Physical Sciences and Mathematics Commons^™

Multi-Color Observations Of Short Grb Afterglows: 20 Events Observed Between 2007 And 2010, A. Nicuesa Guelbenzu, S. Klose, J. Greiner, D. A. Kann, T. Krühler, A. Rossi, S. Schulze, P. M. J. Afonso, J. Elliott, R Filgas, Dieter H. Hartmann, A Kupcu Yoldas, S Mcbreen, M Nardini, F Olivares E., A Rau, S Schmidl, P Schady, V Sudilovsky, A C. Updike, A Yoldas

Publications

We report on follow-up observations of 20 short-duration gamma-ray bursts (GRBs; T90 <2 >s) performed in g'r'i'z' JHKs with the Gamma-Ray Burst Optical Near-Infrared Detector (GROND) between mid-2007 and the end of 2010. This is one of the most compre-hensive data sets on GRB afterglow observations of short bursts published so far. In three cases, GROND was on target within less than 10 min after the trigger, leading to the discovery of the afterglow of GRB 081226A and its faint underlying host galaxy. In addition, GROND was able to image the optical afterglow and follow the light curve evolution in five …

Protein Nano-Object Integrator (Pronoi) For Generating Atomic Style Objects For Molecular Modeling, Nicholas Smith, Brandon Campbell, Lin Li, Chuan Li, Emil Alexov

Publications

Background

With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system.

Results

Here we report the Protein Nano-Object Integrator (ProNOI) which allows for …

Radiation From Accelerated Particles In Relativistic Jets With Shocks, Shear-Flow, And Reconnection, K.-I. Nishikawa, P. Hardee, Y. Mizuno, I. Dutan, B. Zhang, M. Medvedev, E. J. Chor, K. W. Min, J. Niemiec, Y Mizuno, A Nordlund, J T. Frederiksen, H Sol, M Pohl, Dieter H. Hartmann

Publications

We have investigated particle acceleration and shock structure associated with an unmagnetized rel-ativistic jet propagating into an unmagnetized plasma for electron-positron and electron-ion plasmas. Strong magnetic fields generated in the trailing jet shock lead to transverse deflection and acceleration of the electrons. We have self-consistently calculated the radiation from the electrons accelerated in the turbulent magnetic fields for different jet Lorentz factors. We find that the synthetic spectra depend on the bulk Lorentz factor of the jet, the jet temperature, and the strength of the magnetic fields generated in the shock. We have investigated the generation of magnetic fields associated …

An Infrastructure To Support Data Integration And Curation For Higher Educational Research, Linh B. Ngo, Amy W. Apon, Pengfei Xuan, Kimberley Ferguson, Christin Marshall, John Mccann, Yueli Zheng

Publications

The recent challenges for higher education call for research that can offer a comprehensive understanding about the performance and efficiency of higher education institutions in their three primary missions: research, education, and service. In other for this to happen, it is necessary for researchers to have access to a multitude of data sources.However, due to the nature of their academic training, many higher education practitioners do not have access to expertise in working with different data sources. In this work, we describe a design and implementation for an infrastructure that will bring together the tools and the data to provide …

A Deep Search For Host Galaxies Of Grbs With No Detected Optical Afterglow, A. Rossi, S. Klose, P. Ferrero, J. Greiner, L. A. Arnold, E. Gonslaves, Dieter H. Hartmann, A. C. Updike, D. A. Kann, T. Krühler

Publications

Context. Gamma-ray bursts (GRBs) can provide information about star formation at high redshifts. Even in the absence of a bright optical/near-infrared/radio afterglow, the high detection rate of X-ray afterglows by Swift/XRT and its localization precision of 2–3 arcsec facilitates the identification and the study of GRB host galaxies. Aims. We focus on the search for the host galaxies of 17 bursts with arcsec-sized XRT error circles but no detected long-wavelength afterglow, in spite of their deep and rapid follow-up observations. Three of these events can also be classified as truly dark bursts, i.e., the observed upper limit on the optical …

Highly Efficient And Exact Method For Parallelization Of Grid-Based Algorithms And Its Implementation In Delphi, Chuan Li, Lin Li, Jie Zhang, Emil Alexov

Publications

The Gauss–Seidel (GS) method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the GS method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here, we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of processes or computing units. In …

On The Cyclically Fully Commutative Elements Of Coxeter Groups, T. Boothby, J. Burket, M. Eichwald, D. C. Ernst, R. M. Green, Matthew Macauley

Publications

Let W be an arbitrary Coxeter group. If two elements have expressions that are cyclic shifts of each other (as words), then they are conjugate (as group elements) in W. We say that w is cyclically fully commutative (CFC) if every cyclic shift of any reduced expression for w is fully commutative (i.e., avoids long braid relations). These generalize Coxeter elements in that their reduced expressions can be described combinatorially by acyclic directed graphs, and cyclically shifting corresponds to source-to-sink conversions. In this paper, we explore the combinatorics of the CFC elements and enumerate them in all Coxeter groups. …

The Gas/Dust Ratio Of Circumstellar Disks: Testing Models Of Planetesimal Formation, David Horne, Erika Gibb, Terrence W. Rettig, Sean D. Brittain, David Tilley, Dinshaw Balsara

Publications

We present high-resolution, near-infrared NIRSPEC observations of CO absorption toward six class II T Tauri stars: AA Tau, DG Tau, IQ Tau, RY Tau, CW Tau, and Haro 6–5b. 12CO overtone absorption lines originating from the circumstellar disk of each object were used to calculate line-of-sight gas column densities toward each source. We measured the gas/dust ratio as a function of disk inclination, utilizing measured visual extinctions and inclinations for each star. The majority of our sources show further evidence for a correlation between the gas/dust columndensity ratio and disk inclination similar to that found by Rettig et al.

Elastic Properties Of The Zintl Ferromagnet Yb14mnsb11, Sriparna Bhattacharya, D C. Marinescu, James R. Morris, Ivan A. Sergienko, Brian Sales, David Madrus, Veerle Keppens

Publications

We report measurements of the elastic moduli as a function of temperature (5–300) K and magnetic field (0–2 T) for the Zintl ferromagnet Yb14MnSb11, which is believed to be a rare example of an underscreened Kondo lattice. The elastic moduli measured below the Curie temperature in this complex ferromagnet exhibit unusual lattice stiffening that is independent of the magnetic field and can be adequately modeled using the Landau theory.

Herschel/Pacs Observations Of Young Sources In Taurus: The Far-Infrared Counterpart Of Optical Jets, L Podio, I Kamp, D Flower, C Howard, G Sandell, A Mora, G Aresu, Sean D. Brittain, W.R.F. Dent, C Pinte, G J. White

Publications

Context. Observations of the atomic and molecular line emission associated with jets and outflows emitted by young stellar objects provide sensitive diagnostics of the excitation conditions, and can be used to trace the various evolutionary stages they pass through as they evolve to become main sequence stars. Aims. To understand the relevance of atomic and molecular cooling in shocks, and how accretion and ejection efficiency evolves with the evolutionary state of the sources, we will study the far-infrared counterparts of bright optical jets associated with Class I and II sources in Taurus (T Tau, DG Tau A, DG Tau B, …

Observations Of Herbig Ae/Be Stars With Herschel/Pacs. The Atomic And Molecular Contents Of Their Protoplanetary Discs, G Meeus, B Montesinos, I Mendigutia, I Kamp, W F. Thi, C Eiroa, C A. Grady, G Mathews, G Sandell, C. Martin-Zaidi, Sean D. Brittain, W.R.F. Dent, C Howard, F Menard, C Pinte, A Roberge, B Vandenbussche, J P. Williams

Publications

We observed a sample of 20 representative Herbig Ae/Be stars and 5 A-type debris discs with PACS onboard Herschel, as part of the GAS in Protoplanetary Systems (GASPS) project. The observations were done in spectroscopic mode, and cover the far-infrared lines of [O i], [C ii], CO, CH+, H2O, and OH. We have a [Oi] 63 μm detection rate of 100% for the Herbig Ae/Be and 0% for the debris discs. The [Oi] 145 μm line is only detected in 25% and CO J = 18–17 in 45% (and fewer cases for higher J transitions) of the Herbig Ae/Be stars, …

Topological Thermoelectric Effects In Spin-Orbit Coupled Electron- And Hole-Doped Semiconductors, E Dumitrescu, Chuanwei Zhang, D C. Marinescu, Sumanta Tewari

Publications

We compute the intrinsic contributions to the Berry-phase mediated anomalous Hall and Nernst effects in electron- and hole-doped semiconductors in the presence of an in-plane magnetic field as well as Rashba and Dresselhaus spin-orbit couplings. For both systems we find that the regime of chemical potential which supports the topological superconducting state in the presence of the superconducting proximity effect can be characterized by plateaus in the topological Hall and Nernst coefficients flanked by well-defined peaks marking the emergence of the topological regime. The plateaus arise from a clear momentum space separation between the region where the Berry curvature is …

Predicting Nonspecific Ion Binding Using Delphi, Marharyta Petukh, Maxim Zhenirovskyy, Chuan Li, Lin Li, Lin Wang, Emil Alexov

Publications

Ions are an important component of the cell and affect the corresponding biological macromolecules either via direct binding or as a screening ion cloud. Although some ion binding is highly specific and frequently associated with the function of the macromolecule, other ions bind to the protein surface nonspecifically, presumably because the electrostatic attraction is strong enough to immobilize them. Here, we test such a scenario and demonstrate that experimentally identified surface-bound ions are located at a potential that facilitates binding, which indicates that the major driving force is the electrostatics. Without taking into consideration geometrical factors and structural fluctuations, we …

Delphi: A Comprehensive Suite For Delphi Software And Associated Resources, Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov

Publications

Background

Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.

Results

Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding …

Energetic Feedback And 26al From Massive Stars And Their Supernovae In The Carina Region, R. Voss, P. Martin, R. Diehl, J. S. Vink, Dieter H. Hartmann, T. Preibisch

Publications

We study the populations of massive stars in the Carina region and their energetic feedback and ejection of 26Al. Methods. We did a census of the stellar populations in young stellar clusters within a few degrees of the Carina nebula. For each star we estimated the mass, based on the spectral type and the host cluster age. We used population synthesis to calculate the energetic feedback and ejection of 26Al from the winds of the massive stars and their supernova explosions. We used 7 years of INTEGRAL observations to measure the 26Al signal from the region. Results. The INTEGRAL 26Al …

Weak Localization In A Lateral Superlattice With Rashba And Dresselhaus Spin-Orbit Interaction, D C. Marinescu, Andrei Manolescu

Publications

We calculate the weak localization (WL) correction to the conductivity of a lateral superlattice (LSL) with Rashba (R)-Dresselhaus (D) spin-orbit interaction (SOI). The superlattice is modeled as a sequence of parallel wires that support tunneling between adjacent sites, leading to the formation of extended Bloch states along its axis and a miniband in the energy spectrum. Our results, obtained by calculating the eigenvalues of the Cooperon operator in the diffusion approximation, indicate that the electron dephasing rate that determines the antilocalization correction is enhanced by a term proportional with the LSL potential and the bandwidth. Within the same formalism, the …

Bl Lacertae Objects Beyond Redshift 1.3 - Uv-To-Nir Photometry And Photometric Redshift For Fermi/Lat Blazars, A. Rau, P. Schady, J. Greiner, M. Salvato, M. Ajello, E. Bottacini, N. Gehrels, P.M. J. Afonso, J. Elliott, R Filgas, D A. Kann, S Klose, T Krühler, M Nardini, A Nicuesa Guelbenzu, F Olivares E., A Rossi, V Sudilovsky, A C. Updike, Dieter H. Hartmann

Publications

Context.Observations of the γ -ray sky with Fermi led to significant advances towards understanding blazars, the most extreme classof Active Galactic Nuclei. A large fraction of the population detected by Fermi is formed by BL Lacertae (BL Lac) objects, whosesample has always suff ered from a severe redshift incompleteness due to the quasi-featureless optical spectra.Aims.Our goal is to provide a significant increase of the number of confirmed high-redshift BL Lac objects contained in the 2 LACFermi/LAT cataloge.Methods.For 103 Fermi/LAT blazars, photometric redshifts using spectral energy distribution fitting have been obtained. The pho-tometry includes 13 broad-band filters from the far ultraviolet …

Cxom31 J004253.1+411422: The First Ultraluminous X-Ray Transient In M 31, A. Kaur, M. Henze, F. Haberl, W. Pietsch, J. Greiner, A. Rau, Dieter H. Hartmann, G. Sala, M. Hernanz

Publications

Context. We seek clarification of the nature of X-ray sources detected in M 31. Here we focus on CXOM31 J004253.1+411422, the brightness of which suggests that it belongs to the class of ultraluminous X-ray sources. Aims. We determine the X-ray properties of sources detected in the XMM-Newton/Chandra monitoring program. We investigate spectral properties and search for periodic or quasi-periodic oscillations. Methods. A multicomponent model was applied to the spectra obtained from XMM-Newton data to evaluate the relative contributions from thermal and nonthermal emission. The time dependence of this ratio was evaluated over a period of forty days. We simultaneously fit …

Analyzing Effects Of Naturally Occurring Missense Mutations, Zhe Zhang, Maria A. Miteva, Lin Wang, Emil Alexov

Publications

Single-point mutation in genome, for example, single-nucleotide polymorphism (SNP) or rare genetic mutation, is the change of a single nucleotide for another in the genome sequence. Some of them will produce an amino acid substitution in the corresponding protein sequence (missense mutations); others will not. This paper focuses on genetic mutations resulting in a change in the amino acid sequence of the corresponding protein and how to assess their effects on protein wild-type characteristics. The existing methods and approaches for predicting the effects of mutation on protein stability, structure, and dynamics are outlined and discussed with respect to their underlying …

Nested Canalyzing Depth And Network Stability, Lori Layne, Elena Dimitrova, Matthew Macauley

Publications

We introduce the nested canalyzing depth of a function, which measures the extent to which it retains a nested canalyzing structure. We characterize the structure of functions with a given depth and compute the expected activities and sensitivities of the variables. This analysis quantifies how canalyzation leads to higher stability in Boolean networks. It generalizes the notion of nested canalyzing functions (NCFs), which are precisely the functions with maximum depth. NCFs have been proposed as gene regulatory network models, but their structure is frequently too restrictive and they are extremely sparse. We find that functions become decreasingly sensitive to input …

Loft: The Observatory For X-Ray Timing, M. Feroci, J. W. Den Herder, E. Bozzo, D. Barret, S. Brandt, M. Hernanz, M. Van Der Klis, M. Pohl, A. Santangelo, L Stella, A Watts, J Wilms, S Zane

Publications

The LOFT mission concept is one of four candidates selected by ESA for the M3 launch opportunity as Medium Size missions of the Cosmic Vision programme. The launch window is currently planned for between 2022 and 2024. LOFT is designed to exploit the diagnostics of rapid X-ray flux and spectral variability that directly probe the motion of matter down to distances very close to black holes and neutron stars, as well as the physical state of ultradense matter. These primary science goals will be addressed by a payload composed of a Large Area Detector (LAD) and a Wide Field Monitor …

Measuring The Stellar Accretion Rates Of Herbig Ae/Be Stars, Brian Donehew, Sean D. Brittain

Publications

The accretion rate of young stars is a fundamental characteristic of these systems.While accretion onto T Tauri stars has been studied extensively, little work has been done on measuring the accretion rate of their intermediate-mass analogs, the Herbig Ae/Be stars. Measuring the stellar accretion rate of Herbig Ae/Bes is not straightforward both because of the dearth of metal absorption lines available for veiling measurements and the intrinsic brightness of Herbig Ae/Be stars at ultraviolet wavelengths where the brightness of the accretion shock peaks. Alternative approaches to measuring the accretion rate of young stars by measuring the luminosity of proxies such …