci-Cooper-Harbourne. We also introduce the
symbolic polyhedron of a monomial ideal and use this to explore symbolic powers
of non-square-free monomial ideals.


title: 3-extra connectivity of 3-ary n-cube networks

abstract:
  Let G be a connected graph and S be a set of vertices. The h-extra
connectivity of G is the cardinality of a minimum set S such that G-S is
disconnected and each component of G-S has at least h+1 vertices. The h-extra
connectivity is an important parameter to measure the reliability and fault
tolerance ability of large interconnection networks. The h-extra connectivity
for h=1,2 of k-ary n-cube are gotten by Hsieh et al. in [Theoretical Computer
Science, 443 (2012) 63-69] for k>=4 and Zhu et al. in [Theory of Computing
Systems, arxiv.org/pdf/1105.0991v1 [cs.DM] 5 May 2011] for k=3. In this paper,
we show that the h-extra connectivity of the 3-ary n-cube networks for h=3 is
equal to 8n-12, where n>=3.


title: Constraining Light Dark Matter with Low-Energy e+e- Colliders

abstract:
  We investigate the power of low-energy, high-luminosity electron--positron
colliders to probe hidden sectors with a mass below ~10 GeV that couple to
Standard Model particles through a light mediator. Such sectors provide
well-motivated dark matter candidates, and can give rise to distinctive
mono-photon signals at B-factories and similar experiments. We use data from an
existing mono-photon search by BaBar to place new constraints on this class of
models, and give projections for the sensitivity of a similar search at a
future B-factory such as Belle II. We find that the sensitivity of such
searches are more powerful than searches at other collider or fixed-target
facilities for hidden-sector mediators and particles with masses between a few
hundred MeV and 10 GeV. Mediators produced on-shell and decaying invisibly to
hidden-sector particles such as dark matter can be probed particularly well.
Sensitivity to light dark matter produced through an off-shell mediator is more
limited, but may be improved with a better control of backgrounds, allowing
background estimation and a search for kinematic edges. We compare our results
to existing and future direct detection experiments and show that low-energy
colliders provide an indispensable and complementary avenue to search for light
dark matter. The implementation of a mono-photon trigger at Belle II would
provide an unparalleled window into such light hidden sectors.


title: Linking dynamical heterogeneity to static amorphous order

abstract:
  Glass-forming liquids grow dramatically sluggish upon cooling. This slowdown
has long been thought to be accompanied by a growing correlation length.
Characteristic dynamical and static length scales, however, have been observed
to grow at different rates, which perplexes the relationship between the two
and with the slowdown. Here, we show the existence of a direct link between
dynamical sluggishness and static point-to-set correlations, holding at the
local level as we probe different environments within a liquid. This link,
which is stronger and more general than that observed with locally preferred
structures, suggests the existence of an intimate relationship between
structure and dynamics in a broader range of glass-forming liquids than
previously thought.


title: Holographic s+p Superconductors

abstract:
  We study the phase diagram of a holographic model realizing a U(2) global
symmetry on the boundary and show that at low temperature a phase with both
scalar s and vector p condensates exists. This is the s+p-wave phase where the
global U(2) symmetry and also the spatial rotational symmetry are spontaneously
broken. By studying the free energy we show that this phase is preferred when
it exists. We also consider unbalanced configurations where a second chemical
potential is turned on. They present a rich phase diagram characterized by the
competition and coexistence of the s and p order parameters.


title: Sparse sampling, galaxy bias, and voids

abstract:
  To study the impact of sparsity and galaxy bias on void statistics, we use a
single large-volume, high-resolution N-body simulation to compare voids in
multiple levels of subsampled dark matter, halo populations, and mock galaxies
from a Halo Occupation Distribution model tuned to different galaxy survey
densities. We focus our comparison on three key observational statistics:
number functions, ellipticity distributions, and radial density profiles. We
use the hierarchical tree structure of voids to interpret the impacts of
sampling density and galaxy bias, and theoretical and empirical functions to
describe the statistics in all our sample populations. We are able to make
simple adjustments to theoretical expectations to offer prescriptions for
translating from analytics to the void properties measured in realistic
observations. We find that sampling density has a much larger effect on void
sizes than galaxy bias. At lower tracer density, small voids disappear and the
remaining voids are larger, more spherical, and have slightly steeper profiles.
When a proper lower mass threshold is chosen, voids in halo distributions
largely mimic those found in galaxy populations, except for ellipticities,
where galaxy bias leads to higher values. We use the void density profile of
Hamaus et al. (2014) to show that voids follow a self-similar and universal
trend, allowing simple translations between voids studied in dark matter and
voids identified in galaxy surveys. We have added the mock void catalogs used
in this work to the Public Cosmic Void Catalog at http://www.cosmicvoids.net.


title: A Simple Holographic Model of Nonlinear Conductivity

abstract:
  We present a simple analytic gravitational solution which describes the
holographic dual of a 2+1-dimensional conductor which goes beyond the usual
linear response. In particular it includes Joule heating. We find that the
nonlinear frequency-dependent conductivity is a constant. Surprisingly, the
pressure remains isotropic. We also apply an electric field to a holographic
insulator and show that there is a maximum electric field below which it can
remain an insulator. Above this critical value, we argue that it becomes a
conductor due to pair creation of charged particles. Finally, we study 1+1 and
3+1 dimensional conductors at the nonlinear level; here exact solutions are not
available and a perturbative analysis shows that the current becomes time
dependent, but in a way that is captured by a time-dependent effective
temperature.


title: Conformal Field Theories in Fractional Dimensions

abstract:
  We study the conformal bootstrap in fractional space-time dimensions,
obtaining rigorous bounds on operator dimensions. Our results show strong
evidence that there is a family of unitary CFTs connecting the 2D Ising model,
the 3D Ising model, and the free scalar theory in 4D. We give numerical
predictions for the leading operator dimensions and central charge in this
family at different values of D and compare these to calculations of phi^4
theory in the epsilon-expansion.


title:
Intermolecular interactions and substrate effects for an adamantane
  monolayer on the Au(111) surface

abstract:
  We study theoretically and experimentally the infrared (IR) spectrum of an
adamantane monolayer on a Au(111) surface. Using a new STM-based IR
spectroscopy technique (IRSTM) we are able to measure both the nanoscale
structure of an adamantane monolayer on Au(111) as well as its infrared
spectrum, while DFT-based ab initio calculations allow us to interpret the
microscopic vibrational dynamics revealed by our measurements. We find that the
IR spectrum of an adamantane monolayer on Au(111) is substantially modified
with respect to the gas-phase IR spectrum. The first modification is caused by
the adamantane--adamantane interaction due to monolayer packing and it reduces
the IR intensity of the 2912 cm$^{-1}$ peak (gas phase) by a factor of 3.5. The
second modification originates from the adamantane--gold interaction and it
increases the IR intensity of the 2938 cm$^{-1}$ peak (gas phase) by a factor
of 2.6, and reduces its frequency by 276 cm$^{-1}$. We expect that the
techniques described here can be used for an independent estimate of substrate
effects and intermolecular interactions in other diamondoid molecules, and for
other metallic substrates.


title:
Baryogenesis, dark matter and inflation in the Next-to-Minimal
  Supersymmetric Standard Model

abstract:
  Explaining baryon asymmetry, dark matter and inflation are important elements
of a successful theory that extends beyond the Standard Model of particle
physics. In this paper we explore these issues within the Next-to-Minimal
Supersymmetric Standard Model (NMSSM), by studying the conditions for a
strongly first order electroweak phase transition, the abundance of the
lightest supersymmetric particle (LSP), and inflation driven by a gauge
invariant flat direction of MSSM made up of right handed squarks. We present
the regions of parameter space which can yield successful predictions for
cosmic microwave background (CMB) radiation, the observed relic density for the
neutralino LSP, and successful baryogenesis constrained by collider
measurements, such as the recent Higgs mass bound, branching ratios of rare,
flavour violating decays, and the invisible Z decay width. We also explore
where dark matter interactions with xenon nuclei would fall within current
bounds of XENON100 and the projected limits for the XENON1T and LUX
experiments.


title:
Constraining Globular Cluster Formation Through Studies of Young Massive
  Clusters: I. A lack of ongoing star formation within young clusters

abstract:
  We present a survey of 130 Galactic and extragalactic young massive clusters
(YMCs, $10^4 < M/\msun < 10^8$, $10 < t/{\rm Myr} < 1000$) with integrated
spectroscopy or resolved stellar photometry (40 presented here and 90 from the
literature) and use the sample to search for evidence of ongoing star-formation
within the clusters. Such episodes of secondary (or continuous) star-formation
are predicted by models that attempt to explain the observed chemical and
photometric anomalies observed in globular clusters as being due to the
formation of a second stellar population within an existing first population.
Additionally, studies that have claimed extended star-formation histories
within LMC/SMC intermediate age clusters (1-2 Gyr), also imply that many young
massive clusters should show ongoing star-formation. Based on visual inspection
of the spectra and/or the colour-magnitude diagrams, we do not find evidence
for ongoing star-formation within any of the clusters, and use this to place
constraints on the above models. Models of continuous star-formation within
clusters, lasting for hundreds of Myr, are ruled out at high significance
(unless stellar IMF variations are invoked). Models for the (nearly
instantaneous) formation of a secondary population within an existing first
generation are not favoured, but are not formally discounted due to the finite
sampling of age/mass-space.


title:
Coexistence of two vector order parameters: a holographic model for
  ferromagnetic superconductivity

abstract:
  We study a generalization of the standard holographic p-wave superconductor
featuring two interacting vector order parameters. Basing our argument on the
symmetry and linear response properties of the model, we propose it as a
holographic effective theory describing a strongly coupled ferromagnetic
superconductor. We show that the two order parameters undergo concomitant
condensations as a manifestation of an intrinsically interlaced
electric/magnetic dynamics. Such intertwined dynamics is confirmed by the study
of the transport properties. We characterize thoroughly the equilibrium and the
linear response (i.e. optical conductivity and magnetic susceptibility) of the
model at hand by means of a probe approximation analysis. Some insight about
the effects of backreaction in the normal phase can be gained by analogy with
the s-wave unbalanced holographic superconductor.


title: Hedging under multiple risk constraints

abstract:
  Motivated by the asset-liability management of a nuclear power plant
operator, we consider the problem of finding the least expensive portfolio,
which outperforms a given set of stochastic benchmarks. For a specified loss
function, the expected shortfall with respect to each of the benchmarks
weighted by this loss function must remain bounded by a given threshold. We
consider different alternative formulations of this problem in a complete
market setting, establish the relationship between these formulations, present
a general resolution methodology via dynamic programming in a non-Markovian
context and give explicit solutions in special cases.


title:
Weakly holomorphic modular forms and rank two hyperbolic Kac-Moody
  algebras

abstract:
  In this paper, we compute basis elements of certain spaces of weight 0 weakly
holomorphic modular forms and consider the integrality of Fourier coefficients
of the modular forms. We use the results to construct automorphic correction of
the rank 2 hyperbolic Kac-Moody algebras H(a), a=4,5,6, through Hilbert modular
forms explicitly given by Borcherds lifts of the weakly holomorphic modular
forms. We also compute asymptotic of the Fourier coefficients as they are
related to root multiplicities of the rank 2 hyperbolic Kac-Moody algebras.
This work is a continuation of the previous paper, where automorphic correction
was constructed for H(a), a=3, 11, 66.


title:
Differential-Dunkl Operators and Nonstandard Solutions to the Classical
  Yang-Baxter Equation

abstract:
  For every pair of positive coprime integers, m and n, with m<n, there is an
associated generalized Cremmer-Gervais r-matrix r_{m,n} for the Lie algebra
sl_n which provides a nonstandard quasitriangular solution to the classical
Yang-Baxter equation. We give an interpretation of r_{n-2,n} (for n odd) in
terms of differential-Dunkl operators related to the polynomial representation
of dihedral-type rational Cherednik algebras. Finally, we use this
interpretation to partially answer a conjecture of Gerstenhaber and Giaquinto
concerning boundary solutions to the classical Yang-Baxter equation.


title:
Weighing "El Gordo" with a Precision Scale: Hubble Space Telescope
  Weak-lensing Analysis of the Merging Galaxy Cluster ACT-CL J0102-4915 at
  z=0.87

abstract:
  (Abridged) We present a HST weak-lensing study of the merging galaxy cluster
"El Gordo" (ACT-CL J0102-4915) at z=0.87 discovered by the Atacama Cosmology
Telescope collaboration as the strongest SZ decrement in its ~1000 sq. deg
survey. Our weak-lensing analysis confirms that ACT-CL J0102-4915 is indeed an
extreme system consisting of two massive (~10^15 Msun each) subclusters with a
projected separation of ~0.7 Mpc. This binary mass structure revealed by our
lensing study is consistent with the cluster galaxy distribution and the
dynamical study carried out with 89 spectroscopic members. We estimate the mass
of ACT-CL J0102-4915 by simultaneously fitting two axisymmetric NFW profiles
allowing their centers to vary. Our MCMC analysis shows that the masses of the
northwestern (NW) and the southeastern (SE) components are M200c=(1.38+-0.22) x
10^15 Msun and (0.78+-0.20) x 10^15 Msun, respectively. The lensing-based
velocity dispersions are consistent with their spectroscopic measurements. The
centroids of both components are tightly constrained (~4") and close to the
optical luminosity centers. The X-ray and mass peaks are spatially offset by
~8" (~62 kpc), which is significant at the ~2 sigma confidence level and
confirms that the baryonic and dark matter in this cluster are disassociated.
The dark matter peak, however, does not lead the gas peak in the direction
expected if we are viewing the cluster soon after first core passage during a
high speed merger. Under the assumption that the merger is happening in the
plane of the sky, extrapolation of the two NFW halos to a radius r200a=2.4 Mpc
yields a combined mass of M200a=(3.13+-0.56) x 10^15 Msun. This extrapolated
total mass is consistent with our two-component-based dynamical analysis and
previous X-ray measurements, projecting ACT-CL J0102-4915 to be the most
massive cluster at z>0.6 known to date.


title:
Gas lines from the 5-Myr old optically thin disk around HD141569A.
  Herschel observations and modeling

abstract:
  At the distance of 99-116 pc, HD141569A is one of the nearest HerbigAe stars
that is surrounded by a tenuous disk, probably in transition between a massive
primordial disk and a debris disk. We observed the fine-structure lines of OI
at 63 and 145 micron and the CII line at 157 micron with the PACS instrument
onboard the Herschel Space Telescope as part of the open-time large programme
GASPS. We complemented the atomic line observations with archival Spitzer
spectroscopic and photometric continuum data, a ground-based VLT-VISIR image at
8.6 micron, and 12CO fundamental ro-vibrational and pure rotational J=3-2
observations. We simultaneously modeled the continuum emission and the line
fluxes with the Monte Carlo radiative transfer code MCFOST and the
thermo-chemical code ProDiMo to derive the disk gas- and dust properties
assuming no dust settling. The models suggest that the oxygen lines are emitted
from the inner disk around HD141569A, whereas the [CII] line emission is more
extended. The CO submillimeter flux is emitted mostly by the outer disk.
Simultaneous modeling of the photometric and line data using a realistic disk
structure suggests a dust mass derived from grains with a radius smaller than 1
mm of 2.1E-7 MSun and from grains with a radius of up to 1 cm of 4.9E-6 MSun.
We constrained the polycyclic aromatic hydrocarbons (PAH) mass to be between
2E-11 and 1..4E-10 MSun assuming circumcircumcoronene (C150H30) as the
representative PAH. The associated PAH abundance relative to hydrogen is lower
than those found in the interstellar medium (3E-7) by two to three orders of
magnitude. The disk around HD141569A is less massive in gas (2.5 to 4.9E-4 MSun
or 67 to 164 MEarth) and has a flat opening angle (<10%). [abridged]


title: A mean curvature type flow in space forms

abstract:
  In this article, we introduce a new type of mean curvature flow for bounded
star-shaped domains in space forms and prove its longtime existence,
exponential convergence without any curvature assumption. Along this flow, the
enclosed volume is a constant and the surface area evolves monotonically.
Moreover, for a bounded convex domain in R n+1, the quermassintegrals evolve
monotonically along the flow which allows us to prove a class of
Alexandrov-Fenchel inequalities of quermassintegrals.


title: The Star Formation Law in Molecule-Poor Galaxies

abstract:
  In this paper, I investigate the processes that regulate the rate of star
formation in regions of galaxies where the neutral interstellar medium is
predominantly composed of non-star-forming HI. In such regions, found today
predominantly in low-metallicity dwarf galaxies and in the outer parts of large
spirals, the star formation rate per unit area and per unit mass is much
smaller than in more molecule-rich regions. While in molecule-rich regions the
ultraviolet radiation field produced by efficient star formation forces the
density of the cold neutral medium to a value set by two-phase equilibrium, I
show that the low rates of star formation found in molecule-poor regions
preclude this condition. Instead, the density of the cold neutral gas is set by
the requirements of hydrostatic balance. Using this result, I extend the
Krumholz, McKee, & Tumlinson model for star formation and the atomic to
molecular transition to the molecule-poor regime. This "KMT+" model matches a
wide range of observations of the star formation rate and the balance between
the atomic and molecular phases in dwarfs and in the outer parts of spirals,
and is well-suited to implementation as a subgrid recipe for star formation in
cosmological simulations and semi-analytic models. I discuss the implications
of this model for star formation over cosmological times.


title: Exact Lagrangian caps of Legendrian knots

abstract:
  We prove that any Legendrian knot in $(S^3,\xi_{std})$ bounds an exact
Lagrangian surface in $\mathbb{R}^4\setminus B^4$ after a sufficient number of
stabilizations. In order to show this, we construct a family combinatorial
moves on knot projections with some additional data that correspond to
Lagrangian cobordisms between knots.


title:
Structural and Electronic Recovery Pathways of a Photoexcited Ultrathin
  VO2 Film

abstract:
  The structural and electronic recovery pathways of a photoexcited ultrathin
VO2 film at nanosecond time scales have been studied using time-resolved x-ray
diffraction and transient optical absorption techniques. The recovery pathways
from the tetragonal metallic phase to the monoclinic insulating phase are
highly dependent on the optical pump fluence. At pump fluences higher than the
saturation fluence of 14.7 mJ/cm2, we observed a transient structural state
with lattice parameter larger than that of the tetragonal phase, which is
decoupled from the metal-to-insulator phase transition. Subsequently, the
photoexcited VO2 film recovered to the ground state at characteristic times
dependent upon the pump fluence, as a result of heat transport from the film to
the substrate. We present a procedure to measure the time-resolved film
temperature by correlating photoexcited and temperature-dependent x-ray
diffraction measurements. A thermal transport model that incorporates changes
of the thermal parameters across the phase transition reproduces the observed
recovery dynamics. The optical excitation and fast recovery of ultrathin VO2
films provides a practical method to reversibly switch between the monoclinic
insulating and tetragonal metallic state at nanosecond time scales.


title: The effect of amplitude fluctuations on the BKT transition

abstract:
  The Berezinskii-Kosterlitz-Thouless (BKT) transition is a generic transition
describing the loss of coherence in two dimensional systems, and has been
invoked, for example, to describe the superconductor-insulator transition in
thin films. However, recent experiments have shown that the BKT transition,
driven by phase fluctuations, is not sufficient to describe the loss of
superconducting order, and amplitude fluctuations have also to be taken into
account. The standard models that are extensively used to model two-dimensional
superconductors are the Hubbard and XY models. Whereas the XY model allows only
phase fluctuations, the Hubbard model has an extra degree of freedom: amplitude
fluctuations. In this paper we compare two Hubbard models with the same
critical temperature but with different interaction, and deduce the role of the
amplitude fluctuations in the superconducting transition. For this purpose, a
novel approximation is presented and used. We derive an effective phase-only
(XY) Hamiltonian, incorporating amplitude fluctuations in an explicit
temperature dependence of the phase rigidity. We study the relation between
amplitude fluctuations and coupling strength. Our results support existing
claims about the suppression of phase rigidity due to amplitude fluctuations
not present in the XY model.


title:
Near-Field Optical Effect of a Core-Shell Nanostructure In Proximity to
  a Flat Surface

abstract:
  We provide an analytical solution to study the near field optical effect of a
core-shell nanostructure in proximity to a flat surface, within quasi-static
approximation. The distribution of electrostatic potential and field
enhancement in this complex geometry are obtained by solving a set of linear
equations. This analytical result can be applied to a wide range of systems
associated with near field optics and surface plasmon polaritons. As an
illustration of the power of this technique, we study the field attenuation
effect of oxidized shell in a silver tip in near field scanning microscope. The
thickness of oxidized layer can be monitored by measuring the light intensity.
In addition, we propose a novel method to detect local temperature with spatial
resolution down to nm scale, based on a Ag-Au core-shell structure.


title: Subspace identification of large-scale interconnected systems

abstract:
  We propose a decentralized subspace algorithm for identification of
large-scale, interconnected systems that are described by sparse (multi) banded
state-space matrices. First, we prove that the state of a local subsystem can
be approximated by a linear combination of inputs and outputs of the local
subsystems that are in its neighborhood. Furthermore, we prove that for
interconnected systems with well-conditioned, finite-time observability
Gramians (or observability matrices), the size of this neighborhood is
relatively small. On the basis of these results, we develop a subspace
identification algorithm that identifies a state-space model of a local
subsystem from the local input-output data. Consequently, the developed
algorithm is computationally feasible for interconnected systems with a large
number of local subsystems. Numerical results confirm the effectiveness of the
new identification algorithm.


title:
The Altshuler-Shklovskii Formulas for Random Band Matrices I: the
  Unimodular Case

abstract:
  We consider the spectral statistics of large random band matrices on
mesoscopic energy scales. We show that the two-point correlation function of
the local eigenvalue density exhibits a universal power law behaviour that
differs from the Wigner-Dyson-Mehta statistics. This law had been predicted in
the physics literature by Altshuler and Shklovskii [4]; it describes the
correlations of the eigenvalue density in general metallic samples with weak
disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas
for band matrices. In two dimensions, where the leading term vanishes owing to
an algebraic cancellation, we identify the first non-vanishing term and show
that it differs substantially from the prediction of Kravtsov and Lerner [33].


title:
The Altshuler-Shklovskii Formulas for Random Band Matrices II: the
  General Case

abstract:
  The Altshuler-Shklovskii formulas [1] predict, for any disordered quantum
system in the diffusive regime, a universal power law behaviour for the
correlation functions of the mesoscopic eigenvalue density. In this paper and
its companion [2], we prove these formulas for random band matrices. In [2] we
introduced a diagrammatic approach and presented robust estimates on general
diagrams under certain simplifying assumptions. In this paper we remove these
assumptions by giving a general estimate of the subleading diagrams. We also
give a precise analysis of the leading diagrams which give rise to the
Altschuler-Shklovskii power laws. Moreover, we introduce a family of general
random band matrices which interpolates between real symmetric $(\beta=1)$ and
complex Hermitian $(\beta=2)$ models, and track the transition for the
mesoscopic density-density correlation. Finally, we address the higher-order
correlation functions by proving that they behave asymptotically according to a
Gaussian process whose covariance is given by the Altshuler-Shklovskii
formulas.


title: Study of excited nucleons and their structure

abstract:
  Recent advances in the study of excited nucleons are discussed. Much of the
progress has been achieved due to the availability of high precision meson
production data in the photoproduction and electroproduction sectors, the
development of multi-channel partial wave analysis techniques, and advances in
Lattice QCD with predictions of the full excitation spectrum.


title:
Network Structure and Biased Variance Estimation in Respondent Driven
  Sampling

abstract:
  This paper explores bias in the estimation of sampling variance in Respondent
Driven Sampling (RDS). Prior methodological work on RDS has focused on its
problematic assumptions and the biases and inefficiencies of its estimators of
the population mean. Nonetheless, researchers have given only slight attention
to the topic of estimating sampling variance in RDS, despite the importance of
variance estimation for the construction of confidence intervals and hypothesis
tests. In this paper, we show that the estimators of RDS sampling variance rely
on a critical assumption that the network is First Order Markov (FOM) with
respect to the dependent variable of interest. We demonstrate, through
intuitive examples, mathematical generalizations, and computational experiments
that current RDS variance estimators will always underestimate the population
sampling variance of RDS in empirical networks that do not conform to the FOM
assumption. Analysis of 215 observed university and school networks from
Facebook and Add Health indicates that the FOM assumption is violated in every
empirical network we analyze, and that these violations lead to substantially
biased RDS estimators of sampling variance. We propose and test two alternative
variance estimators that show some promise for reducing biases, but which also
illustrate the limits of estimating sampling variance with only partial
information on the underlying population social network.


title: An ant colony optimization algorithm for job shop scheduling problem

abstract:
  The nature has inspired several metaheuristics, outstanding among these is
Ant Colony Optimization (ACO), which have proved to be very effective and
efficient in problems of high complexity (NP-hard) in combinatorial
optimization. This paper describes the implementation of an ACO model algorithm
known as Elitist Ant System (EAS), applied to a combinatorial optimization
problem called Job Shop Scheduling Problem (JSSP). We propose a method that
seeks to reduce delays designating the operation immediately available, but
considering the operations that lack little to be available and have a greater
amount of pheromone. The performance of the algorithm was evaluated for
problems of JSSP reference, comparing the quality of the solutions obtained
regarding the best known solution of the most effective methods. The solutions
were of good quality and obtained with a remarkable efficiency by having to
make a very low number of objective function evaluations.


title: Global attractivity in almost periodic single species models

abstract:
  Using properties of asymptotically almost periodic solutions we prove
existence theorem for piece-wise continuous almost periodic solutions of
differential equations with delay and impulses. We apply these results to study
almost periodic single species model with stage structure and impulses.


title: Asymmetry of radiation damage properties in Al-Ti nanolayers

abstract:
  Molecular dynamics (MD) simulations were employed with empirical potentials
to study the effects of multilayer interfaces and interface spacing in Al-Ti
nanolayers. Several model interfaces derived from stacking of close-packed
layers or face-centered cubic \{100\} layers were investigated. The simulations
reveal significant and important asymmetries in defect production with
$\sim$60% of vacancies created in Al layers compared to Ti layers within the
Al-Ti multilayer system. The asymmetry in the creation of interstitials is even
more pronounced. The asymmetries cause an imbalance in the ratio of vacancies
and interstitials in films of dissimilar materials leading to $>$90% of the
surviving interstitials located in the Al layers. While in the close-packed
nanolayers the interstitials migrate to the atomic layers adjacent to the
interface of the Al layers, in the \{100\} nanolayers the interstitials migrate
to the center of the Al layers and away from the interfaces. The degree of
asymmetry and defect ratio imbalance increases as the layer spacing decreases
in the multilayer films. Underlying physical processes are discussed including
the interfacial strain fields and the individual elemental layer stopping power
in nanolayered systems. In addition, experimental work was performed on
low-dose (10$^{16}$ atoms/cm$^2$) helium (He) irradiation on Al/Ti nanolayers
(5 nm per film), resulting in He bubble formation $\sim$1 nm in diameter in the
Ti film near the interface. The correlation between the preferential flux of
displaced atoms from Ti films to Al films during the defect production that is
revealed in the simulations and the morphology and location of He bubbles from
the experiments is discussed.


title:
Hot medium effects on J/psi production in p+Pb collisions at
  sqrt{s_{NN}}=5.02 TeV

abstract:
  Based on a kinetic description of J/psi dissociation and production in an
expanding quark-gluon plasma that is described by a 2+1 dimensional ideal
hydrodynamics, we have studied the hot medium effects on J/psi production in
p+Pb collisions at sqrt{s_{NN}}=5.02 TeV. Including also the cold nuclear
matter effects, we are able to reproduce recent experimental results on the
nuclear modification factor R_{pPb}(J/psi) measured by the ALICE Collaboration.
We have also made predictions for the R_{pPb} of J/psi and the double ratio
R_{pPb}^{pro}(psi')/R_{pPb}^{pro}(J/psi) of prompt quarkonia produced in the
most central 10% p+Pb collisions. We find that different from the cold nuclear
matter effects, the R_{pPb}(J/psi) is slightly smaller than that in the minimum
bias collisions, and the double ratio is significantly less than one at
backward rapidity.


title:
Nonperturbative renormalization of the chiral nucleon-nucleon
  interaction up to next-to-next-to-leading order

abstract:
  We study the nonperturbative renormalization of the nucleon-nucleon (NN)
interaction at next-to-leading order (NLO) and next-to-next-to-leading order
(NNLO) of chiral effective field theory. A systematic variation of the cutoff
parameter is performed for values below the chiral symmetry breaking scale of
about 1 GeV. The accuracy of the predictions is determined by calculating the
$\chi^2$ for the reproduction of the NN data for energy intervals below
pion-production threshold. At NLO, the NN data are described well up to about
100 MeV laboratory energy and, at NNLO, up to about 200 MeV---with,
essentially, cutoff independence for cutoffs between about 450 and 850 MeV.


title: Neutrino oscillations in the presence of the crust magnetization

abstract:
  It is noted that the crustal magnetic spectrum exhibits the signal from the
partly correlated domain dipoles on the space-scale up to approximately 500 km.
This suggests the nonzero correlation among the dynamical variables of the
ferromagnetic magnetization phenomenon on the small domain scale inside the
earth's crust also. Therefore the influence of the mean of the zero component
of the polarization on the CP matter-induced violation indexes is discussed.


title: Combinatorics of balanced carries

abstract:
  We study the combinatorics of addition using balanced digits, deriving an
analog of Holte's "amazing matrix" for carries in usual addition. The
eigenvalues of this matrix for base b balanced addition of n numbers are found
to be 1,1/b,...,1/b^n, and formulas are given for its left and right
eigenvectors. It is shown that the left eigenvectors can be identified with
hyperoctahedral Foulkes characters, and that the right eigenvectors can be
identified with hyperoctahedral Eulerian idempotents. We also examine the
carries that occur when a column of balanced digits is added, showing this
process to be determinantal. The transfer matrix method and a serendipitous
diagonalization are used to study this determinantal process.


title: Diagnostics for Variational Bayes approximations

abstract:
  Variational Bayes (VB) has shown itself to be a powerful approximation method
in many application areas. This paper describes some diagnostics methods which
can assess how well the VB approximates the true posterior, particularly with
regards to its covariance structure. The methods proposed also allow us to
generate simple corrections when the approximation error is large. It looks at
joint, marginal and conditional aspects of the approximate posterior and shows
how to apply these techniques in both simulated and real data examples.


title:
Worldwide Patterns of Ancestry, Divergence, and Admixture in
  Domesticated Cattle

abstract:
  The domestication and development of cattle has considerably impacted human
societies, but the histories of cattle breeds have been poorly understood
especially for African, Asian, and American breeds. Using genotypes from 43,043
autosomal single nucleotide polymorphism markers scored in 1,543 animals, we
evaluate the population structure of 134 domesticated bovid breeds. Regardless
of the analytical method or sample subset, the three major groups of Asian
indicine, Eurasian taurine, and African taurine were consistently observed.
Patterns of geographic dispersal resulting from co-migration with humans and
exportation are recognizable in phylogenetic networks. All analytical methods
reveal patterns of hybridization which occurred after divergence. Using 19
breeds, we map the cline of indicine introgression into Africa. We infer that
African taurine possess a large portion of wild African auroch ancestry,
causing their divergence from Eurasian taurine. We detect exportation patterns
in Asia and identify a cline of Eurasian taurine/indicine hybridization in
Asia. We also identify the influence of species other than Bos taurus in the
formation of Asian breeds. We detect the pronounced influence of Shorthorn
cattle in the formation of European breeds. Iberian and Italian cattle possess
introgression from African taurine. American Criollo cattle are shown to be of
Iberian, and not African, decent. Indicine introgression into American cattle
occurred in the Americas, and not Europe. We argue that cattle migration,
movement and trading followed by admixture have been important forces in
shaping modern bovine genomic variation.


title: Wave packet dynamics in the one-dimensional extended Hubbard model

abstract:
  Using time-dependent density-matrix renormalization group, we study the time
evolution of electronic wave packets in the one-dimensional extended Hubbard
model with on-site and nearest neighbor repulsion, U and V, respectively. As
expected, the wave packets separate into spin-only and charge-only excitations
(spin-charge separation). Charge and spin velocities exhibit non-monotonic
dependence on V. For small and intermediate values of V, both velocities
increase with V. However, the charge velocity exhibits a stronger dependence
than that of the spin, leading to a more pronounced spin-charge separation.
Charge fractionalization, on the other hand, is weakly affected by V. The
results are explained in terms of Luttinger liquid theory in the weak-coupling
limit, and an effective model in the strong-coupling regime.


title: Nonlinear fluctuations of weakly asymmetric interacting particle systems

abstract:
  We introduce what we call the second-order Boltzmann-Gibbs principle, which
allows to replace local functionals of a conservative, one-dimensional
stochastic process by a possibly nonlinear function of the conserved quantity.
This replacement opens the way to obtain nonlinear stochastic evolutions as the
limit of the fluctuations of the conserved quantity around stationary states.
As an application of this second-order Boltzmann-Gibbs principle, we introduce
the notion of energy solutions of the KPZ and stochastic Burgers equations.
Under minimal assumptions, we prove that the density fluctuations of
one-dimensional, stationary, weakly asymmetric, conservative particle systems
are sequentially compact and that any limit point is given by energy solutions
of the stochastic Burgers equation. We also show that the fluctuations of the
height function associated to these models are given by energy solutions of the
KPZ equation in this sense. Unfortunately, we lack a uniqueness result for
these energy solutions. We conjecture these solutions to be unique, and we show
some regularity results for energy solutions of the KPZ/Burgers equation,
supporting this conjecture.


title: Quantum dynamics with an ensemble of Hamiltonians

abstract:
  We review recent progress in the nonequilibrium dynamics of thermally
isolated many-body quantum systems, evolving with an ensemble of Hamiltonians
as opposed to deterministic evolution with a single time-dependent Hamiltonian.
Such questions arise in (i) quantum dynamics of disordered systems, where
different realizations of disorder give rise to an ensemble of real-time
quantum evolutions. (ii) quantum evolution with noisy Hamiltonians (temporal
disorder), which leads to stochastic Schrodinger equations, and, (iii) in the
broader context of quantum optimal control, where one needs to analyze an
ensemble of permissible protocols in order to find one that optimizes a given
figure of merit. The theme of ensemble quantum evolution appears in several
emerging new directions in noneqilibrium quantum dynamics of thermally isolated
many-body systems, which include many-body localization, noise-driven systems,
and shortcuts to adiabaticity.


title: Variational Bayes inference and Dirichlet process priors

abstract:
  This paper shows how the variational Bayes method provides a computational
efficient technique in the context of hierarchical modelling using Dirichlet
process priors, in particular without requiring conjugate prior assumption. It
shows, using the so called parameter separation parameterization, a simple
criterion under which the variational method works well. Based on this
framework, its provides a full variational solution for the Dirichlet process.
The numerical results show that the method is very computationally efficient
when compared to MCMC. Finally, we propose an empirical method to estimate the
truncation level for the truncated Dirichlet process.


title: Isotropic stars in general relativity

abstract:
  We present a general solution of the Einstein gravitational field equations
for the static spherically symmetric gravitational interior spacetime of an
isotropic fluid sphere. The solution is obtained by transforming the pressure
isotropy condition, a second order ordinary differential equation, into a
Riccati type first order differential equation, and using a general
integrability condition for the Riccati equation. This allows us to obtain an
exact non-singular solution of the interior field equations for a fluid sphere,
expressed in the form of infinite power series. The physical features of the
solution are studied in detail numerically by cutting the infinite series
expansions, and restricting our numerical analysis by taking into account only
$n=21$ terms in the power series representations of the relevant astrophysical
parameters. In the present model all physical quantities (density, pressure,
speed of sound etc.) are finite at the center of the sphere. The physical
behavior of the solution essentially depends on the equation of state of the
dense matter at the center of the star. The stability properties of the model
are also analyzed in detail for a number of central equations of state, and it
is shown that it is stable with respect to the radial adiabatic perturbations.
The astrophysical analysis indicates that this solution can be used as a
realistic model for static general relativistic high density objects, like
neutron stars.


title: Multi-layer graph analysis for dynamic social networks

abstract:
  Modern social networks frequently encompass multiple distinct types of
connectivity information; for instance, explicitly acknowledged friend
relationships might complement behavioral measures that link users according to
their actions or interests. One way to represent these networks is as
multi-layer graphs, where each layer contains a unique set of edges over the
same underlying vertices (users). Edges in different layers typically have
related but distinct semantics; depending on the application multiple layers
might be used to reduce noise through averaging, to perform multifaceted
analyses, or a combination of the two. However, it is not obvious how to extend
standard graph analysis techniques to the multi-layer setting in a flexible
way. In this paper we develop latent variable models and methods for mining
multi-layer networks for connectivity patterns based on noisy data.


title: Arithmetic Groups (Banff, Alberta, April 14-19, 2013)

abstract:
  We present detailed summaries of the talks that were given during a week-long
workshop on Arithmetic Groups at the Banff International Research Station in
April 2013. The vast majority of these reports are based on abstracts that were
kindly provided by the speakers. Video recordings of many of the lectures are
available online.


title: The third-order term in the normal approximation for singular channels

abstract:
  For a singular and symmetric discrete memoryless channel with positive
dispersion, the third-order term in the normal approximation is shown to be
upper bounded by a constant. This finding completes the characterization of the
third-order term for symmetric discrete memoryless channels. The proof method
is extended to asymmetric and singular channels with constant composition
codes, and its connection to existing results, as well as its limitation in the
error exponents regime, are discussed.


title:
Using the Palomar Transient Factory to Search for Ultra-Long-Period
  Cepheid Candidates in M31

abstract:
  Ultra-long-period Cepheids (ULPCs) are important in distance-scale studies
due to their potential for determining distance beyond ~100 Mpc. We performed a
comprehensive search for ULPCs in M31, a local benchmark to calibrate the
distance ladders. We use data from the Palomar Transient Factory (PTF), which
has imaged M31 using a 1.2-m telescope equipped with a ~7.26 deg2 field-of-view
(FOV) camera, usually with daily sampling, since the beginning of 2010. The
large FOV, together with the regular monitoring, enables us to probe ULPCs in
the bulge, disk, and even out to the halo of M31. Using a difference imaging
analysis technique, we found and characterized 3 promising ULPC candidates
based on their luminosities, amplitudes and Fourier parameters. The mean
absolute magnitude for these 3 ULPC candidates, calibrated with latest M31
distance, is M_R=-6.47mag. Two out of the 3 ULPC candidates have been reported
in literature, however their published periods from Magnier et al. are about
half of the periods we found in this work. The third ULPC candidate is a new
discovery. We studied 5 other candidates and determined that they are probably
Mira-like or ultra-long-period variables, but not ULPCs.


title: A Swiss Pocket Knife for Computability

abstract:
  This research is about operational- and complexity-oriented aspects of
classical foundations of computability theory. The approach is to re-examine
some classical theorems and constructions, but with new criteria for success
that are natural from a programming language perspective.
  Three cornerstones of computability theory are the S-m-ntheorem; Turing's
"universal machine"; and Kleene's second recursion theorem. In today's
programming language parlance these are respectively partial evaluation,
self-interpretation, and reflection. In retrospect it is fascinating that
Kleene's 1938 proof is constructive; and in essence builds a self-reproducing
program.
  Computability theory originated in the 1930s, long before the invention of
computers and programs. Its emphasis was on delimiting the boundaries of
computability. Some milestones include 1936 (Turing), 1938 (Kleene), 1967
(isomorphism of programming languages), 1985 (partial evaluation), 1989 (theory
implementation), 1993 (efficient self-interpretation) and 2006 (term register
machines).
  The "Swiss pocket knife" of the title is a programming language that allows
efficient computer implementation of all three computability cornerstones,
emphasising the third: Kleene's second recursion theorem. We describe
experiments with a tree-based computational model aiming for both fast program
generation and fast execution of the generated programs.


title: A Proof System with Names for Modal Mu-calculus

abstract:
  Fixpoints are an important ingredient in semantics, abstract interpretation
and program logics. Their addition to a logic can add considerable expressive
power. One general issue is how to define proof systems for such logics. Here
we examine proof systems for modal logic with fixpoints. We present a tableau
proof system for checking validity of formulas which uses names to keep track
of unfoldings of fixpoint variables as devised by Jungteerapanich.


title: A Comparison of Well-Quasi Orders on Trees

abstract:
  Well-quasi orders such as homeomorphic embedding are commonly used to ensure
termination of program analysis and program transformation, in particular
supercompilation.
  We compare eight well-quasi orders on how discriminative they are and their
computational complexity. The studied well-quasi orders comprise two very
simple examples, two examples from literature on supercompilation and four new
proposed by the author.
  We also discuss combining several well-quasi orders to get well-quasi orders
of higher discriminative power. This adds 19 more well-quasi orders to the
list.


title:
Abstract interpretation-based approaches to Security - A Survey on
  Abstract Non-Interference and its Challenging Applications

abstract:
  In this paper we provide a survey on the framework of abstract
non-interference. In particular, we describe a general formalization of
abstract non-interference by means of three dimensions (observation, protection
and semantics) that can be instantiated in order to obtain well known or even
new weakened non-interference properties. Then, we show that the notions of
abstract non-interference introduced in language-based security are instances
of this more general framework which allows to better understand the different
components of a non-interference policy. Finally, we consider two challenging
research fields concerning security where abstract non-interference seems a
promising approach providing new perspectives and new solutions to open
problems: Code injection and code obfuscation.


title: Notions of Monad Strength

abstract:
  Over the past two decades the notion of a strong monad has found wide
applicability in computing. Arising out of a need to interpret products in
computational and semantic settings, different approaches to this concept have
arisen. In this paper we introduce and investigate the connections between
these approaches and also relate the results to monad composition. We also
introduce new methods for checking and using the required laws associated with
such compositions, as well as provide examples illustrating problems and issues
that arise.


title: Abstract Interpretation as a Programming Language

abstract:
  In David Schmidt's PhD work he explored the use of denotational semantics as
a programming language. It was part of an effort to not only treat formal
semantics as specifications but also as interpreters and input to compiler
generators. The semantics itself can be seen as a program and one may examine
different programming styles and ways to represent states.
  Abstract interpretation is primarily a technique for derivation and
specification of program analysis. As with denotational semantics we may also
view abstract interpretations as programs and examine the implementation. The
main focus in this paper is to show that results from higher-order strictness
analysis may be used more generally as fixpoint operators for higher-order
functions over lattices and thus provide a technique for immediate
implementation of a large class of abstract interpretations. Furthermore, it
may be seen as a programming paradigm and be used to write programs in a
circular style.


title: Formal Contexts, Formal Concept Analysis, and Galois Connections

abstract:
  Formal concept analysis (FCA) is built on a special type of Galois
connections called polarities. We present new results in formal concept
analysis and in Galois connections by presenting new Galois connection results
and then applying these to formal concept analysis. We also approach FCA from
the perspective of collections of formal contexts. Usually, when doing FCA, a
formal context is fixed. We are interested in comparing formal contexts and
asking what criteria should be used when determining when one formal context is
better than another formal context. Interestingly, we address this issue by
studying sets of polarities.


title: Coroutining Folds with Hyperfunctions

abstract:
  Fold functions are a general mechanism for computing over recursive data
structures. First-order folds compute results bottom-up. With higher-order
folds, computations that inherit attributes from above can also be expressed.
In this paper, we explore folds over a form of recursive higher-order function,
called hyperfunctions, and show that hyperfunctions allow fold computations to
coroutine across data structures, as well as compute bottom up and top down. We
use the compiler technique of foldr-build as an exemplar to show how
hyperfunctions can be used.


title: Adaptation dynamics in densely clustered chemoreceptors

abstract:
  In many sensory systems, transmembrane receptors are spatially organized in
large clusters. Such arrangement may facilitate signal amplification and the
integration of multiple stimuli. However, this organization likely also affects
the kinetics of signaling since the cytoplasmic enzymes that modulate the
activity of the receptors must localize to the cluster prior to receptor
modification. Here we examine how these spatial considerations shape signaling
dynamics at rest and in response to stimuli. As a model, we use the chemotaxis
pathway of Escherichia coli, a canonical system for the study of how organisms
sense, respond, and adapt to environmental stimuli. In bacterial chemotaxis,
adaptation is mediated by two enzymes that localize to the clustered receptors
and modulate their activity through methylation-demethylation. Using a novel
stochastic simulation, we show that distributive receptor methylation is
necessary for successful adaptation to stimulus and also leads to large
fluctuations in receptor activity in the steady state. These fluctuations arise
from noise in the number of localized enzymes combined with saturated
modification kinetics between localized enzymes and receptor substrate. An
analytical model explains how saturated enzyme kinetics and large fluctuations
can coexist with an adapted state robust to variation in the expression level
of the pathway constituents, a key requirement to ensure the functionality of
individual cells within a population. This contrasts with the well-mixed
covalent modification system studied by Goldbeter and Koshland in which mean
activity becomes ultrasensitive to protein abundances when the enzymes operate
at saturation. Large fluctuations in receptor activity have been quantified
experimentally. Here we clarify their mechanistic relationship with
well-studied aspects of the chemotaxis system, precise adaptation and
functional robustness.


title: Online partial evaluation of sheet-defined functions

abstract:
  We present a spreadsheet implementation, extended with sheet-defined
functions, that allows users to define functions using only standard
spreadsheet concepts such as cells, formulas and references, requiring no new
syntax. This implements an idea proposed by Peyton-Jones and others.
  As the main contribution of this paper, we then show how to add an online
partial evaluator for such sheet-defined functions. The result is a
higher-order functional language that is dynamically typed, in keeping with
spreadsheet traditions, and an interactive platform for function definition and
function specialization.
  We describe an implementation of these ideas, present some performance data
from microbenchmarks, and outline desirable improvements and extensions.


title: Modular Construction of Shape-Numeric Analyzers

abstract:
  The aim of static analysis is to infer invariants about programs that are
precise enough to establish semantic properties, such as the absence of
run-time errors. Broadly speaking, there are two major branches of static
analysis for imperative programs. Pointer and shape analyses focus on inferring
properties of pointers, dynamically-allocated memory, and recursive data
structures, while numeric analyses seek to derive invariants on numeric values.
Although simultaneous inference of shape-numeric invariants is often needed,
this case is especially challenging and is not particularly well explored.
Notably, simultaneous shape-numeric inference raises complex issues in the
design of the static analyzer itself.
  In this paper, we study the construction of such shape-numeric, static
analyzers. We set up an abstract interpretation framework that allows us to
reason about simultaneous shape-numeric properties by combining shape and
numeric abstractions into a modular, expressive abstract domain. Such a modular
structure is highly desirable to make its formalization and implementation
easier to do and get correct. To achieve this, we choose a concrete semantics
that can be abstracted step-by-step, while preserving a high level of
expressiveness. The structure of abstract operations (i.e., transfer, join, and
comparison) follows the structure of this semantics. The advantage of this
construction is to divide the analyzer in modules and functors that implement
abstractions of distinct features.


title:
Verification of Imperative Programs by Constraint Logic Program
  Transformation

abstract:
  We present a method for verifying partial correctness properties of
imperative programs that manipulate integers and arrays by using techniques
based on the transformation of constraint logic programs (CLP). We use CLP as a
metalanguage for representing imperative programs, their executions, and their
properties. First, we encode the correctness of an imperative program, say
prog, as the negation of a predicate 'incorrect' defined by a CLP program T. By
construction, 'incorrect' holds in the least model of T if and only if the
execution of prog from an initial configuration eventually halts in an error
configuration. Then, we apply to program T a sequence of transformations that
preserve its least model semantics. These transformations are based on
well-known transformation rules, such as unfolding and folding, guided by
suitable transformation strategies, such as specialization and generalization.
The objective of the transformations is to derive a new CLP program TransfT
where the predicate 'incorrect' is defined either by (i) the fact 'incorrect.'
(and in this case prog is not correct), or by (ii) the empty set of clauses
(and in this case prog is correct). In the case where we derive a CLP program
such that neither (i) nor (ii) holds, we iterate the transformation. Since the
problem is undecidable, this process may not terminate. We show through
examples that our method can be applied in a rather systematic way, and is
amenable to automation by transferring to the field of program verification
many techniques developed in the field of program transformation.


title: Abstraction and Learning for Infinite-State Compositional Verification

abstract:
  Despite many advances that enable the application of model checking
techniques to the verification of large systems, the state-explosion problem
remains the main challenge for scalability. Compositional verification
addresses this challenge by decomposing the verification of a large system into
the verification of its components. Recent techniques use learning-based
approaches to automate compositional verification based on the assume-guarantee
style reasoning. However, these techniques are only applicable to finite-state
systems. In this work, we propose a new framework that interleaves abstraction
and learning to perform automated compositional verification of infinite-state
systems. We also discuss the role of learning and abstraction in the related
context of interface generation for infinite-state components.


title: Denotational Semantics of A User-Oriented, Domain-Specific Language

abstract:
  This paper presents the formal definition of a domain-specific language,
named Pantagruel, following the methodology proposed by David Schmidt for
language development. This language is dedicated to programming applications
that orchestrate networked entities. It targets developers that are
professionals in such domains as building management and assisted living, and
want to leverage networked entities to support daily tasks.
  Pantagruel has a number of features that address the requirements of the
domain of entity orchestration. Furthermore, Pantagruel provides high-level
constructs that make it accessible to developers that do not necessarily have
programming skills. It has been used to develop a number of applications by
non-programmers.
  We show how the user-oriented programming concepts of Pantagruel are
expressed in the denotational semantics of Pantagruel. This formal definition
has been used to derive an interpreter for Pantagruel and to provide a basis to
reason about Pantagruel programs.


title: Simulation of Two-Way Pushdown Automata Revisited

abstract:
  The linear-time simulation of 2-way deterministic pushdown automata (2DPDA)
by the Cook and Jones constructions is revisited. Following the semantics-based
approach by Jones, an interpreter is given which, when extended with
random-access memory, performs a linear-time simulation of 2DPDA. The recursive
interpreter works without the dump list of the original constructions, which
makes Cook's insight into linear-time simulation of exponential-time automata
more intuitive and the complexity argument clearer. The simulation is then
extended to 2-way nondeterministic pushdown automata (2NPDA) to provide for a
cubic-time recognition of context-free languages. The time required to run the
final construction depends on the degree of nondeterminism. The key mechanism
that enables the polynomial-time simulations is the sharing of computations by
memoization.


title:
Higher-Order Process Modeling: Product-Lining, Variability Modeling and
  Beyond

abstract:
  We present a graphical and dynamic framework for binding and execution of
business) process models. It is tailored to integrate 1) ad hoc processes
modeled graphically, 2) third party services discovered in the (Inter)net, and
3) (dynamically) synthesized process chains that solve situation-specific
tasks, with the synthesis taking place not only at design time, but also at
runtime. Key to our approach is the introduction of type-safe stacked
second-order execution contexts that allow for higher-order process modeling.
Tamed by our underlying strict service-oriented notion of abstraction, this
approach is tailored also to be used by application experts with little
technical knowledge: users can select, modify, construct and then pass
(component) processes during process execution as if they were data. We
illustrate the impact and essence of our framework along a concrete, realistic
(business) process modeling scenario: the development of Springer's
browser-based Online Conference Service (OCS). The most advanced feature of our
new framework allows one to combine online synthesis with the integration of
the synthesized process into the running application. This ability leads to a
particularly flexible way of implementing self-adaption, and to a particularly
concise and powerful way of achieving variability not only at design time, but
also at runtime.


title: A Simple Semantics and Static Analysis for Stack Inspection

abstract:
  The Java virtual machine and the .NET common language runtime feature an
access control mechanism specified operationally in terms of run-time stack
inspection. We give a denotational semantics in "eager" form, and show that it
is equivalent to the "lazy" semantics using stack inspection. We give a static
analysis of safety, i.e., the absence of security errors, that is simpler than
previous proposals. We identify several program transformations that can be
used to remove run-time checks. We give complete, detailed proofs for safety of
the analysis and for the transformations, exploiting compositionality of the
eager semantics.


title: The Immune System: the ultimate fractionated cyber-physical system

abstract:
  In this little vision paper we analyze the human immune system from a
computer science point of view with the aim of understanding the architecture
and features that allow robust, effective behavior to emerge from local sensing
and actions. We then recall the notion of fractionated cyber-physical systems,
and compare and contrast this to the immune system. We conclude with some
challenges.


title: A Survey on Product Operators in Abstract Interpretation

abstract:
  The aim of this paper is to provide a general overview of the product
operators introduced in the literature as a tool to enhance the analysis
accuracy in the Abstract Interpretation framework. In particular we focus on
the Cartesian and reduced products, as well as on the reduced cardinal power,
an under-used technique whose features deserve to be stressed for their
potential impact in practical applications.


title: A short note on Simulation and Abstraction

abstract:
  This short note is written in celebration of David Schmidt's sixtieth
birthday. He has now been active in the program analysis research community for
over thirty years and we have enjoyed many interactions with him. His work on
characterising simulations between Kripke structures using Galois connections
was particularly influential in our own work on using probabilistic abstract
interpretation to study Larsen and Skou's notion of probabilistic bisimulation.
We briefly review this work and discuss some recent applications of these ideas
in a variety of different application areas.


title: Automatic Repair of Overflowing Expressions with Abstract Interpretation

abstract:
  We consider the problem of synthesizing provably non-overflowing integer
arithmetic expressions or Boolean relations among integer arithmetic
expressions. First we use a numerical abstract domain to infer numerical
properties among program variables. Then we check if those properties guarantee
that a given expression does not overflow. If this is not the case, we
synthesize an equivalent, yet not-overflowing expression, or we report that
such an expression does not exists.
  The synthesis of a non-overflowing expression depends on three, orthogonal
factors: the input expression (e.g., is it linear, polynomial,... ?), the
output expression (e.g., are case splits allowed?), and the underlying
numerical abstract domain - the more precise the abstract domain is, the more
correct expressions can be synthesized.
  We consider three common cases: (i) linear expressions with integer
coefficients and intervals; (ii) Boolean expressions of linear expressions; and
(iii) linear expressions with templates. In the first case we prove there
exists a complete and polynomial algorithm to solve the problem. In the second
case, we have an incomplete yet polynomial algorithm, whereas in the third we
have a complete yet worst-case exponential algorithm.


title:
Pretty-big-step-semantics-based Certified Abstract Interpretation
  (Preliminary version)

abstract:
  We present a technique for deriving semantic program analyses from a natural
semantics specification of the programming language. The technique is based on
a particular kind of semantics called pretty-big-step semantics. We present a
pretty-big-step semantics of a language with simple objects called O'While and
specify a series of instrumentations of the semantics that explicitates the
flows of values in a program. This leads to a semantics-based dependency
analysis, at the core, e.g., of tainting analysis in software security. The
formalization has been realized with the Coq proof assistant.


title: Iterable Forward Reachability Analysis of Monitor-DPNs

abstract:
  There is a close connection between data-flow analysis and model checking as
observed and studied in the nineties by Steffen and Schmidt. This indicates
that automata-based analysis techniques developed in the realm of
infinite-state model checking can be applied as data-flow analyzers that
interpret complex control structures, which motivates the development of such
analysis techniques for ever more complex models. One approach proposed by
Esparza and Knoop is based on computation of predecessor or successor sets for
sets of automata configurations. Our goal is to adapt and exploit this approach
for analysis of multi-threaded Java programs. Specifically, we consider the
model of Monitor-DPNs for concurrent programs. Monitor-DPNs precisely model
unbounded recursion, dynamic thread creation, and synchronization via
well-nested locks with finite abstractions of procedure- and thread-local
state. Previous work on this model showed how to compute regular predecessor
sets of regular configurations and tree-regular successor sets of a fixed
initial configuration. By combining and extending different previously
developed techniques we show how to compute tree-regular successor sets of
tree-regular sets. Thereby we obtain an iterable, lock-sensitive forward
reachability analysis. We implemented the analysis for Java programs and
applied it to information flow control and data race detection.


title: Model Checking in Bits and Pieces

abstract:
  Fully automated verification of concurrent programs is a difficult problem,
primarily because of state explosion: the exponential growth of a program state
space with the number of its concurrently active components. It is natural to
apply a divide and conquer strategy to ameliorate state explosion, by analyzing
only a single component at a time. We show that this strategy leads to the
notion of a "split" invariant, an assertion which is globally inductive, while
being structured as the conjunction of a number of local, per-component
invariants. This formulation is closely connected to the classical Owicki-Gries
method and to Rely-Guarantee reasoning. We show how the division of an
invariant into a number of pieces with limited scope makes it possible to apply
new, localized forms of symmetry and abstraction to drastically simplify its
computation. Split invariance also has interesting connections to parametric
verification. A quantified invariant for a parametric system is a split
invariant for every instance. We show how it is possible, in some cases, to
invert this connection, and to automatically generalize from a split invariant
for a small instance of a system to a quantified invariant which holds for the
entire family of instances.


title:
A Case for Dynamic Reverse-code Generation to Debug Non-deterministic
  Programs

abstract:
  Backtracking (i.e., reverse execution) helps the user of a debugger to
naturally think backwards along the execution path of a program, and thinking
backwards makes it easy to locate the origin of a bug. So far backtracking has
been implemented mostly by state saving or by checkpointing. These
implementations, however, inherently do not scale. Meanwhile, a more recent
backtracking method based on reverse-code generation seems promising because
executing reverse code can restore the previous states of a program without
state saving. In the literature, there can be found two methods that generate
reverse code: (a) static reverse-code generation that pre-generates reverse
code through static analysis before starting a debugging session, and (b)
dynamic reverse-code generation that generates reverse code by applying dynamic
analysis on the fly during a debugging session. In particular, we espoused the
latter one in our previous work to accommodate non-determinism of a program
caused by e.g., multi-threading. To demonstrate the usefulness of our dynamic
reverse-code generation, this article presents a case study of various
backtracking methods including ours. We compare the memory usage of various
backtracking methods in a simple but nontrivial example, a bounded-buffer
program. In the case of non-deterministic programs such as this bounded-buffer
program, our dynamic reverse-code generation outperforms the existing
backtracking methods in terms of memory efficiency.


title:
Probing the high-density behavior of symmetry energy with gravitational
  waves

abstract:
  Gravitational wave (GW) astronomy opens up an entirely new window on the
Universe to probe the equations of state (EOS) of neutron-rich matter. With the
advent of next generation GW detectors, measuring the gravitational radiation
from coalescing binary neutron star systems, mountains on rotating neutron
stars, and stellar oscillation modes may become possible in the near future.
Using a set of model EOSs satisfying the latest constraints from terrestrial
nuclear experiments, state of the art nuclear many-body calculations of the
pure neutron matter EOS, and astrophysical observations consistently, we study
various GW signatures of the high-density behavior of the nuclear symmetry
energy, which is considered among the most uncertain properties of dense
neutron-rich nucleonic matter. In particular, we find the tidal polarizability
of neutron stars, potentially measurable in binary systems just prior to
merger, is more sensitive to the high density component of the nuclear symmetry
energy than the symmetry energy at nuclear saturation density. We also find
that the upper limit on the GW strain amplitude from elliptically deformed
stars is very sensitive to the density dependence of the symmetry energy. This
suggests that future developments in modeling of the neutron star crust, and
direct gravitational wave signals from accreting binaries will provide a wealth
of information on the EOS of neutron-rich matter. We also review the
sensitivity of the $r$-mode instability window to the density dependence of the
symmetry energy. Whereas models with larger values of the density slope of the
symmetry energy at saturation seem to be disfavored by the current
observational data, within a simple $r$-mode model, we point out that a
subsequent softer behavior of the symmetry energy at high densities (hinted at
by recent observational interpretations) could rule them in.


title: Diophantine properties of continued fractions on the Heisenberg group

abstract:
  We provide several results on the diophantine properties of continued
fractions on the Heisenberg group, many of which are analogous to classical
results for real continued fractions. In particular, we show an analog of
Khinchin's theorem and that convergents are also best approximants up to a
constant factor of the denominator.


title: The face vector of a half-open hypersimplex

abstract:
  The half-open hypersimplex $\Delta'_{n,k}$ consists of those $x = (x_{1},
\ldots, x_{n}) \in[0,1]^n$ with $k-1<x_1+\cdots+x_n\le k$, where $0 < k \leq
n$. The $f$-vector of a half-open hypersimplex and related generating functions
are explicitly studied.


title: Statistical Mechanics of Labor Markets

abstract:
  We introduce a probabilistic model of labor markets for university graduates,
in particular, in Japan. To make a model of the market efficiently, we take
into account several hypotheses. Namely, each company fixes the (business year
independent) number of opening positions for newcomers. The ability of
gathering newcomers depends on the result of job matching process in past
business years. This fact means that the ability of the company is weaken if
the company did not make their quota or the company gathered applicants too
much over the quota. All university graduates who are looking for their jobs
can access the public information about the ranking of companies. Assuming the
above essential key points, we construct the local energy function of each
company and describe the probability that an arbitrary company gets students at
each business year by a Boltzmann-Gibbs distribution. We evaluate the relevant
physical quantities such as the employment rate. We find that the system
undergoes a sort of `phase transition' from the `good employment phase' to
`poor employment phase' when one controls the degree of importance for the
ranking.


title: Level sets of the lapse function in static GR

abstract:
  We present a novel physical interpretation of the level sets of the
(canonical) lapse function in static isolated general relativistic space-times.
Our interpretation uses a notion of 'constrained test particles'. It leads to a
definition of gravitational force on test particles and to a previously unknown
uniqueness result for the lapse function.
  In Section 5, we discuss 'photon spheres' in static isolated relativistic
space-times and relate them to the level sets of the lapse function.


title: Dynamics of probabilistic labor markets: statistical physics perspective

abstract:
  We introduce a toy probabilistic model to analyze job-matching processes in
recent Japanese labor markets for university graduates by means of statistical
physics. We show that the aggregation probability of each company is rewritten
by means of non-linear map under several conditions. Mathematical treatment of
the map enables us to discuss the condition on which the rankings of arbitrary
two companies are reversed during the dynamics. The so-called `mismatch'
between students and companies is discussed from both empirical and theoretical
viewpoints.


title: General Formalism For the BRST Symmetry

abstract:
  In this paper we will discuss Faddeev-Popov method for field theories with a
gauge symmetry in an abstract way. We will then develope a general formalism
for dealing with the BRST symmetry. This formalism will make it possible to
analyse the BRST symmetry for any theory.


title: Classification of 4d N=2 gauge theories

abstract:
  We classify all possible four-dimensional N=2 supersymmetric UV-complete
gauge theories composed of semi-simple gauge groups and hypermultiplets. We
also give appropriate references for all theories with known Seiberg-Witten
solutions.


title: Curiosity about the dust matter in the cosmological context

abstract:
  We propose a model for the dust matter in the cosmological context. The model
contains a scalar field with a kinetic term nonminimally coupled to gravity. By
investigating the background and perturbative equations, it is demonstrated
that the scalar field has the same dynamics as the dust matter. We have also
considered the cosmological constant in the model. It turns out that the model
has not exotic behavior. Thus, a universe including the scalar field and the
cosmological constant evolves just as our Universe. Moreover, we have added the
quadratic term in the action. It is shown that the quadratic term can be ruled
out by its consequences.


title: Relaxation of dark matter halos: how to match observational data?

abstract:
  We show that moderate energy relaxation in the formation of dark matter halos
invariably leads to profiles that match those observed in the central regions
of galaxies. The density profile of the central region is universal and
insensitive to either the seed perturbation shape or the details of the
relaxation process. The profile has a central core; the multiplication of the
central density by the core radius is almost independent of the halo mass, in
accordance with observations. In the core area the density distribution behaves
as an Einasto profile with low index ($n\sim 0.5$); it has an extensive region
with $\rho\propto r^{-2}$ at larger distances. This is exactly the shape that
observations suggest for the central region of galaxies. On the other hand,
this shape does not fit the galaxy cluster profiles. A possible explanation of
this fact is that the relaxation is violent in the case of galaxy clusters;
however, it is not violent enough when galaxies or smaller dark matter
structures are considered. We discuss the reasons for this.


title: On invariant Schreier structures

abstract:
  Schreier graphs, which possess both a graph structure and a Schreier
structure (an edge-labeling by the generators of a group), are objects of
fundamental importance in group theory and geometry. We study the Schreier
structures with which unlabeled graphs may be endowed, with emphasis on
structures which are invariant in some sense (e.g. conjugation-invariant, or
sofic). We give proofs of a number of "folklore" results, such as that every
regular graph of even degree admits a Schreier structure, and show that, under
mild assumptions, the space of invariant Schreier structures over a given
invariant graph structure is very large, in that it contains uncountably many
ergodic measures. Our work is directly connected to the theory of invariant
random subgroups, a field which has recently attracted a great deal of
attention.


abstract:
  Assessing the consistency between short-term global temperature trends in
observations and climate model projections is a challenging problem. While
climate models capture many processes governing short-term climate
fluctuations, they are not expected to simulate the specific timing of these
somewhat random phenomena - the occurrence of which may impact the realized
trend. Therefore, to assess model performance, we develop distributions of
projected temperature trends from a collection of climate models running the
IPCC A1B emissions scenario. We evaluate where observed trends of length 5 to
15 years fall within the distribution of model trends of the same length. We
find that current trends lie near the lower limits of the model distributions,
with cumulative probability-of-occurrence values typically between 5 percent
and 20 percent, and probabilities below 5 percent not uncommon. Our results
indicate cause for concern regarding the consistency between climate model
projections and observed climate behavior under conditions of increasing
anthropogenic greenhouse-gas emissions.


title:
Ab-Initio Calculation of Molecular Aggregation Effects: a Coumarin-343
  Case Study

abstract:
  We present time-dependent density functional theory (TDDFT) calculations for
single and dimerized Coumarin-343 molecules in order to investigate the quantum
mechanical effects of chromophore aggregation in extended systems designed to
function as a new generation of sensors and light-harvesting devices. Using the
single-chromophore results, we describe the construction of effective
Hamiltonians to predict the excitonic properties of aggregate systems. We
compare the electronic coupling properties predicted by such effective
Hamiltonians to those obtained from TDDFT calculations of dimers, and to the
coupling predicted by the transition density cube (TDC) method. We determine
the accuracy of the dipole-dipole approximation and TDC with respect to the
separation distance and orientation of the dimers. In particular, we
investigate the effects of including Coulomb coupling terms ignored in the
typical tight-binding effective Hamiltonian. We also examine effects of orbital
relaxation which cannot be captured by either of these models.


title:
Refining the M_BH-V_c scaling relation with HI rotation curves of water
  megamaser galaxies

abstract:
  Black hole - galaxy scaling relations provide information about the
coevolution of supermassive black holes and their host galaxies. We compare the
black hole mass - circular velocity (MBH - Vc) relation with the black hole
mass - bulge stellar velocity dispersion (MBH - sigma) relation, to see whether
the scaling relations can passively emerge from a large number of mergers, or
require a physical mechanism, such as feedback from an active nucleus. We
present VLA H I observations of five galaxies, including three water megamaser
galaxies, to measure the circular velocity. Using twenty-two galaxies with
dynamical MBH measurements and Vc measurements extending to large radius, our
best-fit MBH - Vc relation, log MBH = alpha + beta log(Vc /200 km s^-1), yields
alpha = 7.43+/-0.13, beta = 3.68+1.23/-1.20, and intrinsic scatter epsilon_int
= 0.51+0.11/-0.09. The intrinsic scatter may well be higher than 0.51, as we
take great care to ascribe conservatively large observational errors. We find
comparable scatter in the MBH - sigma relations, epsilon_int = 0.48+0.10/-0.08,
while pure merging scenarios would likely result in a tighter scaling with the
dark halo (as traced by Vc) than baryonic (sigma) properties. Instead, feedback
from the active nucleus may act on bulge scales to tighten the MBH - sigma
relation with respect to the MBH - Vc relation, as observed.


title:
Monte Carlo Study of an Effective Ising Model for the Spin-ice type
  Kondo Lattice Model

abstract:
  An effective Ising model for the spin-ice type Kondo lattice model is
investigated by the classical Monte Carlo simulation. We clarify the magnetic
phase diagram with four phases: ice-ferro, ice-(0,0,2\pi), 32-sublattice, and
all-in/all-out ordered states. The result well reproduces the phase diagram of
the Kondo lattice model studied previously [H. Ishizuka et al.: J. Phys. Soc.
Jpn. 81 (2012) 113706], which suggests that the RKKY interactions up to third
neighbors are sufficient to describe the magnetic properties of the itinerant
electron model. We discuss the peculiar nature of phase transitions: the
suppression of the critical temperatures down to zero temperature between two
ice phases and the presence of the tricritical points on the phase boundary of
the 32-sublattice ordered state.


title:
Internal modes of a skyrmion in the ferromagnetic background in chiral
  magnets

abstract:
  A spin texture called skyrmion has been recently observed in certain chiral
magnets without inversion symmetry. The observed skyrmions are extended objects
with typical linear sizes of 10 nm to 100 nm that contain $10^3$ to $10^5$
spins and can be deformed in response to external perturbations. Weak
deformations are characterized by the internal modes which are localized around
the skyrmion center. Knowledge of internal modes is crucial to assess the
stability and rigidity of these topological textures. Here we compute the
internal modes of a skyrmion in the ferromagnetic background state by numerical
diagonalization of the dynamical matrix. We find several internal modes below
the magnon continuum, such as the mode corresponding to the translational
motion, and different kinds of breathing modes. The number of internal modes is
larger for lower magnetic fields. Indeed, several modes become gapless in the
low field region indicating that the single skyrmion solution becomes unstable,
although a skyrmion lattice is thermodynamically stable. On the other hand, at
high fields only three internal modes exist and the skyrmion is stable even at
higher fields when the ferromagnetic state is thermodynamically stable. We also
show that the presence of out-of-plane easy-axis anisotropy stabilizes the
single skyrmion solution. Finally, we discuss the effects of damping and
possible experimental observations of these internal modes.


title:
Silicon-Vacancy Color Centers in Nanodiamonds: Cathodoluminescence
  Imaging Marker in the Near Infrared

abstract:
  We demonstrate that nanodiamonds fabricated to incorporate silicon-vacancy
(Si-V) color centers provide bright, spectrally narrow, and stable
cathodoluminescence (CL) in the near-infrared. Si-V color centers containing
nanodiamonds are promising as non-bleaching optical markers for correlated CL
and secondary electron microscopy, including applications to nanoscale
bioimaging.