338 research outputs found
Piecewise adiabatic population transfer in a molecule via a wave packet
We propose a class of schemes for robust population transfer between quantum
states that utilize trains of coherent pulses and represent a generalized
adiabatic passage via a wave packet. We study piecewise Stimulated Raman
Adiabatic Passage with pulse-to-pulse amplitude variation, and piecewise
chirped Raman passage with pulse-to-pulse phase variation, implemented with an
optical frequency comb. In the context of production of ultracold ground-state
molecules, we show that with almost no knowledge of the excited potential,
robust high-efficiency transfer is possibleComment: 4 pages, 5 figures. Submitted to Phys. Rev. Let
Spectral components in the bright, long GRB 061007: properties of the photosphere and the nature of the outflow
We present a time-resolved spectral analysis of the bright, long GRB 061007
(z=1.261) using Swift BAT and Suzaku WAM data. We find that the prompt emission
of GRB 061007 can be equally well explained by a photospheric component
together with a power law as by a Band function, and we explore the
implications of the former model. The photospheric component, which we model
with a multicolour blackbody, dominates the emission and has a very stable
shape throughout the burst. This component provides a natural explanation for
the hardness-intensity correlation seen within the burst and also allows us to
estimate the bulk Lorentz factor and the radius of the photosphere. The
power-law component dominates the fit at high energies and has a nearly
constant slope of -1.5. We discuss the possibility that this component is of
the same origin as the high-energy power laws recently observed in some Fermi
LAT bursts.Comment: Accepted for publication in MNRA
Bounded Representations of Interval and Proper Interval Graphs
Klavik et al. [arXiv:1207.6960] recently introduced a generalization of
recognition called the bounded representation problem which we study for the
classes of interval and proper interval graphs. The input gives a graph G and
in addition for each vertex v two intervals L_v and R_v called bounds. We ask
whether there exists a bounded representation in which each interval I_v has
its left endpoint in L_v and its right endpoint in R_v. We show that the
problem can be solved in linear time for interval graphs and in quadratic time
for proper interval graphs.
Robert's Theorem states that the classes of proper interval graphs and unit
interval graphs are equal. Surprisingly the bounded representation problem is
polynomially solvable for proper interval graphs and NP-complete for unit
interval graphs [Klav\'{\i}k et al., arxiv:1207.6960]. So unless P = NP, the
proper and unit interval representations behave very differently.
The bounded representation problem belongs to a wider class of restricted
representation problems. These problems are generalizations of the
well-understood recognition problem, and they ask whether there exists a
representation of G satisfying some additional constraints. The bounded
representation problems generalize many of these problems
Ultracold dense gas of deeply bound heteronuclear molecules
Recently, the quest for an ultracold and dense ensemble of polar molecules
has attracted strong interest. Polar molecules have bright prospects for novel
quantum gases with long-range and anisotropic interactions, for quantum
information science, and for precision measurements. However, high-density
clouds of ultracold polar molecules have so far not been produced. Here, we
report a key step towards this goal. Starting from an ultracold dense gas of
heteronuclear 40K-87Rb Feshbach molecules with typical binding energies of a
few hundred kHz and a negligible dipole moment, we coherently transfer these
molecules into a vibrational level of the ground-state molecular potential
bound by >10 GHz. We thereby increase the binding energy and the expected
dipole moment of the 40K-87Rb molecules by more than four orders of magnitude
in a single transfer step. Starting with a single initial state prepared with
Feshbach association, we achieve a transfer efficiency of 84%. While dipolar
effects are not yet observable, the presented technique can be extended to
access much more deeply bound vibrational levels and ultimately those
exhibiting a significant dipole moment. The preparation of an ultracold quantum
gas of polar molecules might therefore come within experimental reach.Comment: 5 pages, 5 figure
A Mathematical Framework for Agent Based Models of Complex Biological Networks
Agent-based modeling and simulation is a useful method to study biological
phenomena in a wide range of fields, from molecular biology to ecology. Since
there is currently no agreed-upon standard way to specify such models it is not
always easy to use published models. Also, since model descriptions are not
usually given in mathematical terms, it is difficult to bring mathematical
analysis tools to bear, so that models are typically studied through
simulation. In order to address this issue, Grimm et al. proposed a protocol
for model specification, the so-called ODD protocol, which provides a standard
way to describe models. This paper proposes an addition to the ODD protocol
which allows the description of an agent-based model as a dynamical system,
which provides access to computational and theoretical tools for its analysis.
The mathematical framework is that of algebraic models, that is, time-discrete
dynamical systems with algebraic structure. It is shown by way of several
examples how this mathematical specification can help with model analysis.Comment: To appear in Bulletin of Mathematical Biolog
Modeling the high-energy emission in GRB 110721A and implications on the early multiwavelength and polarimetric observations
GRB 110721A was detected by the Gamma-ray Burst Monitor and the Large Area
Telescope (LAT) onboard the Fermi satellite and the Gamma-ray Burst Polarimeter
onboard the IKAROS solar mission. Previous analysis done of this burst showed:
i) a linear polarization signal with position angle stable () and high degree of , ii) an extreme peak
energy of a record-breaking at 152 MeV, and iii) a subdominant prompt
thermal component observed right after the onset of this burst. In this paper,
the LAT data around the reported position of GRB 110721A are analysed with the
most recent software and then, the LAT light curve above 100 MeV was obtained.
The LAT light curve is modelled in terms of adiabatic early-afterglow external
shocks when the outflow propagates into a stellar wind. Additionally, we
discuss the possible origins and also study the implications of the
early-afterglow external shocks on the extreme peak energy observed at 152
MeV, the polarization observations and the subdominant prompt thermal
component.Comment: 9 pages and one figure. Accepted for publication in Ap
Impacts of selected Ecological Focus Area options in European farmed landscapes on climate regulation and pollination services: a systematic map protocol
Background: This systematic map protocol responds to an urgent policy need to evaluate key environmental benefits of new compulsory greening measures in the European Union’s Common Agricultural Policy (CAP), with the aim of building a policy better linked to environmental performance. The systematic map will focus on Ecological Focus Areas (EFAs), in which larger arable farmers must dedicate 5% of their arable land to ecologically beneficial habitats, landscape features and land uses. The European Commission’s Joint Research Centre has used a software tool called the ‘EFA calculator’ to inform the European Commission about environmental benefits of EFA implementation. However, there are gaps in the EFA calculator’s coverage of ecosystem services, especially ‘global climate regulation’, and an opportunity to use systematic mapping methods to enhance its capture of evidence, in advance of forthcoming CAP reforms. We describe a method for assembling a database of relevant, peer-reviewed research conducted in all agricultural landscapes in Europe and neighbouring countries with similar biogeography, addressing the primary question: what are the impacts of selected EFA features in agricultural land on two policy-relevant ecosystem service outcomes—global climate regulation and pollination? The method is streamlined to allow results in good time for the current, time-limited opportunity to influence reforms of the CAP greening measures at European and Member State level. Methods: We will search four bibliographic databases in English, using a predefined and tested search string that focuses on a subset of EFA options and ecosystem service outcomes. The options and outcomes are selected as those with particular policy relevance and traction. Only articles in English will be included. We will screen search results at title, abstract and full text levels, recording the number of studies deemed non-relevant (with reasons at full text). A systematic map database that displays the meta-data (i.e. descriptive summary information about settings and methods) of relevant studies will be produced following full text assessment. The systematic map database will be published as a MS-Excel database. The nature and extent of the evidence base will be discussed, and the applicability of methods to convert the available evidence into EFA calculator scores will be assessed
Quantum-inspired interferometry with chirped laser pulses
We introduce and implement an interferometric technique based on chirped
femtosecond laser pulses and nonlinear optics. The interference manifests as a
high-visibility (> 85%) phase-insensitive dip in the intensity of an optical
beam when the two interferometer arms are equal to within the coherence length
of the light. This signature is unique in classical interferometry, but is a
direct analogue to Hong-Ou-Mandel quantum interference. Our technique exhibits
all the metrological advantages of the quantum interferometer, but with signals
at least 10^7 times greater. In particular we demonstrate enhanced resolution,
robustness against loss, and automatic dispersion cancellation. Our
interferometer offers significant advantages over previous technologies, both
quantum and classical, in precision time delay measurements and biomedical
imaging.Comment: 6 pages, 4 figure
Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets
Current genome-wide association studies (GWAS) use commercial genotyping microarrays that can assay over a million single nucleotide polymorphisms (SNPs). The number of SNPs is further boosted by advanced statistical genotype-imputation algorithms and large SNP databases for reference human populations. The testing of a huge number of SNPs needs to be taken into account in the interpretation of statistical significance in such genome-wide studies, but this is complicated by the non-independence of SNPs because of linkage disequilibrium (LD). Several previous groups have proposed the use of the effective number of independent markers (Me) for the adjustment of multiple testing, but current methods of calculation for Me are limited in accuracy or computational speed. Here, we report a more robust and fast method to calculate Me. Applying this efficient method [implemented in a free software tool named Genetic type 1 error calculator (GEC)], we systematically examined the Me, and the corresponding p-value thresholds required to control the genome-wide type 1 error rate at 0.05, for 13 Illumina or Affymetrix genotyping arrays, as well as for HapMap Project and 1000 Genomes Project datasets which are widely used in genotype imputation as reference panels. Our results suggested the use of a p-value threshold of ~10−7 as the criterion for genome-wide significance for early commercial genotyping arrays, but slightly more stringent p-value thresholds ~5 × 10−8 for current or merged commercial genotyping arrays, ~10−8 for all common SNPs in the 1000 Genomes Project dataset and ~5 × 10−8 for the common SNPs only within genes
A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data
Motivation: Copy Number Variants (CNVs) are important genetic factors for studying human diseases. While high-throughput whole genome re-sequencing provides multiple lines of evidence for detecting CNVs, computational algorithms need to be tailored for different type or size of CNVs under different experimental designs. Results: To achieve optimal power and resolution of detecting CNVs at low depth of coverage, we implemented a Hidden Markov Model that integrates both depth of coverage and mate-pair relationship. The novelty of our algorithm is that we infer the likelihood of carrying a deletion jointly from multiple mate pairs in a region without the requirement of a single mate pairs being obvious outliers. By integrating all useful information in a comprehensive model, our method is able to detect medium-size deletions (200-2000bp) at low depth (<10× per sample). We applied the method to simulated data and demonstrate the power of detecting medium-size deletions is close to theoretical values. Availability: A program implemented in Java, Zinfandel, is available at http://www.cs.columbia.edu/~itsik/zinfandel
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