Random Graph Models with Hidden Color

We demonstrate how to generalize two of the most well-known random graph models, the classic random graph, and random graphs with a given degree distribution, by the introduction of hidden variables in the form of extra degrees of freedom, color, applied to vertices or stubs (half-edges). The color is assumed unobservable, but is allowed to affect edge probabilities. This serves as a convenient method to define very general classes of models within a common unifying formalism, and allowing for a non-trivial edge correlation structure.Comment: 17 pages, 2 figures; contrib. to the Workshop on Random Geometry in Krakow, May 200

Deterministic Annealing and Nonlinear Assignment

For combinatorial optimization problems that can be formulated as Ising or Potts spin systems, the Mean Field (MF) approximation yields a versatile and simple ANN heuristic, Deterministic Annealing. For assignment problems the situation is more complex -- the natural analog of the MF approximation lacks the simplicity present in the Potts and Ising cases. In this article the difficulties associated with this issue are investigated, and the options for solving them discussed. Improvements to existing Potts-based MF-inspired heuristics are suggested, and the possibilities for defining a proper variational approach are scrutinized.Comment: 15 pages, 3 figure

The Diagonalisation of the Lund Fragmentation Model I

We will in this note show that it is possible to diagonalise the Lund Fragmentation Model. We show that the basic original result, the Lund Area law, can be factorised into a product of transition operators, each describing the production of a single particle and the two adjacent breakup points (vertex positions) of the string field. The transition operator has a discrete spectrum of (orthonormal) eigenfunctions, describing the vertex positions (which in a dual way corresponds to the momentum transfers between the produced particles) and discrete eigenvalues, which only depend upon the particle produced. The eigenfunctions turn out to be the well-known two- dimensional harmonic oscillator functions and the eigenvalues are the analytic continuations of these functions to time-like values (corresponding to the particle mass). In this way all observables in the model can be expressed in terms of analytical formulas. In this note only the 1+1-dimensional version of the model is treated but we end with remarks on the extensions to gluonic radiation, transverse momentum generation etc, to be performed in future papers.Comment: 15 pages, 7 figure

The Lund Fragmentation Process for a Multi-gluon String According to the Area Law

The Lund Area Law describes the probability for the production of a set of colourless hadrons from an initial set of partons, in the Lund string fragmentation model. In this paper we will present a general method to implement the Area Law for a multi-gluon string state. The partonic states are in general given by a perturbative QCD cascade and are consequently defined only down to a cutoff in the energy momentum fluctuations. We will show that our method defines the states down to the hadronic mass scale inside an analytically calculable scenario. We will then show that there is a differential version of our process which is closely related to the generalised rapidity range \lambda, which has been used as a measure on the partonic states. We identify \lambda as the area spanned between the directrix curve (the curve given by the parton energy momentum vectors laid out in colour order, which determines the string surface) and the average curve (to be called the P-curve) of the stochastic X-curves (curves obtained when the hadronic energy-momentum vectors are laid out in rank order). Finally we show that from the X-curve corresponding to a particular stochastic fragmentation situation it is possible to reproduce the directrix curve (up to one starting vector and a set of sign choices, one for each hadron).Comment: 1 title page + 36 pages, 20 figure

Adjustment in Property Space Markets: Estimates from the Stockholm Office Market

Markets for property space adjust only gradually because tenants are constrained by long-term leases and landlords and tenants face transactions and information costs. Not only do rents adjust slowly, but space occupancy may differ from demand at current rent, giving rise to %u201Chidden vacancies%u201D. We estimate the joint dynamics of office rents and vacancies using an error-correction model using a new lease rent series for Stockholm offices 1977­2002 estimated on 2,500 leases. It takes 5-10 years for the market to adjust to a shock. In a model simulation of a positive employment shock open vacancies fall from the natural level of 7 percent to below 4 percent, while hidden vacancies increase by about as much. Most of the variation in hidden vacancies over time is explained by the difference between demand at current and average rent on existing leases, which we calculate using data on contract lease length.

Optical advantages and function of multifocal spherical fish lenses

The spherical crystalline lenses in the eyes of many fish species are well-suited models for studies on how natural selection has influenced the evolution of the optical system. Many of these lenses exhibit multiple focal lengths when illuminated with monochromatic light. Similar multifocality is present in a majority of vertebrate eyes, and it is assumed to compensate for the defocusing effect of longitudinal chromatic aberration. In order to identify potential optical advantages of multifocal lenses, we studied their information transfer capacity by computer modeling. We investigated four lens types: the lens of Astatotilapia burtoni, an African cichlid fish species, an equivalent monofocal lens, and two artificial multifocal lenses. These lenses were combined with three detector arrays of different spectral properties: the cone photoreceptor system of A. burtoni and two artificial arrays. The optical properties compared between the lenses were longitudinal spherical aberration curves, point spread functions, modulation transfer functions, and imaging characteristics. The multifocal lenses had a better balance between spatial and spectral information than the monofocal lenses. Additionally, the lens and detector array had to be matched to each other for optimal function. (C) 2012 Optical Society of Americ

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

The role of the mammalian DNA end-processing enzyme polynucleotide kinase 3'-phosphatase in spinocerebellar ataxia Type 3 pathogenesis

DNA strand-breaks (SBs) with non-ligatable ends are generated by ionizing radiation, oxidative stress, various chemotherapeutic agents, and also as base excision repair (BER) intermediates. Several neurological diseases have already been identified as being due to a deficiency in DNA end-processing activities. Two common dirty ends, 3'-P and 5'-OH, are processed by mammalian polynucleotide kinase 3'-phosphatase (PNKP), a bifunctional enzyme with 3'-phosphatase and 5'-kinase activities. We have made the unexpected observation that PNKP stably associates with Ataxin-3 (ATXN3), a polyglutamine repeat-containing protein mutated in spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph Disease (MJD). This disease is one of the most common dominantly inherited ataxias worldwide; the defect in SCA3 is due to CAG repeat expansion (from the normal 14-41 to 55-82 repeats) in the ATXN3 coding region. However, how the expanded form gains its toxic function is still not clearly understood. Here we report that purified wild-type (WT) ATXN3 stimulates, and by contrast the mutant form specifically inhibits, PNKP's 3' phosphatase activity in vitro. ATXN3-deficient cells also show decreased PNKP activity. Furthermore, transgenic mice conditionally expressing the pathological form of human ATXN3 also showed decreased 3'-phosphatase activity of PNKP, mostly in the deep cerebellar nuclei, one of the most affected regions in MJD patients' brain. Finally, long amplicon quantitative PCR analysis of human MJD patients' brain samples showed a significant accumulation of DNA strand breaks. Our results thus indicate that the accumulation of DNA strand breaks due to functional deficiency of PNKP is etiologically linked to the pathogenesis of SCA3/MJD.This research was supported by USPHS grant NS073976 (TKH) and P30 ES 06676 that support the NIEHS Center Cell Biology Core and Molecular Genomics Core of UTMB’s NIEHS Center for DNA sequencing. TKP is supported by CA129537 and CA154320. This work was also supported by Fundação para a Ciência e Tecnologia through the project [PTDC/SAU-GMG/101572/2008] and through fellowships [SFRH/BPD/91562/2012 to ASF, SFRH/BD/51059/2010 to ANC]. IB is supported by NIEHS R01 ES018948 and NIAID/AI06288