Physical Sciences and Mathematics Commons^™

Early-Time Chromatic Variations In The Wind-Swept Medium Of Grb 021211 And The Faintness Of Its Afterglow, M. C. Nysewander, D. E. Reichart, H.-S. Park, G. G. Williams, K. Kinugasa, D. Q. Lamb, A. A. Henden, S. Klose, T. Kato, A Harper, H Yamaoka, C Laws, K Torii, D G. York, J C. Barentine, J Dembicky, R J. Mcmillan, J A. Moran, Dieter H. Hartmann, B Ketzeback, M B. Bayliss, J A. Crain, A C. Foster, M Schwartz, P Holvorcem, P A. Price, R Canterna, G B. Crew, G R. Ricker, S D. Barthelmy

Publications

We present Follow-Up Network for Gamma-Ray Bursts (FUN GRB) Collaboration observations of the optical afterglow of GRB 021211 made between 143 s and 102 days after the burst. Our unique data set includes the earliest filtered detections and color information for an afterglow in the pre-Swift era. We find that the afterglow is best described by (1) a propagation through a wind-swept medium, (2) a cooling break that is blueward of the observed optical frequencies, and (3) a hard electron energy distribution. However, superimposed on this ‘‘standard model’’ behavior we find, one and possibly two, significant chromatic variations during the …

Predicting Residue Contacts Using Pragmatic Correlated Mutations Method: Reducing The False Positives, Petras J. Kundrotas, Emil Alexov

Publications

Background

Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins.

Results

Here we report a new implementation of the CM method with an added set of selection rules (filters). The parameters of the algorithm were optimized against fifteen high resolution crystal …

A Case Study On Grid Performance Modeling, Amy Apon, Baochuan Lu, Larry Dowdy, Frank Robinson, Doug Hoffman, Denny Brewer

Publications

The purpose of this case study is to develop a performance model for an enterprise grid for performance management and capacity planning1. The target environment includes grid applications such as health-care and financial services where the data is located primarily within the resources of a worldwide corporation. The approach is to build a discrete event simulation model for a representative work-flow grid. Five work-flow classes, found using a customized k-means clustering algorithm characterize the workload of the grid. Analyzing the gap between the simulation and measurement data validates the model. The case study demonstrates that the simulation model can be …

The Grb 060218/Sn 2006aj Event In The Context Of Other Gamma-Ray Burst Supernovae, P. Ferreo, D. A. Kann, A. Zeh, S. Klose, E. Pian, E. Palazzi, N. Masetti, Dieter H. Hartmann, J. Sollerman, J. Deng, A V. Filippenko, J Greiner, M A. Hughes, P Mazzali, W Li, E Rol, R J. Smith, N R. Tanvir

Publications

The supernova SN 2006aj associated with GRB 060218 is the second-closest GRB-SN observed to date (z =0.033). We present Very Large Telescope, Liverpool Telescope, and Katzman Automatic Imaging Telescope multi-color photometry of SN 2006aj. This super-nova is found to be subluminous and rapidly evolving. Its early light curve includes an additional wavelength-dependent component, which can be interpreted as shock break-out. We compare the photometric evolution of multi-band light curves with the corresponding properties of the present sample of more than 10 GRB-SNe with precisely known redshifts. Using host-galaxy extinction measure-ments, we derive extinction-corrected GRB-SN luminosities and place SN 2006aj in …

Protcom: Searchable Database Of Protein Complexes Enhanced With Domain-Domain Structures, Petras Kundrotas, Emil Alexov

Publications

The database of protein complexes (PROTCOM) is a compilation of known 3D structures of protein–protein complexes enriched with artificially created domain–domain structures using the available entries in the Protein Data Bank. The domain–domain structures are generated by parsing single chain structures into loosely connected domains and are important features of the database. The database (http://www.ces.clemson.edu/compbio/protcom) could be used for benchmarking purposes of the docking and other algorithms for predicting 3D structures of protein–protein complexes. The database can be utilized as a template database in the homology or threading methods for modeling the 3D structures of unknown protein–protein complexes. …

Neutrino Oscillation Effects On Supernova Light Element Synthesis, Takashi Yoshida, Toshitaka Kajino, Hidekazu Yokomakura, Keichi Kimura, Akira Takamura, Dieter H. Hartmann

Publications

Neutrion oscillations affect light-element synthesis through the v-process in supernova explosions. The 7Li and 11B yields produced in a supernova explosion of a 16.2 M ⊙ star model increase by factors of 1.9 and 1.3 in the case of the large mixing angle solution with a normal mass hierarchy of sin^2 2θ13 >~ 2x10^-3 compared with those without the oscillations. In the case of an inerted mass hierarchy or a nonadiabatic 1-3 mixing resonance, the increment of their yields is much smaller. Neutrino oscillations raise the reaction rates of charged-current v-process reactions in the region outside oxygen-rich layers. The number …

Electrostatic Properties Of Protein-Protein Complexes, Petras J. Kundrotas, Emil Alexov

Publications

Statistical electrostatic analysis of 37 protein-protein complexes extracted from the previously developed database of protein complexes (ProtCom, http://www.ces.clemson.edu/compbio/protcom) is presented. It is shown that small interfaces have a higher content of charged and polar groups compared to large interfaces. In a vast majority of the cases the average pK_a shifts for acidic residues induced by the complex formation are negative, indicating that complex formation stabilizes their ionizable states, whereas the histidines are predicted to destabilize the complex. The individual pK_a shifts show the same tendency since 80% of the interfacial acidic groups were found to lower their …

The Great Plains Network (Gpn) Middleware Test Bed, Amy Apon, Gregory Monaco, Gordon Springer

Publications

GPN (Great Plains Network) is a consortium of public universities in seven mid-western states. GPN goals include regional strategic planning and the development of a collaboration environment, middleware services and a regional grid for sharing computational, storage and data resources. A major challenge is to arrive at a common authentication and authorization service, based on the set of heterogeneous identity providers at each institution. GPN has built a prototype middleware test bed that includes Shibboleth and other NMI-EDIT middleware components. The test bed includes several prototype end-user applications, and is being used to further our research into fine-grained access control …

Dust Stratification In Young Circumstellar Disks, Terrence Rettig, Sean D. Brittain, Theodore Simon, Erika Gibb, Dinshaw S. Balsara, David A. Tilley, Craig Kulesa

Publications

We present high-resolution infrared spectra of four YSOs (T Tau N, T Tau S, RNO 91, and HL Tau). The spectra exhibit narrow absorption lines of 12CO, 13CO, and C18O, as well as broad emission lines of gas-phase 12CO. The narrow absorption lines of CO are shown to originate from the colder circumstellar gas. We find that the line-of-sight gas column densities resulting from the CO absorption lines are much higher than expected for the measured extinction for each source and suggest the gas/dust ratio is measuring the dust settling and/or grain coagulation in these extended disks. We provide a …

Probing Cosmic Chemical Evolution With Gamma-Ray Bursts: Grb060206 At Z=4.048, J. P. U. Frynbo, R. L. C. Starling, C. Ledoux, K. Wiersema, C. C. Thöne, J. Sollerman, P. Jakobsson, J. Hjorth, D. Watson, P M. Vreeswijk, P Møller, E Rol, J Gorosabel, J Näränen, R.A.M.J. Wijers, G Björnsson, J M. Castro Cerón, P Curran, Dieter H. Hartmann, S T. Holland, B L. Jensen, A J. Levan, M Limousin, C Kouveliotou, G Nelemans, K Pedersen, R S. Priddey, N R. Tanvir

Publications

Aims. We present early optical spectroscopy of the afterglow of the gamma-ray burst GRB 060206 with the aim of determining the metallicity of the GRB absorber and the physical conditions in the circumburst medium. We also discuss how GRBs may be important complementary probes of cosmic chemical evolution. Methods. Absorption line study of the GRB afterglow spectrum. Results. We determine the redshift of the GRB to be z =4.04795 ±0.00020. Based on the measurement of the neutral hydrogen column density from the damped Lyman-αline and the metal content from weak, unsaturated S ii lines we derive a metallicity of [S/H] …

Are Ti44-Producing Supernovae Exceptional?, L.-S. The, Donald D. Clayton, R Diehl, Dieter H. Hartmann, A F. Iyudin, M D. Leising, B S. Meyer, Y Motizuki, V Schönfelder

Publications

According to standard models supernovae produce radioactive ⁴⁴Ti, which should be visible in gamma-rays following decay to ⁴⁴Ca for a few centuries. ⁴⁴Ti production is believed to be the source of cosmic ⁴⁴Ca, whose abundance is well established. Yet, gamma-ray telescopes have not seen the expected young remnants of core collapse events. The ⁴⁴Ti mean life of 89 y and the Galactic supernova rate of 3/100 y imply several detectable ⁴⁴Ti gamma-ray sources, but only one is clearly seen, the 340-year-old Cas A SNR. Furthermore, supernovae which produce much ⁴⁴Ti are expected …

Architectural Tradeoffs For Unifying Campus Grid Resources, Amy Apon, Bart Taylor

Publications

Most universities have a powerful collection of computing resources on campus for use in areas from high performance computing to general access student labs. However, these resources are rarely used to their full potential. Grid computing offers a way to unify these resources and to better utilize the capability they provide. The complexity of some grid tools makes learning to use them a daunting task for users not familiar with using the command line. Combining these tools together into a single web portal interface provides campus faculty and students with an easy way to access the campus resources. This paper …

Post-Outburst Infrared Spectra Of V1647 Ori, The Illuminating Star Of Mcneil's Nebula, E L. Gibb, T W. Rettig, Sean D. Brittain, D Wasikowski, Theodore Simon, William D. Vacca, Michael C. Cushing, C Kulesa

Publications

V1647 Ori is a low mass star in the L1630 star-forming region that underwent an outburst in late 2003/early 2004. We present post-outburst infrared spectra obtained with NIRSPEC (Keck II) and SpeX (IRTF) and compare these to spectra taken during the outburst. The results show that the temperature of the hot CO formed in the inner part of the disk has declined by ~800 K, while the water and CO ice and low-J CO gas features remained unchanged, consistent with previous assertions that the latter, low-temperature features arise in the foreground cloud. The P-Cygni profiles of the Paschen series that …

Inital Starting Point Analysis For K-Means Clustering: A Case Study, Amy Apon, Frank Robinson, Denny Brewer, Larry Dowdy, Doug Hoffman, Baochuan Lu

Publications

Workload characterization is an important part of systems performance modeling. Clustering is a method used to find classes of jobs within workloads. K-Means is one of the most popular clustering algorithms. Initial starting point values are needed as input parameters when performing k-means clustering. This paper shows that the results of the running the k-means algorithm on the same workload will vary depending on the values chosen as initial starting points. Fourteen methods of composing initial starting point values are compared in a case study. The results indicate that a synthetic method, scrambled midpoints, is an effective starting point method …

Growth Of Carbon Grains In Supernova Ejecta, Ethan A-N. Deneault, Donald D. Clayton, Bradley S. Meyer

Publications

We present a chemical reaction network that describes the condensation chemistry of carbon dust grains in an expanding supernova shell. We assume that the region of interest consists solely of gaseous free carbon and oxygen atoms and that the buildup of CO is counteracted by the radioactive decay of 56Co, which breaks up the CO mol-ecule and allows C to condense into solids. Our chemical model takes C to first form linear chains, which, at some critical length, transition into ringed isomers. These isomers are more resistant to oxidation than linear chains. These ringed isomers form the nuclei for the …

Radioactive 26al And Massive Stars In The Galaxy, Roland Diehl, Hubert Halloin, Karsten Kretschmer, Giselher G. Lichiti, Volker Schönfelder, Andrew W. Strong, Andreas Von Kienlin, Wei Wang, Pierre Jean, Jürgen Knödlseder, Jean-Pierre Roques, Georg Weidenspointner, Stephane Schanne, Dieter H. Hartmann, Christoph Winkler, Cornelia Wunderer

Publications

Gamma-rays from radioactive 26Al (half life ~7.2 105 yr) provide a 'snapshot' view of ongoing nucleosynthesis in the Galaxy1. The Galaxy is relatively transparent to such gamma-rays, and emission has been found concentrated along the plane of the Galaxy2. This led to the conclusion1 that massive stars throughout the Galaxy dominate the production of 26Al. On the other hand, meteoritic data show locally-produced 26Al, perhaps from spallation reactions in the protosolar disk. Furthermore, prominent gamma-ray emission from the Cygnus region2,3 suggests that a substantial fraction of Galactic 26Al could originate in localized star-forming regions. Here we report high spectral resolution …