Physical Sciences and Mathematics Commons^™

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 …

Lithium In The Upper Centaurus Lupus And Lower Centaurus Crux Subgroups Of Scorpius-Centaurus, Eric J. Bubar, Marc Schaeuble, Jeremy R. King, Eric E. Mamajek, John R. Stauffer

Publications

We utilize spectroscopically derived model atmosphere parameters and the Li i λ6104 subordinate line and the λ6708 doublet to derive lithium abundances for 12 members of the Upper Centaurus Lupus and Lower Centaurus Crux subgroups of the Scorpius–Centaurus OB Association. The results indicate any intrinsic Li scatter in our 0.9–1.4 M stars is limited to ∼0.15 dex, consistent with the lack of dispersion in 1.0 M stars in the 100 Myr Pleiades and 30–50 Myr IC 2391 and 2602 clusters. Both ab initio uncertainty estimates and the derived abundances themselves indicate that the λ6104 line yields abundances with equivalent or …

Progress In The Prediction Of Pka Values In Proteins, Emil Alexov, Ernest L. Mehler, Nathan Baker, Antonio Baptista, Yong Huang, Francesca Milletti, Jens Erik Nielsen, Damien Farrell, Tommy Carstensen, Mats H.M. Olsson, Jana K. Shen, Jim Warwicker, Sarah Williams, J Michael Word

Publications

The pK_a-cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pK_a values and protein electrostatics in general. The first round of the pK_a-cooperative, which challenged computational labs to carry out blind predictions against pK_as experimentally determined in the laboratory of Bertrand Garcia-Moreno, was completed and results discussed at the Telluride meeting (July 6–10, 2009). This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics. …

Developing Hybrid Approaches To Predict Pka Values Of Ionizable Groups, Shawn Witham, Kemper Talley, Lin Wang, Zhe Zhang, Daquan Gao, Wei Yang, Emil Alexov

Publications

Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure. On another hand, if the change of the charge state is accompanied by a structural reorganization of the target protein, then the relevant conformational changes have to be taken into account in the pKa calculations. Here we report a hybrid …

Electronic Charge And Spin Density Distribution In A Quantum Ring With Spin-Orbit And Coulomb Interactions, Csaba Daday, Andrei Manolescu, D C. Marinescu, Vidar Gudmundsson

Publications

Charge and spin density distributions are studied within a nanoring structure endowed with Rashba and Dresselhaus spin-orbit interactions (SOIs). For a small number of electrons, in the presence of an external magnetic field and of the Coulomb interaction, the energy spectrum of the system is calculated through an exact numerical diagonalization procedure. The eigenstates thus determined are used to estimate the charge and spin densities around the ring. We find that when more than two electrons are considered, the charge density deformations induced by SOIs are dramatically flattened by the Coulomb repulsion, while the spin density deformations are amplified.

Detailed Abundances Of The Solar Twins 16 Cygni And B Cygni: Constraining Planet Formation Models, Simon C. Schuler, Katia Cunha, Verne V. Smith, Luan Ghezzi, Jeremy R. King, Constantine P. Deliyannis, Ann Merchant Boesgaard

Publications

Results of a detailed abundance analysis of the solar twins 16 Cyg A and 16 Cyg B based on high-resolution, high signal-to-noise ratio echelle spectroscopy are presented. 16 Cyg B is known to host a giant planet while no planets have yet been detected around 16 Cyg A. Stellar parameters are derived directly from our high-quality spectra, and the stars are found to be physically similar, with ΔTeff = +43 K, Δ log g =−0.02 dex, and Δξ = +0.10 km s−1 (in the sense of A − B), consistent with previous findings. Abundances of 15 elements are derived and …

X-Ray Monitoring Of Classical Novae In The Central Region Of M 31 Iii. Autumn And Winter 2007/2008 And 2008/2009, M. Henze, W. Pietsch, F. Haberl, M. Hernanz, G. Sala, D. Hartzidimitriou, M. Della Velle, A. Rau, Dieter H. Hartmann, V. Burwitz

Publications

Context. Classical novae (CNe) represent the major class of supersoft X-ray sources (SSSs) in the central region of the galaxy M 31. Aims. We performed a dedicated monitoring of the M 31 central region with XMM-Newton and Chandra between Nov. 2007 and Feb. 2008 and between Nov. 2008 and Feb. 2009, respectively, to find SSS counterparts of CNe, determine the duration of their SSS phase, and derive physical outburst parameters. Methods. We systematically searched our data for X-ray counterparts of CNe, determined their X-ray light curves and characterised their spectra using blackbody fits and white dwarf (WD) atmosphere models. Additionally, …

A Missense Mutation In Clic2 Associated With Intellectual Disability Is Predicted By In Silico Modeling To Affect Protein Stability And Dynamics, Shawn Witham, Kyoko Takano, Charles Schwartz, Emil Alexov

Publications

Large-scale next generation resequencing of X chromosome genes identified a missense mutation in the CLIC2 gene on Xq28 in a male with X-linked intellectual disability (XLID) and not found in healthy individuals. At the same time, numerous nsSNPs (nonsynonomous SNP) have been reported in the CLIC2 gene in healthy individuals indicating that the CLIC2 protein can tolerate amino acid substitutions and be fully functional. To test the possibility that p.H101Q is a disease-causing mutation, we performed in silico simulations to calculate the effects of the p.H101Q mutation on CLIC2 stability, dynamics, and ionization states while comparing the effects obtained for …

Helical Antiferromagnetic Ordering In The Lowest Landau Level Of A Semiconductor Superlattice, Liqiu Zheng, D C. Marinescu

Publications

When subjected to a tilted magnetic field, the ground state of a semiconductor superlattice (SL) with two identical quantum wells per unit cell is shown to exhibit different magnetic configurations that are dependent on the strength and direction of the field and the SL characteristics. Intra- and interunit cell tunneling between the wells, assumed to be infinitely attractive, generate an energy miniband structure of the lowest Landau level that, in cooperation with the Zeeman splitting, creates, at certain points in the momentum space, an energy difference between opposite-spin single-particle states that can be overcome by the Coulomb interaction. Within the …

Nova M31n 2007-12b: Supersoft X-Rays Reveal An Intermediate Polar?, W. Pietsch, M. Henze, F. Haberl, M. Hernanz, G. Sala, Dieter H. Hartmann, M. Della Valle

Publications

Context. In the central part of M 31, a high number of optical novae can be targeted within the field of view of the XMM-Newton EPIC and Chandra HRC-I X-ray detectors. A special monitoring program of the area has allowed us to investigate supersoft emission of individual novae in detail and perform a statistical analysis of the sample. Aims. For the He/N nova M31N 2007-12b, we aimed to constrain the time of appearance of a supersoft source (SSS) and the duration of the SSS state as well as determine the spectral and time variability while the source was bright. Methods. …

Thermal Conductance Of A Two-Channel Kondo Model, C P. Moca, A Roman, D C. Marinescu

Publications

A theory of thermal transport in a two-channel Kondo system, such as the one formed by a small quantum dot coupled to two leads and to a larger dot, is formulated. The interplay of the two screening constants allow an exploration of the Fermi liquid and non-Fermi liquid regimes. By using analytical, as well as numerical, renormalization group methods, we study the temperature dependence of the thermal conductance and the Lorentz number. We find that in the low-temperature limit, the Lorentz number attains its universal value, irrespective of the nature of the ground state.

Ro-Vibrational Co Detected In The Β Pictoris Circumstellar Disk, Matthew R. Troutman, Kenneth H. Hinkle, Joan R. Najita, Terrence W. Rettig, Sean D. Brittain

Publications

We present high-resolution near-infrared spectra of β Pictoris—a nearby young star with a debris disk. Fundamental low-J CO absorption lines are detected and strict upper limits are placed on the flux of v = 2–1 low-J CO emission lines. The limit on the UV fluorescent emission flux in the v = 2–1 lines is used to place a tight constraint on the inner extent of the CO gas. Assuming Hi is the primary collision partner, the sub-thermal population of the low-J v = 0 rotational levels constrains the density of the gas in the disk to nH = (2.5+7.1 −1.2)×105 …

On The Role Of Electrostatics In Protein–Protein Interactions, Zhe Zhang, Shawn Witham, Emil Alexov

Publications

The role of electrostatics in protein–protein interactions and binding is reviewed in this paper. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and the basic electrostatic effects occurring upon the formation of the complex are discussed. The effect of the salt concentration and pH of the water phase on protein–protein binding free energy is demonstrated which indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge–charge interactions across the interface. It is pointed out that the pH-optimum (pH of …

Order Independence In Asynchronous Cellular Automata, Matthew Macauley, Jon Mccammond, Henning S. Mortveit

Publications

A sequential dynamical system, or SDS, consists of an undirected graph Y, a vertex-indexed list of local functions F_Y, and a permutation pi of the vertex set (or more generally, a word w over the vertex set) that describes the order in which these local functions are to be applied. In this article we investigate the special case where Y is a circular graph with n vertices and all of the local functions are identical. The 256 possible local functions are known as Wolfram rules and the resulting sequential dynamical systems are called finite asynchronous elementary cellular automata, or ACAs, …

Grips - Gamma-Ray Imaging, Polarimetry And Spectroscopy, Jochen Greiner, Karl Mannheim, Felix Aharonian, Marco Ajello, Lajos G. Balaz, Guido Barbiellini, Ronaldo Bellazzini, Shawn Bishop, Gennady S. Bisnoyatij-Kogan, Steven Boggs, Andrej Bykov, Guido Dicocco, Roland Diehl, Dominik Elsasser, Suzanne Foley, Claes Fransson, Neil Gehrels, Lorraine Hanlon, Dieter H. Hartmann

Publications

We propose to perform a continuously scanning all-sky survey from 200 keV to 80 MeV achieving a sensitivity which is better by a factor of 40 or more compared to the previous missions in this energy range (COMPTEL, INTEGRAL; see Fig. 1). The Gamma-Ray Imaging, Polarimetry and Spectroscopy (“GRIPS”) mission addresses fundamental questions in ESA’s Cosmic Vision plan. Among the major themes of the strategic plan, GRIPS has its focus on the evolving, vio-lent Universe, exploring a unique energy window. We propose to investigate γ-ray bursts and blazars, the mechanisms behind supernova explosions, nucleosynthesis and spallation, the enigmatic origin of …

Simulation Of Relativistic Jets And Associated Self-Consistent Radiation, K.-I. Nishikawa, E. J. Choi, K. Min, P. Hardee, Y. Mizuno, C. Zhang, J. Niemiec, M. Medvedev, A. Norlund, J Frederiksen, M Pohl, H Sol, Dieter H. Hartmann, G J. Fishman

Publications

Plasma instabilities excited in collisionless shocks are responsible for particle acceleration. We have investigated the particle acceleration and shock structure associated with an unmagnetized relativistic electron-positron jet propagating into an unmagnetized electron-positron plasma. Cold jet electrons are thermalized and slowed while the ambient electrons are swept up to create a par-tially developed hydrodynamic-like shock structure. In the leading shock, electron density increases by a factor of about 3.5 in the simulation frame. Strong electromagnetic fields are generated in the trailing shock and provide an emission site. These magnetic fields contribute to the electrons transverse deflection behind the shock. Our initial …

Abundances Of Stars With Planets: Trends With Condensation Temperature, Simon C. Schuler, Davin Flateau, Katia Cunha, Jeremy R. King, Luan Ghezzi, Verne V. Smith

Publications

Precise abundances of 18 elements have been derived for 10 stars known to host giant planets from high signal-to-noise ratio, high-resolution echelle spectroscopy. Internal uncertainties in the derived abundances are typically 0.05 dex. The stars in our sample have all been previously shown to have abundances that correlate with the condensation temperature (Tc) of the elements in the sense of increasing abundances with increasing Tc; these trends have been interpreted as evidence that the stars may have accreted H-depleted planetary material. Our newly derived abundances also correlate positively with Tc, although slopes of linear least-square fits to the [m/H]–Tc relations …

In Silico And In Vitro Investigations Of The Mutability Of Disease-Causing Missense Mutation Sites In Spermine Synthase, Zhe Zhang, Joy Norris, Charles Schwartz, Emil Alexov

Publications

Background

Spermine synthase (SMS) is a key enzyme controlling the concentration of spermidine and spermine in the cell. The importance of SMS is manifested by the fact that single missense mutations were found to cause Snyder-Robinson Syndrome (SRS). At the same time, currently there are no non-synonymous single nucleoside polymorphisms, nsSNPs (harmless mutations), found in SMS, which may imply that the SMS does not tolerate amino acid substitutions, i.e. is not mutable.

Methodology/Principal Findings

To investigate the mutability of the SMS, we carried out in silico analysis and in vitro experiments of the effects of amino acid substitutions at the …