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Sample records for starburst molecular structure

  1. Molecular outflows in starburst nuclei

    NASA Astrophysics Data System (ADS)

    Roy, Arpita; Nath, Biman B.; Sharma, Prateek; Shchekinov, Yuri

    2016-12-01

    Recent observations have detected molecular outflows in a few nearby starburst nuclei. We discuss the physical processes at work in such an environment in order to outline a scenario that can explain the observed parameters of the phenomenon, such as the molecular mass, speed and size of the outflows. We show that outflows triggered by OB associations, with NOB ≥ 105 (corresponding to a star formation rate (SFR)≥1 M⊙ yr-1 in the nuclear region), in a stratified disc with mid-plane density n0 ˜ 200-1000 cm-3 and scaleheight z0 ≥ 200(n0/102 cm-3)-3/5 pc, can form molecules in a cool dense and expanding shell. The associated molecular mass is ≥107 M⊙ at a distance of a few hundred pc, with a speed of several tens of km s-1. We show that an SFR surface density of 10 ≤ ΣSFR ≤ 50 M⊙ yr-1 kpc-2 favours the production of molecular outflows, consistent with observed values.

  2. HIGH-DENSITY MOLECULAR GAS PROPERTIES OF THE STARBURST GALAXY NGC 1614 REVEALED WITH ALMA

    SciTech Connect

    Imanishi, Masatoshi; Nakanishi, Kouichiro

    2013-09-15

    We present the results of HCN/HCO{sup +}/HNC J = 4-3 transition line observations of the nearby starburst galaxy NGC 1614, obtained with ALMA Cycle 0. We find that high density molecular gas traced with these lines shows a velocity structure such that the northern (southern) side of the nucleus is redshifted (blueshifted) with respect to the nuclear velocity of this galaxy. The redshifted and blueshifted emission peaks are offset by {approx}0.''6 at the northern and southern sides of the nucleus, respectively. At these offset positions, observations at infrared >3 {mu}m indicate the presence of active dusty starbursts, supporting the picture that high-density molecular gas is the site of active starbursts. The enclosed dynamical mass within the central {approx}2'' in radius, derived from the dynamics of the high-density molecular gas, is {approx}10{sup 9} M{sub Sun }, which is similar to previous estimates. Finally, the HCN emission is weaker than HCO{sup +} but stronger than HNC for J = 4-3 for all starburst regions of NGC 1614, as seen for J = 1-0 transition lines in starburst-dominated galaxies.

  3. Extragalactic molecular line surveys: the starburst galaxy NGC253

    NASA Astrophysics Data System (ADS)

    Martín, S.; Mauersberger, R.; Martín-Pintado, J.; Henkel, C.; García-Burillo, S.

    Figure 1 shows the first spectral line survey towards an extragalactic source, the starburst galaxy NGC253. The scan, carried out at the IRAM 30m telescope, covers ~86% of the observable 2mm atmospheric window from 129.1 to 175.2GHz. A total of ~ 100 spectral features have been identified as transitions from 25 different molecular species. Ten out of these 25 molecules have been detected for the first time towards a starbust galaxy. NO, NS, SO2, H2S and H2CS were reported by Martín et al.(2003), Martín et al.(2005) while C2S, CH2NH, NH2CN, HOCO+ and C3H are tentatively detected in the survey. These new detections implies an increase of ~ 40% in the 27 molecular species previosly detected outside the galaxy (Mauersberger & Henkel(1993), Mauersberger et al.(1995), Sage & Ziurys(1995), Heikkila et al.(1999).) Additionaly, DNC and N2D+, two deuterated species never obseved in the extragalactic ISM, are tentatively identified. The molecular abundances derived for each species in NGC253 have been compared with five Galactic sources known to be prototypes of different types of chemistry. The chemical complexity of NGC253 resembles closely that observed towards prototypical Galactic Center molecular clouds (SgrB2(OH) in, thought to be mainly dominated by low velocity shocks Martín-Pintado et al.(2001). This comparison certainly indicates that the chemistry of the molecular environment within the nuclear region of NGC253 and that in Galactic Center molecular clouds are driven by similar physical processes. Also a comparison has been performed with five selected prominent galaxies which clearly shows up the chemical differenciation between nuclei of galaxies. The chemical complexity of IC342, and also that of NGC4945 except for the observed lack of SiO, clearly resemble that of NGC253. On the other hand, it is remarkable the different chemical complexity observed between the starburst nuclei within NGC253 and M82. This difference has been interpreted in terms of the

  4. How Does Dense Molecular Gas Contribute to Star Formation in the Starburst Galaxy NGC 2146?

    NASA Astrophysics Data System (ADS)

    Wofford, Alia

    2017-01-01

    The starburst galaxy NGC 2146 is believed to have been formed approximately 800 Myr ago, when two galaxies collided with each other possibly leading to a burst of star formation. NGC 2146 is known as a starburst galaxy for the high frequency of star formation going on in its molecular clouds. These clouds serve as nurseries for star formation to occur. Hydrogen Cyanide (HCN) and Carbon monoxide (CO) are molecules found in molecular gas clouds. HCN molecules are tracers for high density star forming gas. Whereas, CO molecules are tracers for low density star forming gas. In this project, we are observing these two molecules and their proximity to where the stars are forming in the galaxy to determine if the star formation is occurring in the same area as the high and low density molecular gas areas in starburst galaxy NGC 2146.

  5. Structure of the Interacting Starburst Galaxy II Zw 23

    NASA Astrophysics Data System (ADS)

    Cigan, P. J.; Gallagher, J. S.; Rudie, G.; Wehner, E. H.

    2005-09-01

    II Zw 23 (UGC 3179) is a luminous (MB -21) nearby compact narrow emission line starburst galaxy with blue optical colors and strong emission lines. We present a photometric and morphological study of II Zw 23 and its interacting companion, PC016099, using data obtained with the WIYN 3.5-m telescope in combination with a WFPC2 image from the HST archives. II Zw 23 has a highly disturbed outer structure with long trails of debris that may be feeding tidal dwarfs. Its central regions appear disk-like, a structure that is consistent with the overall rotation pattern observed in the Hα emission line velocity field measured from Densepak observations obtained with WIYN. We discuss these results in terms of the different evolutionary paths followed by stars and gas during strong interactions and the possibility of rapid secondary galactic disk formation in such events.

  6. Suppression of star formation in the galaxy NGC 253 by a starburst-driven molecular wind.

    PubMed

    Bolatto, Alberto D; Warren, Steven R; Leroy, Adam K; Walter, Fabian; Veilleux, Sylvain; Ostriker, Eve C; Ott, Jürgen; Zwaan, Martin; Fisher, David B; Weiss, Axel; Rosolowsky, Erik; Hodge, Jacqueline

    2013-07-25

    The under-abundance of very massive galaxies in the Universe is frequently attributed to the effect of galactic winds. Although ionized galactic winds are readily observable, most of the expelled mass (that is, the total mass flowing out from the nuclear region) is likely to be in atomic and molecular phases that are cooler than the ionized phases. Expanding molecular shells observed in starburst systems such as NGC 253 (ref. 12) and M 82 (refs 13, 14) may facilitate the entrainment of molecular gas in the wind. Although shell properties are well constrained, determining the amount of outflowing gas emerging from such shells and the connection between this gas and the ionized wind requires spatial resolution better than 100 parsecs coupled with sensitivity to a wide range of spatial scales, a combination hitherto not available. Here we report observations of NGC 253, a nearby starburst galaxy (distance ∼ 3.4 megaparsecs) known to possess a wind, that trace the cool molecular wind at 50-parsec resolution. At this resolution, the extraplanar molecular gas closely tracks the Hα filaments, and it appears to be connected to expanding molecular shells located in the starburst region. These observations allow us to determine that the molecular outflow rate is greater than 3 solar masses per year and probably about 9 solar masses per year. This implies a ratio of mass-outflow rate to star-formation rate of at least 1, and probably ∼3, indicating that the starburst-driven wind limits the star-formation activity and the final stellar content.

  7. Stellar feedback as the origin of an extended molecular outflow in a starburst galaxy.

    PubMed

    Geach, J E; Hickox, R C; Diamond-Stanic, A M; Krips, M; Rudnick, G H; Tremonti, C A; Sell, P H; Coil, A L; Moustakas, J

    2014-12-04

    Recent observations have revealed that starburst galaxies can drive molecular gas outflows through stellar radiation pressure. Molecular gas is the phase of the interstellar medium from which stars form, so these outflows curtail stellar mass growth in galaxies. Previously known outflows, however, involve small fractions of the total molecular gas content and have typical scales of less than a kiloparsec. In at least some cases, input from active galactic nuclei is dynamically important, so pure stellar feedback (the momentum return into the interstellar medium) has been considered incapable of rapidly terminating star formation on galactic scales. Molecular gas has been detected outside the galactic plane of the archetypal starburst galaxy M82 (refs 4 and 5), but so far there has been no evidence that starbursts can propel substantial quantities of cold molecular gas to the same galactocentric radius (about 10 kiloparsecs) as the warmer gas that has been traced by metal ion absorbers in the circumgalactic medium. Here we report observations of molecular gas in a compact (effective radius 100 parsecs) massive starburst galaxy at redshift 0.7, which is known to drive a fast outflow of ionized gas. We find that 35 per cent of the total molecular gas extends approximately 10 kiloparsecs, and one-third of this extended gas has a velocity of up to 1,000 kilometres per second. The kinetic energy associated with this high-velocity component is consistent with the momentum flux available from stellar radiation pressure. This demonstrates that nuclear bursts of star formation are capable of ejecting large amounts of cold gas from the central regions of galaxies, thereby strongly affecting their evolution by truncating star formation and redistributing matter.

  8. OBSERVATIONAL CONSTRAINTS ON THE MOLECULAR GAS CONTENT IN NEARBY STARBURST DWARF GALAXIES

    SciTech Connect

    McQuinn, Kristen B. W.; Skillman, Evan D.; Dalcanton, Julianne J.; Weisz, Daniel R.; Williams, Benjamin F.; Dolphin, Andrew E.; Cannon, John M.; Holtzman, Jon

    2012-06-01

    Using star formation histories derived from optically resolved stellar populations in 19 nearby starburst dwarf galaxies observed with the Hubble Space Telescope, we measure the stellar mass surface densities of stars newly formed in the bursts. By assuming a star formation efficiency (SFE), we then calculate the inferred gas surface densities present at the onset of the starbursts. Assuming an SFE of 1%, as is often assumed in normal star-forming galaxies, and assuming that the gas was purely atomic, translates to very high H I surface densities ({approx}10{sup 2}-10{sup 3} M{sub Sun} pc{sup -2}), which are much higher than have been observed in dwarf galaxies. This implies either higher values of SFE in these dwarf starburst galaxies or the presence of significant amounts of H{sub 2} in dwarfs (or both). Raising the assumed SFEs to 10% or greater (in line with observations of more massive starbursts associated with merging galaxies), still results in H I surface densities higher than observed in 10 galaxies. Thus, these observations appear to require that a significant fraction of the gas in these dwarf starbursts galaxies was in the molecular form at the onset of the bursts. Our results imply molecular gas column densities in the range 10{sup 19}-10{sup 21} cm{sup -2} for the sample. In the galaxies where CO observations have been made, these densities correspond to values of the CO-H{sub 2} conversion factor (X{sub CO}) in the range >(3-80) Multiplication-Sign 10{sup 20} cm{sup -2} (K km s{sup -1}){sup -1}, or up to 40 Multiplication-Sign greater than Galactic X{sub CO} values.

  9. Dense Molecular Gas Tracers in the Outflow of the Starburst Galaxy NGC 253

    NASA Astrophysics Data System (ADS)

    Walter, Fabian; Bolatto, Alberto D.; Leroy, Adam K.; Veilleux, Sylvain; Warren, Steven R.; Hodge, Jacqueline; Levy, Rebecca C.; Meier, David S.; Ostriker, Eve C.; Ott, Jürgen; Rosolowsky, Erik; Scoville, Nick; Weiss, Axel; Zschaechner, Laura; Zwaan, Martin

    2017-02-01

    We present a detailed study of a molecular outflow feature in the nearby starburst galaxy NGC 253 using ALMA. We find that this feature is clearly associated with the edge of NGC 253's prominent ionized outflow, has a projected length of ∼300 pc, with a width of ∼50 pc, and a velocity dispersion of ∼40 km s‑1, which is consistent with an ejection from the disk about 1 Myr ago. The kinematics of the molecular gas in this feature can be interpreted (albeit not uniquely) as accelerating at a rate of 1 km s‑1 pc‑1. In this scenario, the gas is approaching an escape velocity at the last measured point. Strikingly, bright tracers of dense molecular gas (HCN, CN, HCO+, CS) are also detected in the molecular outflow: we measure an HCN(1–0)/CO(1–0) line ratio of ∼ 1/10 in the outflow, similar to that in the central starburst region of NGC 253 and other starburst galaxies. By contrast, the HCN/CO line ratio in the NGC 253 disk is significantly lower (∼ 1/30), similar to other nearby galaxy disks. This strongly suggests that the streamer gas originates from the starburst, and that its physical state does not change significantly over timescales of ∼1 Myr during its entrainment in the outflow. Simple calculations indicate that radiation pressure is not the main mechanism for driving the outflow. The presence of such dense material in molecular outflows needs to be accounted for in simulations of galactic outflows.

  10. Optical depth of molecular gas in starburst galaxies - Is M82 the prototype?

    NASA Technical Reports Server (NTRS)

    Verter, F.; Rickard, L. J.

    1989-01-01

    An attempt is made to survey the CO(2-1) emission toward the centers of 17 IR-luminous galaxies which have previously been detected in CO(1-0). These galaxies span a wide range of size and L(FIR)/L(B) ratio, many have multiple-wavelength studies establishing them as starbursts, and some bear a morphological resemblance to M 82. Nine galaxies are detected and useful upper limits are placed on the remaining eight. Using the CO(2-1)/CO(1-0) ratio of antenna temperature as a diagnostic of optical depth, it is found that all of the galaxies contain predominantly optically thick molecular gas. This implies that the phase of starburst during which the molecular gas is optically thin, currently witnessed in M 82, is either uncommon or short-lived.

  11. Evolution of molecular clouds in the starburst galaxy NGC 1808 revealed with ALMA

    NASA Astrophysics Data System (ADS)

    Salak, D.; Nakai, N.; Miyamoto, Y.

    2015-05-01

    We present large-field CO(1-0) observations of the starburst galaxy NGC 1808 conducted with ALMA. High-resolution (˜100 pc) images reveal a high concentration of molecular gas in the nucleus, 500-pc ring, gas-rich bar, and spiral arms. We derived the bar pattern speed and found an offset between CO and Hα emission peaks in the offset ridges along the bar. The results indicate that the evolution of molecular clouds on the galactic scale is driven by bar dynamics.

  12. The Green Bank Telescope Maps the Dense Molecular Gas in the Starburst Galaxy M82

    NASA Astrophysics Data System (ADS)

    Kepley, Amanda A.; Leroy, A. K.; Frayer, D. T.; Usero, A.; Marvil, J.; Walter, F.

    2014-01-01

    In both the Milky Way and nearby galaxies, the presence of dense molecular gas is correlated with recent star formation, suggesting that the formation of this gas may represent a key regulating step in the star formation process. Testing this idea requires wide-area, high-resolution maps of dense molecular gas in galaxies to explore how local physical conditions drive dense gas formation. Until now, these observations have been limited by the faintness of dense gas tracers like HCN and HCO+, but new instruments like the 4mm receiver on Robert C. Byrd Green Bank Telescope (GBT) -- the largest single-dish millimeter telescope -- are poised to change this picture. We present GBT maps of the dense gas tracers HCN and HCO+ in the prototypical nearby starburst galaxy M82. The HCN and HCO+ in the disk of M82 correlates both with recent star formation and the diffuse molecular gas and shows kinematics consistent with a rotating torus. HCO+ emission is also associated with the outflow of molecular gas previously identified in CO. These observations mark the first time that dense molecular gas like HCO+ has been associated with an outflow in a nearby galaxy and suggests that the outflow of dense molecular gas from the center of galaxies like M82 may regulate the star formation globally. Finally, the CO-to-HCN and CO-to-HCO+ line ratios reveal that there is more dense gas at the center of M82, pointing to the starburst as a key driver of this relationship. These results establish that the GBT can efficiently map the dense molecular gas at 90 GHz in nearby galaxies; this capability will increase further with the 16-element feed array currently being built for the GBT.

  13. The radio core structure of the luminous infrared galaxy NGC 4418. A young clustered starburst revealed?

    NASA Astrophysics Data System (ADS)

    Varenius, E.; Conway, J. E.; Martí-Vidal, I.; Aalto, S.; Beswick, R.; Costagliola, F.; Klöckner, H.-R.

    2014-06-01

    Context. The galaxy NGC 4418 contains one of the most compact obscured nuclei within a luminous infrared galaxy (LIRG) in the nearby Universe. This nucleus contains a rich molecular gas environment and an unusually high ratio of infrared-to-radio luminosity (q-factor). The compact nucleus is powered by either a compact starburst or an active galactic nucleus (AGN). Aims: The aim of this study is to constrain the nature of the nuclear region (starburst or AGN) within NGC 4418 via very-high-resolution radio imaging. Methods: Archival data from radio observations using the European Very Long Baseline Interferometry Network (EVN) and Multi-Element Radio Linked Interferometer Network (MERLIN) interferometers are imaged. Sizes and flux densities are obtained by fitting Gaussian intensity distributions to the image. The average spectral index of the compact radio emission is estimated from measurements at 1.4 GHz and 5.0 GHz. Results: The nuclear structure of NGC 4418 visible with EVN and MERLIN consists of eight compact (<49 mas i.e. <8 pc) features spread within a region of 250 mas, i.e. 41 pc. We derive an inverted spectral index α ≥ 0.7 (Sν ∝ να) for the compact radio emission. Conclusions: Brightness temperatures >104.8 K indicate that these compact features cannot be HII-regions. The complex morphology and inverted spectrum of the eight detected compact features is evidence against the hypothesis that an AGN alone is powering the nucleus of NGC 4418. The compact features could be super star clusters with intense star formation, and their associated free-free absorption could then naturally explain both their inverted radio spectrum and the low radio-to-IR ratio of the nucleus. The required star formation area density is extreme, however, and close to the limit of what can be observed in a well-mixed thermal/non-thermal plasma produced by star formation, and is also close to the limit of what can be physically sustained.

  14. FORMATION OF DENSE MOLECULAR GAS AND STARS AT THE CIRCUMNUCLEAR STARBURST RING IN THE BARRED GALAXY NGC 7552

    SciTech Connect

    Pan, Hsi-An; Lim, Jeremy; Matsushita, Satoki; Wong, Tony; Ryder, Stuart

    2013-05-01

    We present millimeter molecular line complemented by optical observations, along with a reanalysis of archival centimeter H I and continuum data, to infer the global dynamics and determine where dense molecular gas and massive stars preferentially form in the circumnuclear starburst ring of the barred-spiral galaxy NGC 7552. We find diffuse molecular gas in a pair of dust lanes each running along the large-scale galactic bar, as well as in the circumnuclear starburst ring. We do not detect dense molecular gas in the dust lanes, but find such gas concentrated in two knots where the dust lanes make contact with the circumnuclear starburst ring. When convolved to the same angular resolution as the images in dense gas, the radio continuum emission of the circumnuclear starburst ring also exhibits two knots, each lying downstream of an adjacent knot in dense gas. The results agree qualitatively with the idea that massive stars form from dense gas at the contact points, where diffuse gas is channeled into the ring along the dust lanes, and later explode as supernovae downstream of the contact points. Based on the inferred rotation curve, however, the propagation time between the respective pairs of dense gas and centimeter continuum knots is about an order of magnitude shorter than the lifetimes of OB stars. We discuss possible reasons for this discrepancy, and conclude that either the initial mass function is top-heavy or massive stars in the ring do not form exclusively at the contact points where dense molecular gas is concentrated.

  15. Bifunctional star-burst amorphous molecular materials for OLEDs: achieving highly efficient solid-state luminescence and carrier transport induced by spontaneous molecular orientation.

    PubMed

    Kim, Jun Yun; Yasuda, Takuma; Yang, Yu Seok; Adachi, Chihaya

    2013-05-21

    Bifunctional star-burst amorphous molecular materials displaying both efficient solid-state luminescence and high hole-transport properties are developed in this study. A high external electroluminescence quantum efficiency up to 5.9% is attained in OLEDs employing the developed amorphous materials. It is revealed that the spontaneous horizontal orientation of these light-emitting molecules in their molecular-condensed states leads to a remarkable enhancement of the electroluminescence efficiencies and carrier-transport properties.

  16. Evolution of the ISM in main-sequence versus starburst galaxies: A motivation for molecular deep fields

    NASA Astrophysics Data System (ADS)

    Aravena, Manuel

    In the last decade, significant progress has been made to understand the evolution with redshift of star formation processes in galaxies. Its is now clear that the majority of galaxies at z<3 form a nearly linear correlation between their stellar mass and star formation rates and appear to create most of their stars in timescales of ~1 Gyr. At the highest luminosities, a significant fraction of galaxies deviate from this main-sequence, showing short duty cycles and thus producing most of their stars in a single burst of star formation within ~100 Myr, being likely driven by major merger activity. Despite the large luminosities of starbursts, main-sequence galaxies appear to dominate the star formation density of the Universe at its peak. While progress has been impressive, a number of questions are still unanswered. In this paper, I briefly review our current observational understanding of this main-sequence vs starburst galaxy paradigm, and address how future observations will help us to have better insights into the fundamental properties of the interstellar medium of these galaxies. Finally, I show recent attempts to conduct molecular deep field observations and the motivation to perform molecular deep field spectroscopy with the Atacama Large Millimeter/submillimeter Array.

  17. Models of the Molecular Interstellar Medium in Starbursts and AGN from z=0-6

    NASA Astrophysics Data System (ADS)

    Narayanan, Desika T.; Cox, T.; Chakrabarti, S.; Dave, R.; Di Matteo, T.; Kelly, B.; Hernquist, L.; Hopkins, P.; Kulesa, C.; Li, Y.; Robertson, B.; Walker, C.

    2006-12-01

    Recent pioneering CO observations of infrared luminous galaxies and AGN at high-z allow us to study coevolution of black hole growth and star formation in galaxies during the heydey of massive galaxy formation. However, little is known concerning the physical nature of these crucial galaxies, and the relationship between the central AGN, ISM, and host galaxy properties to the observed CO emission. In order to provide a framework for an interpretation of these observations, I investigate the nature of the CO emission in starburst galaxies and quasars by combining a 3D non-LTE radiative transfer code with cosmological and galaxy merger hydrodynamic simulations. Here, I highlight recent results from these simulations. Specifically, I will discuss the following: 1. The effect of black hole growth and starbursts on CO emission patterns; 2. The role of galactic winds on CO emission morphologies and line profiles; 3. The nature of CO emission in z 6 Quasars, and how we might use this to constrain models of primordial galaxy formation.

  18. Starburst galaxies

    NASA Technical Reports Server (NTRS)

    Weedman, Daniel W.

    1987-01-01

    The infrared properties of star-forming galaxies, primarily as determined by the Infrared Astronomy Satellite (IRAS), are compared to X-ray, optical, and radio properties. Luminosity functions are reviewed and combined with those derived from optically discovered samples using 487 Markarian galaxies with redshifts and published IRAS 60 micron fluxes, and 1074 such galaxies in the Center for Astrophysics redshift survey. It is found that the majority of infrared galaxies which could be detected are low luminosity sources already known from the optical samples, but non-infrared surveys have found only a very small fraction of the highest luminosity sources. Distributions of infrared to optical fluxes and available spectra indicate that the majority of IRAS-selected galaxies are starburst galaxies. Having a census of starburst galaxies and associated dust allow severl important global calculations. The source counts are predicted as a function of flux limits for both infrared and radio fluxes. These galaxies are found to be important radio sources at faint flux limits. Taking the integrated flux to z = 3 indicates that such galaxies are a significant component of the diffuse X-ray background, and could be the the dominant component depending on the nature of the X-ray spectra and source evolution.

  19. Molecular gas in low-metallicity starburst galaxies:. Scaling relations and the CO-to-H2 conversion factor

    NASA Astrophysics Data System (ADS)

    Amorín, R.; Muñoz-Tuñón, C.; Aguerri, J. A. L.; Planesas, P.

    2016-04-01

    Context. Tracing the molecular gas-phase in low-mass star-forming galaxies becomes extremely challenging due to significant UV photo-dissociation of CO molecules in their low-dust, low-metallicity ISM environments. Aims: We aim to study the molecular content and the star-formation efficiency of a representative sample of 21 blue compact dwarf galaxies (BCDs), previously characterized on the basis of their spectrophotometric properties. Methods: We present CO (1-0) and (2-1) observations conducted at the IRAM-30m telescope. These data are further supplemented with additional CO measurements and multiwavelength ancillary data from the literature. We explore correlations between the derived CO luminosities and several galaxy-averaged properties. Results: We detect CO emission in seven out of ten BCDs observed. For two galaxies these are the first CO detections reported so far. We find the molecular content traced by CO to be correlated with the stellar and Hi masses, star formation rate (SFR) tracers, the projected size of the starburst, and its gas-phase metallicity. BCDs appear to be systematically offset from the Schmidt-Kennicutt (SK) law, showing lower average gas surface densities for a given ΣSFR, and therefore showing extremely low (≲0.1 Gyr) H2 and H2 +Hi depletion timescales. The departure from the SK law is smaller when considering H2 +Hi rather than H2 only, and is larger for BCDs with lower metallicity and higher specific SFR. Thus, the molecular fraction (ΣH2/ ΣHI) and CO depletion timescale (ΣH2/ ΣSFR) of BCDs is found to be strongly correlated with metallicity. Using this, and assuming that the empirical correlation found between the specific SFR and galaxy-averaged H2 depletion timescale of more metal-rich galaxies extends to lower masses, we derive a metallicity-dependent CO-to-H2 conversion factor αCO,Z ∝ (Z/Z⊙)- y, with y = 1.5(±0.3)in qualitative agreement with previous determinations, dust-based measurements, and recent model

  20. The Molecular Clouds Fueling A 1/5 Solar Metallicity Starburst

    NASA Astrophysics Data System (ADS)

    Kepley, Amanda A.; Leroy, Adam K.; Johnson, Kelsey E.; Sandstrom, Karin; Chen, C.-H. Rosie

    2016-09-01

    Using the Atacama Large Millimeter/submillimeter Array, we have made the first high spatial and spectral resolution observations of the molecular gas and dust in the prototypical blue compact dwarf galaxy II Zw 40. The {}12{CO}(2-1) and {}12{CO}(3-2) emission is clumpy and distributed throughout the central star-forming region. Only one of eight molecular clouds has associated star formation. The continuum spectral energy distribution is dominated by free-free and synchrotron; at 870 μm, only 50% of the emission is from dust. We derive a CO-to-H2 conversion factor using several methods, including a new method that uses simple photodissocation models and resolved CO line intensity measurements to derive a relationship that uniquely predicts {α }{co} for a given metallicity. We find that the CO-to-H2 conversion factor is 4-35 times that of the Milky Way (18.1-150.5 {M}⊙ {({{K}}{km}{{{s}}}-1{{pc}}2)}-1). The star formation efficiency of the molecular gas is at least 10 times higher than that found in normal spiral galaxies, which is likely due to the burst-dominated star formation history of II Zw 40 rather than an intrinsically higher efficiency. The molecular clouds within II Zw 40 resemble those in other strongly interacting systems like the Antennae: overall they have high size-linewidth coefficients and molecular gas surface densities. These properties appear to be due to the high molecular gas surface densities produced in this merging system rather than to increased external pressure. Overall, these results paint a picture of II Zw 40 as a complex, rapidly evolving system whose molecular gas properties are dominated by the large-scale gas shocks from its ongoing merger.

  1. THE OPTICAL STRUCTURE OF THE STARBURST GALAXY M82. II. NEBULAR PROPERTIES OF THE DISK AND INNER WIND

    SciTech Connect

    Westmoquette, M. S.; Smith, L. J.; Konstantopoulos, I. S.; Gallagher, J. S.; Trancho, G.

    2009-12-01

    and wind sources provides an ideal environment for broad line emission, and explains the large observed broad/narrow-line flux ratios. We have examined in more detail the discrete outflow channel identified within the inner wind in Paper I. The channel appears as a coherent, expanding cylindrical structure of length >120 pc and width 35-50 pc. The walls maintain an approximately constant (but subsonic) expansion velocity of approx60 km s{sup -1}, and are defined by peaks and troughs in the densities of the different line components. We hypothesize that as the hot wind fluid flows down the channel cavity, it interacts with the cooler, denser walls of the channel and with entrained material within the flow to produce broad-line emission, while the walls themselves emit primarily the narrow lines. We use the channel to examine further the relationship between the narrow and broad component emitting gas within the inner wind. Within the starburst energy injection zone, we find that turbulent motions (as traced by the broad component) appear to play an increasing role with height. Finally, we have argued that a point-like knot identified in GMOS position 4, exhibiting blueshifted (by approx140 km s{sup -1}), broad (approx<350 km s{sup -1}) Halpha emission and enhanced [S II]/Halpha and [N II]/Halpha ratios, is most likely an ejected luminous blue variable-type object.

  2. Space Observations of Starburst Galaxies

    NASA Technical Reports Server (NTRS)

    Heckman, Timothy M.; Leitherer, Claus

    1997-01-01

    Led by JHU postdoc Gerhardt Meurer, we completed our analysis of far-UV HST FOC images of nine nearby starbursts. We have been able to delineate the structure of the regions in which the unusually vigorous star-formation is occurring (Meurer et al 1995). At 0.1 arcsec (2 to 20 pc) resolution, the starbursts are resolved into multiple clumps and bright star clusters distributed over a region several hundred pc to a few kpc in size. This suggests that compact sites of star-formation may propagate from place to place within a larger central gas reservoir over the duration of the burst. The UV and optical properties of these clusters suggest that they may correspond to newly 'minted' globular clusters. These clusters typically produce about 10% to 50% of the far-UV light, and are preferentially located in the heart of the starburst, where the background UV surface brightness is highest. Thus, massive star cluster (globular cluster?) formation is a fundamental part of the starburst phenomenon. This confirms and generalizes the results of Whitmore et al (1993). Our starburst images are also being compared to our recent analysis of the HST FOC image of R136 in the LMC (De Marchi et al 1993). We have also extended our results on the UV photometric structure of starbursts to star-forming galaxies in the early universe (Meurer et al 1997). We show that the most actively- star-forming galaxies at all redshifts seem to have approximately the same bolometric surface-brightness, and that the high redshift galaxies may be larger and more luminous versions of local starbursts.

  3. Starburst models of merging galaxies

    NASA Technical Reports Server (NTRS)

    Prestwich, Andrea H.

    1993-01-01

    In the past decade, infrared observations have shown that interacting and merging galaxies have higher luminosities than isolated systems, with the luminosities in mergers as high as 10(exp 12) solar luminosity. However, the origin of the luminosity found in mergers is controversial, with two main competing theories. The first is the starburst scenario. As two gas rich galaxies start to merge, cloud-cloud collisions induce fast shocks in the molecular gas. This gas cools, collapses, and fragments, producing a blast of star formation. The main rival to this theory is that the infrared luminosity is produced by a dust embedded active nucleus, the merger of two gas rich galaxies providing the 'fuel to feed the monster'. There has even been speculation that there is an evolutionary link between starbursts and active nuclei, and that possibly active galactic nuclei (AGN's) and QSO's were formed from a starburst. Assuming that the infrared luminosity in merging galaxies is due to star formation, there should be ionizing photons produced from the high mass stars, giving rise to recombination line emission. The objective is to use a simple starburst model to test the hypothesis that the extreme infrared luminosity of merging galaxies is due to a starburst.

  4. Starburst Channels

    NASA Technical Reports Server (NTRS)

    2007-01-01

    [figure removed for brevity, see original site] Figure 1

    Translucent carbon dioxide ice covers the polar regions of Mars seasonally. It is warmed and sublimates (evaporates) from below, and escaping gas carves a numerous channel morphologies.

    In this example (figure 1) the channels form a 'starburst' pattern, radiating out into feathery extensions. The center of the pattern is being buried with dust and new darker dust fans ring the outer edges. This may be an example of an expanding morphology, where new channels are formed as the older ones fill and are no longer efficiently channeling the subliming gas out.

    Observation Geometry Image PSP_003443_0980 was taken by the High Resolution Imaging Science Experiment (HiRISE) camera onboard the Mars Reconnaissance Orbiter spacecraft on 21-Apr-2007. The complete image is centered at -81.8 degrees latitude, 76.2 degrees East longitude. The range to the target site was 247.1 km (154.4 miles). At this distance the image scale is 24.7 cm/pixel (with 1 x 1 binning) so objects 74 cm across are resolved. The image shown here has been map-projected to 25 cm/pixel. The image was taken at a local Mars time of 04:52 PM and the scene is illuminated from the west with a solar incidence angle of 71 degrees, thus the sun was about 19 degrees above the horizon. At a solar longitude of 223.4 degrees, the season on Mars is Northern Autumn.

  5. Starbursts and their dynamics

    NASA Technical Reports Server (NTRS)

    Norman, Colin

    1987-01-01

    Detailed mechanisms associated with dynamical process occurring in starburst galaxies are considered including the role of bars, waves, mergers, sinking satellites, self gravitating gas and bulge heating. The current understanding of starburst galaxies both observational and theoretical is placed in the context of theories of galaxy formations, Hubble sequence evolution, starbursts and activity, and the nature of quasar absorption lines.

  6. Optical and Near Infrared studies of the photometric structure and starburst activity of Blue Compact Dwarf Galaxies

    NASA Astrophysics Data System (ADS)

    Noeske, K. G.

    2003-03-01

    This thesis describes three studies of Blue Compact Dwarf Galaxies (BCDs), focussed on the structure of the stellar components, the star-forming activity, and the environment of such galaxies, as well as the physical background of their morphological variety. The analysis of deep Near Infrared (NIR) image data of a significant sample of BCDs allows to study the evolved stellar low surface brightness (LSB) components of BCDs more precisely than previous studies at visible wavelengths. Azimuthally averaged radial surface brightness profiles (SBPs) show an exponential intensity distribution of the stellar LSB components at large galactocentric radii. This result, along with the derived exponential scale lengths which are systematically smaller than those of dwarf Irregular and dwarf Elliptical galaxies, agrees with previous optical studies. Towards smaller radii, however, the NIR data reveal an inwards-flattening of the SBPs of the stellar LSB components with respect to their outer exponential slopes in more than half of the BCDs under study. Such inwards-flattening exponential SBPs are frequent in dwarf Irregulars and dwarf Ellipticals, but were hitherto largely undiscovered in the stellar hosts of BCDs. The physical origin of such SBPs in dwarf galaxies is to date not understood. Empirical approaches to their systematization and quantitative investigation are discussed, along with the various implications of the discovery of such SBPs in many BCDs for the understanding of such galaxies. Based on the derived structural information on the stellar LSB components and the starburst components, the hypothesis is raised that below a certain threshold density of the stellar LSB component, of the order of 0.4 solar masses per cubic parsec, burst-like star formation does not occur in gas-rich dwarf galaxies. On this hypothesis, the observed relations between the structure of the stellar LSB components of BCDs and their luminosity can be reproduced, as well as the systematic

  7. EVOLVING STARBURST MODELING OF FAR-INFRARED/SUBMILLIMETER/MILLIMETER LINE EMISSION. II. APPLICATION TO M 82

    SciTech Connect

    Yao Lihong

    2009-11-01

    We present starburst models for far-infrared/sub-millimeter/millimeter line emission of molecular and atomic gas in an evolving starburst region, which is treated as an ensemble of noninteracting hot bubbles that drive spherical shells of swept-up gas into a surrounding uniform gas medium. These bubbles and shells are driven by stellar winds and supernovae within massive star clusters formed during an instantaneous starburst. The underlying stellar radiation from the evolving clusters affects the properties and structure of photodissociation regions (PDRs) in the shells, and hence the spectral energy distributions (SEDs) of the molecular and atomic line emission from these swept-up shells and the associated parent giant molecular clouds contain a signature of the stage of evolution of the starburst. The physical and chemical properties of the shells and their structure are computed using a simple, well-known similarity solution for the shell expansion, a stellar population synthesis code, and a time-dependent PDR chemistry model. The SEDs for several molecular and atomic lines ({sup 12}CO and its isotope {sup 13}CO, HCN, HCO{sup +}, C, O, and C{sup +}) are computed using a nonlocal thermodynamic equilibrium line radiative transfer model. By comparing our models with the available observed data of nearby infrared bright galaxies, especially M 82, we constrain the models and in the case of M 82, we provide estimates for the ages (5-6 Myr, 10 Myr) of recent starburst activity. We also derive a total H{sub 2} gas mass of approx(2-3.4) x 10{sup 8} M {sub sun} for the observed regions of the central 1 kpc starburst disk of M 82.

  8. Star Formation Quenching in High-redshift Large-scale Structure: Post-starburst Galaxies in the Cl 1604 Supercluster at z ~ 0.9

    NASA Astrophysics Data System (ADS)

    Wu, Po-Feng; Gal, Roy R.; Lemaux, Brian C.; Kocevski, Dale D.; Lubin, Lori M.; Rumbaugh, Nicholas; Squires, Gordon K.

    2014-09-01

    The Cl 1604 supercluster at z ~ 0.9 is one of the most extensively studied high-redshift large-scale structures, with more than 500 spectroscopically confirmed members. It consists of eight clusters and groups, with members numbering from a dozen to nearly a hundred, providing a broad range of environments for investigating the large-scale environmental effects on galaxy evolution. Here we examine the properties of 48 post-starburst galaxies in Cl 1604, comparing them to other galaxy populations in the same supercluster. Incorporating photometry from ground-based optical and near-infrared imaging, along with Spitzer mid-infrared observations, we derive stellar masses for all Cl 1604 members. The colors and stellar masses of the K+A galaxies support the idea that they are progenitors of red sequence galaxies. Their morphologies, residual star formation rates, and spatial distributions suggest that galaxy mergers may be the principal mechanism producing post-starburst galaxies. Interaction between galaxies and the dense intracluster medium (ICM) is also effective, but only in the cores of dynamically evolved clusters. The prevalence of post-starburst galaxies in clusters correlates with the dynamical state of the host cluster, as both galaxy mergers and the dense ICM produce post-starburst galaxies. We also investigate the incompleteness and contamination of K+A samples selected by means of Hδ and [O II] equivalent widths. K+A samples may be up to ~50% incomplete due to the presence of LINERs/Seyferts, and up to ~30% of K+A galaxies could have substantial star formation activity.

  9. Star formation quenching in high-redshift large-scale structure: post-starburst galaxies in the Cl 1604 supercluster at z ∼ 0.9

    SciTech Connect

    Wu, Po-Feng; Gal, Roy R.; Lemaux, Brian C.; Kocevski, Dale D.; Lubin, Lori M.; Rumbaugh, Nicholas; Squires, Gordon K.

    2014-09-01

    The Cl 1604 supercluster at z ∼ 0.9 is one of the most extensively studied high-redshift large-scale structures, with more than 500 spectroscopically confirmed members. It consists of eight clusters and groups, with members numbering from a dozen to nearly a hundred, providing a broad range of environments for investigating the large-scale environmental effects on galaxy evolution. Here we examine the properties of 48 post-starburst galaxies in Cl 1604, comparing them to other galaxy populations in the same supercluster. Incorporating photometry from ground-based optical and near-infrared imaging, along with Spitzer mid-infrared observations, we derive stellar masses for all Cl 1604 members. The colors and stellar masses of the K+A galaxies support the idea that they are progenitors of red sequence galaxies. Their morphologies, residual star formation rates, and spatial distributions suggest that galaxy mergers may be the principal mechanism producing post-starburst galaxies. Interaction between galaxies and the dense intracluster medium (ICM) is also effective, but only in the cores of dynamically evolved clusters. The prevalence of post-starburst galaxies in clusters correlates with the dynamical state of the host cluster, as both galaxy mergers and the dense ICM produce post-starburst galaxies. We also investigate the incompleteness and contamination of K+A samples selected by means of Hδ and [O II] equivalent widths. K+A samples may be up to ∼50% incomplete due to the presence of LINERs/Seyferts, and up to ∼30% of K+A galaxies could have substantial star formation activity.

  10. THE OPTICAL STRUCTURE OF THE STARBURST GALAXY M82. I. DYNAMICS OF THE DISK AND INNER-WIND

    SciTech Connect

    Westmoquette, M. S.; Smith, L. J.; Konstantopoulos, I. S.; Gallagher, J. S.; Trancho, G.

    2009-05-01

    We present Gemini-North GMOS-IFU observations of the central starburst clumps and inner wind of M82, together with WIYN DensePak IFU observations of the inner 2 x 0.9 kpc of the disk. These cover the emission lines of H{alpha}, [N II], [S II], and [S III] at a spectral resolution of 45-80 km s{sup -1}. The high signal-to-noise of the data is sufficient to accurately decompose the emission line profiles into multiple narrow components (FWHM {approx} 30-130 km s{sup -1}) superimposed on a broad (FWHM {approx} 150-350 km s{sup -1}) feature. This paper is the first of a series examining the optical structure of M82's disk and inner wind; here we focus on the ionized gaseous and stellar dynamics and present maps of the relevant emission line properties. Our observations show that ionized gas in the starburst core of M82 is dynamically complex with many overlapping expanding structures located at different radii. Localised line splitting of up to 100 km s{sup -1} in the narrow component is associated with expanding shells of compressed, cool, photoionized gas at the roots of the superwind outflow. We have been able to associate some of this inner-wind gas with a distinct outflow channel characterised by its dynamics and gas density patterns, and we discuss the consequences of this discovery in terms of the developing wind outflow. The broad optical emission line component is observed to become increasingly important moving outward along the outflow channel, and in general with increasing height above/below the plane. Following our recent work on the origins of this component, we associate it with turbulent gas in wind-clump interface layers and hence sites of mass loading, meaning that the turbulent mixing of cooler gas into the outflowing hot gas must become increasingly important with height, and provides powerful direct evidence for the existence of mass-loading over a large, spatially extended area reaching far into the inner wind. We discuss the consequences and

  11. Exploring the Vertical Structure of Nuclear Starburst Disks: A Possible Source of AGN Obscuration at Redshift ~ 1

    NASA Astrophysics Data System (ADS)

    Gohil, Raj; Ballantyne, David R.

    2017-01-01

    Nuclear starburst disks (NSDs) are star-forming regions that could be present at high redshift (z~1) in the vicinity of active galactic nuclei (AGNs). One dimensional analytical models by Thompson et al. (2005) show that, under certain conditions, these disks can be geometrically thick on parsec scales which make them a possible source for AGN obscuration. We construct a 2D model of NSDs where an iterative method is used to obtain vertical solutions for a given annulus. These solutions coherently satisfy the equations of energy balance, hydrostatic, radiative transfer, and the Toomre stability criteria. In comparison to 1D model, a more robust 2D calculation shows the higher scale-height at the outer part of a NSD, but predicts a lower expansion of an atmosphere at the parsec/sub-parsec scale. A total of 96 NSD models are computed under various physical conditions (black hole mass, size of a disk, and a gas fraction) in order to predict the column density distribution along a line of sight. Assuming a random distribution of input parameters, the statistics yield 59% of Type 1, 24% of Compton-thin (CTN), and 17% of Compton-thick (CTK) AGNs. The distribution of obscured AGNs fraction peaks near NH = 1023.5 cm-2. Depending on a viewing angle (θ) of a given NSD, the line of sight NH can vary from 1022 to 1028 cm-2. This supports the unification theory of AGNs as our results show an AGN can appear to be obscured by a CTK (NH > 1024 cm-2) or CTN (1022 cm-2< NH < 1024 cm-2) gas depending on a viewing angle. Using 2D structure, we show any θ is possible for CTN AGNs; however, the maximum allowed θ for CTK AGN is restricted to approximately 60 degrees.

  12. Evolution of Dense Gas with Starburst Age: When Star Formation Versus Dense Gas Relations Break Down

    NASA Astrophysics Data System (ADS)

    Meier, David S.; Turner, J. L.; Schinnerer, E.

    2011-05-01

    Dense gas correlates well with star formation on kpc scales. On smaller scales, motions of individual clouds become comparable to the 100 Myr ages of starbursts. One then expects the star formation rate vs. dense gas relations to break down on giant molecular cloud scales. We exploit this to study the evolutionary history of nuclear starburst in the nearby spiral, IC 342. Maps of the J=5-4 and 16-15 transitions of dense gas tracer HC3N at 20 pc resolution made with the VLA and the Plateau de Bure interferometer are presented. The 5-4 line of HC3N traces very dense gas in the cold phase, while the 16-15 transition traces warm, dense gas. These reveal changes in dense cloud structure on scales of 30 pc among clouds with star formation histories differing by only a few Myrs. HC3N emission does not correlate well with young star formation at these high spatial resolutions, but gas excitation does. The cold, dense gas extends well beyond the starburst region implying large amounts of dense quiescent gas not yet actively forming stars. Close to the starburst the high excitation combined with faint emission indicates that the immediate (30 pc) vicinity of the starburst lacks large masses of very dense gas and has high dense gas star formation efficiencies. The dense gas appears to be in pressure equilibrium with the starburst. We propose a scenario where the starburst is being caught in the act of dispersing or destroying the dense gas in the presence of the expanding HII region. This work is supported by the NSF through NRAO and grant AST-1009620.

  13. Dusty Starbursts within a z=3 Large Scale Structure revealed by ALMA

    NASA Astrophysics Data System (ADS)

    Umehata, Hideki

    The role of the large-scale structure is one of the most important theme in studying galaxy formation and evolution. However, it has been still mystery especially at z>2. On the basis of our ALMA 1.1 mm observations in a z ~ 3 protocluster field, it is suggested that submillimeter galaxies (SMGs) preferentially reside in the densest environment at z ~ 3. Furthermore we find a rich cluster of AGN-host SMGs at the core of the protocluster, combining with Chandra X-ray data. Our results indicate the vigorous star-formation and accelerated super massive black hole (SMBH) growth in the node of the cosmic web.

  14. NGC 1614: A Laboratory for Starburst Evolution

    NASA Technical Reports Server (NTRS)

    Alonso-Herrero, A.; Engelbracht, C. W.; Rieke, M. J.; Rieke, G. H.; Quillen, A. C.

    2000-01-01

    The modest extinction and reasonably face-on viewing geometry make the luminous infrared galaxy NGC 1614 an ideal laboratory for study of a powerful starburst. HST/NICMOS observations show: (1) deep CO stellar absorption, tracing a starburst nucleus about 45 pc in diameter; (2) surrounded by an approx. 600 pc diameter ring of supergiant H II regions revealed in Pa-alpha line emission; (3) lying within a molecular ring indicated by its extinction shadow in H - K; and (4) all at the center of a disturbed spiral galaxy. The luminosities of the giant H II regions in the ring axe extremely high, an order of magnitude brighter than 30 Doradus; very luminous H II regions, comparable with 30 Dor, are also found in the spiral arms of the galaxy. Luminous stellar clusters surround the nucleus and lie in the spiral arms, similar to clusters observed in other infrared luminous and ultraluminous galaxies. The star forming activity may have been initiated by a merger between a disk galaxy and a companion satellite, whose nucleus appears in projection about 300 pc to the NE of the nucleus of the primary galaxy. The relation of deep stellar CO bands to surrounding ionized gas ring to molecular gas indicates that the luminous starburst started in the nucleus and is propagating outward into the surrounding molecular ring. This hypothesis is supported by evolutionary starburst modeling that shows that the properties of NGC 1614 can be fitted with two short-lived bursts of star formation separated by 5 Myr (and by inference by a variety of models with a similar duration of star formation). The total dynamical mass of the starburst region of 1.3 x 10(exp 9) solar masses is mostly accounted for by the old pre-starburst stellar population. Although our starburst models use a modified Salpeter initial mass function (turning over near one solar mass), the tight mass budget suggests that the IMF may contain relatively more 10 - 30 solar masses stars and fewer low mass stars than the

  15. Uv Imaging of Circumnuclear Starburst Rings

    NASA Astrophysics Data System (ADS)

    Colina, Luis

    1996-07-01

    We propose to obtain F218W WFPC images of a well defined sample of nearby galaxies with face-on circumnuclear starburst rings, and covering different levels of activity from pure starbursts to Seyfert 1 {AGNs}. These high resolution images will allow to generate for the first time an homogeneous database with the UV properties of about 60 individual circumnuclear star-forming knots. The use of the database will allow for the first time a direct and quantitative determination of basic ultraviolet properties of individual nuclear/circumnuclear star-forming knots, and of the entire starburst ring, such as: {a} their size and structure, {b} their UV luminosity function and, {c} their contribution to the UV energy output in composite AGN+starburst galaxies. The database will help in our understanding of high redshift blue galaxies, thought to be star-forming galaxies, where the flux detected in optical filters corresponds to flux emitted at UV {1500-3000Angstrom} rest frame wavelengths. The requested UV images will be combined with ROSAT/HRI images to characterize for the first time the high energy end, i.e. UV to soft X-rays, of circumnuclear starburst rings.

  16. Neutral carbon and CO in 76 (U)LIRGs and starburst galaxy centers. A method to determine molecular gas properties in luminous galaxies

    NASA Astrophysics Data System (ADS)

    Israel, F. P.; Rosenberg, M. J. F.; van der Werf, P.

    2015-06-01

    In this paper we present fluxes in the [ CI ] lines of neutral carbon at the centers of some 76 galaxies with far-infrared luminosities ranging from 109 to 1012L⊙, as obtained with the Herschel Space Observatory and ground-based facilities, along with the line fluxes of the J = 7-6, J = 4-3, J = 2-112CO, and J = 2-113CO transitions. With this dataset, we determine the behavior of the observed lines with respect to each other and then investigate whether they can be used to characterize the molecular interstellar medium (ISM) of the parent galaxies in simple ways and how the molecular gas properties define the model results. In most starburst galaxies, the [ CI ] to 13CO line flux ratio is much higher than in Galactic star-forming regions, and it is correlated to the total far-infrared luminosity. The [ CI ] (1-0)/12CO (4-3), the [ CI ] (2-1)/12CO (7-6), and the [ CI ] (2-1)/(1-0) flux ratios are correlated, and they trace the excitation of the molecular gas. In the most luminous infrared galaxies (LIRGs), the ISM is fully dominated by dense (n( H2) = 104-105 cm-3) and moderately warm (Tkin ≈ 30 K) gas clouds that appear to have low [C°]/[CO] and [13CO]/[12CO] abundances. In less luminous galaxies, emission from gas clouds at lower densities becomes progressively more important, and a multiple-phase analysis is required to determine consistent physical characteristics. Neither the 12CO nor the [ CI ] velocity-integrated line fluxes are good predictors of molecular hydrogen column densities in individual galaxies. In particular, so-called X( [ CI ]) conversion factors are not superior to X( 12CO) factors. The methods and diagnostic diagrams outlined in this paper also provide a new and relatively straightforward means of deriving the physical characteristics of molecular gas in high-redshift galaxies up to z = 5, which are otherwise hard to determine.

  17. Understanding molecular structure from molecular mechanics.

    PubMed

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  18. Karl G. Jansky very large array observations of cold dust and molecular gas in starbursting quasar host galaxies at z ∼ 4.5

    SciTech Connect

    Wagg, J.; Carilli, C. L.; Lentati, L.; Maiolino, R.; Hills, R.; Aravena, M.; Cox, P.; McMahon, R. G.; Riechers, D.; Walter, F.; Andreani, P.; Wolfe, A.

    2014-03-10

    We present Karl G. Jansky Very Large Array (VLA) observations of 44 GHz continuum and CO J = 2-1 line emission in BRI 1202–0725 at z = 4.7 (a starburst galaxy and quasar pair) and BRI 1335–0417 at z = 4.4 (also hosting a quasar). With the full 8 GHz bandwidth capabilities of the upgraded VLA, we study the (rest-frame) 250 GHz thermal dust continuum emission for the first time along with the cold molecular gas traced by the low-J CO line emission. The measured CO J = 2-1 line luminosities of BRI 1202–0725 are L{sub CO}{sup ′}=(8.7±0.8)×10{sup 10} K km s{sup –1} pc{sup 2} and L{sub CO}{sup ′}=(6.0 ± 0.5)×10{sup 10} K km s{sup –1} pc{sup 2} for the submillimeter galaxy (SMG) and quasar, respectively, which are equal to previous measurements of the CO J = 5-4 line luminosities implying thermalized line emission, and we estimate a combined cold molecular gas mass of ∼9×10{sup 10} M {sub ☉}. In BRI 1335–0417 we measure L{sub CO}{sup ′}=(7.3±0.6)×10{sup 10} K km s{sup –1} pc{sup 2}. We detect continuum emission in the SMG BRI 1202–0725 North (S {sub 44} {sub GHz} = 51 ± 6 μJy), while the quasar is detected with S {sub 44} {sub GHz} = 24 ± 6 μJy and in BRI 1335–0417 we measure S {sub 44} {sub GHz} = 40 ± 7 μJy. Combining our continuum observations with previous data at (rest-frame) far-infrared and centimeter wavelengths, we fit three-component models in order to estimate the star formation rates. This spectral energy distribution fitting suggests that the dominant contribution to the observed 44 GHz continuum is thermal dust emission, while either thermal free-free or synchrotron emission contributes less than 30%.

  19. Starburst Triggering and Environmental Effects

    NASA Astrophysics Data System (ADS)

    Combes, F.

    Introduction Stability of a two-fluid medium Mechanisms to trigger starbursts Dynamical mechanisms: non-axisymmetry and torques Angular momentum transfer for the stellar component Angular momentum transfer for the gas component feedback and self-regulation Fueling activity by bars The inner Lindblad resonance Nuclear disks and nuclear bars Bar destruction through mass concentration Gas-dominated central disk Environmental effects Numerical codes and gas modelling Star-formation processes Formation of large complexes Lessons from mergers Gas morphology in mergers Tidal tails and dark matter Ring galaxies Groups and clusters Rich clusters Galaxy evolution Evolution along the hubble sequence Fragility of disks Evolution at high redshift Gas and dark matter Hot gas in rich clusters Self-gravity and fractal structure of the ISM Conclusion

  20. The Scaling Relations and Star Formation Laws of Mini-starburst Complexes

    NASA Astrophysics Data System (ADS)

    Nguyen-Luong, Quang; Nguyen, Hans V. V.; Motte, Fredérique; Schneider, Nicola; Fujii, Michiko; Louvet, Fabien; Hill, Tracey; Sanhueza, Patricio; Chibueze, James O.; Didelon, Pierre

    2016-12-01

    The scaling relations and star formation laws for molecular cloud complexes (MCCs) in the Milky Way are investigated. MCCs are mostly large (R > 50 pc), massive (˜106 {\\text{}}{M}⊙ ) gravitationally unbound cloud structures. We compare their masses {M}{gas}, mass surface densities {{{Σ }}}{M{gas}}, radii R, velocity dispersions σ, star formation rates (SFRs), and SFR densities {{{Σ }}}{SFR} with those of structures ranging from cores, clumps, and giant molecular clouds, to MCCs, and galaxies, spanning eight orders of magnitudes in size and 13 orders of magnitudes in mass. This results in the following universal relations:σ ˜ {R}0.5,{M}{gas}˜ {R}2,{{{Σ }}}{SFR}˜ {{{Σ }}}{M{gas}}1.5, {SFR}˜ {{M}{gas}}0.9, {and} {SFR}˜ {σ }2.7. Variations in the slopes and coefficients of these relations are found at individual scales, signifying different physics acting at different scales. Additionally, there are breaks at the MCC scale in the σ {--}R relation and between starburst and normal star-forming objects in the {SFR}{--}{M}{gas} and {{{Σ }}}{SFR}-{{{Σ }}}{{{M}}{gas}} relations. Therefore, we propose to use the Schmidt-Kennicutt diagram to distinguish starburst from normal star-forming structures by applying a {{{Σ }}}{M{gas}} threshold of ˜100 {\\text{}}{M}⊙ pc-2 and a {{{Σ }}}{SFR} threshold of 1 {\\text{}}{M}⊙ yr-1 kpc-2. Mini-starburst complexes are gravitationally unbound MCCs that have enhanced {{{Σ }}}{SFR} (>1 {\\text{}}{M}⊙ yr-1 kpc-2), probably caused by dynamic events such as radiation pressure, colliding flows, or spiral arm gravitational instability. Because of dynamical evolution, gravitational boundedness does not play a significant role in regulating the star formation activity of MCCs, especially the mini-starburst complexes, which leads to the dynamical formation of massive stars and clusters. We emphasize the importance of understanding mini-starbursts in investigating the physics of starburst galaxies.

  1. Feeding IC 342: The nuclear spiral of a starburst galaxy

    NASA Technical Reports Server (NTRS)

    Levine, D.; Turner, J. L.; Hurt, Robert L.

    1993-01-01

    IC 342 is a large nearby (1.8 Mpc, Turner and Hurt, 1991, hereafter T&H) spiral galaxy undergoing a moderate nuclear starburst. T&H have previously mapped the inner arcminute in CO-13(1-0) using the Owens Valley Millimeter Interferometer and found evidence that the nuclear molecular gas takes the form of spiral arms in a density wave pattern. They suggest that radial streaming along the arms may channel gas from the exterior of the galaxy into the nucleus, feeding the starburst. We have mapped the CO-12(1-0) emission of the inner 2 kpc of IC 342 at 2.8 inch resolution using the Owens Valley Radio Observatory (OVRO) Millimeter Interferometer. The greater sensitivity of CO-12 observations has allowed us to trace the spiral pattern out to a total extent of greater than 1 kpc. The CO-12 observations extend considerably the structure observed at CO-13 and offer further evidence that a spiral density wave may extend from the disk into the nucleus of IC 342.

  2. X-Ray Properties of the Central kpc of AGN and Starbursts: The Latest News from Chandra

    NASA Astrophysics Data System (ADS)

    Weaver, Kimberly A.

    The X-ray properties of 15 nearby (v < 3000 kms-1) galaxies that possess AGN and/or starbursts are discussed. Two-thirds have nuclear extended emission on scales from ~0.5 to ~1.5 kpc that is either clearly associated with a nuclear outflow or morphologically resembles an outflow. Galaxies that are AGN-dominated tend to have linear structures while starburst-dominated galaxies tend to have plume-like structures. Significant X-ray absorption is present in the starburst regions, indicating that a circumnuclear starburst is sufficient to block an AGN at optical wavelengths. Galaxies with starburst activity possess more X-ray point sources within their central kpc than non-starbursts. Many of these sources are more luminous than typical X-ray binaries. The Chandra results are discussed in terms of the starburst--AGN connection, a revised unified model for AGN, and possible evolutionary scenarios.

  3. Dynamic molecular graphs: "hopping" structures.

    PubMed

    Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

    2014-05-05

    This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions.

  4. (12)CO (3-2) & (1-0) emission line observations of nearby starburst galaxy nuclei

    NASA Technical Reports Server (NTRS)

    Devereux, Nicholas; Taniguchi, Yoshiaki; Sanders, D. B.; Nakai, N.; Young, J. S.

    1994-01-01

    New measurements of the (12)CO (1-0) and (12)CO (3-2) line emission are presented for the nuclei of seven nearby starburst galaxies selected from a complete sample of 21 nearby starburst galaxies for which the nuclear star formation rates are measured to be comparable to the archetype starburst galaxies M82 and NGC 253. The new observations capitalize on the coincidence between the beam size of the 45 m Nobeyama telescope at 115 GHz and that of the 15 m James Clerk Maxwell Telescope at 345 GHz to measure the value of the (12)CO (3-2)/(1-0) emission line ratio in a 15 sec (less than or equal to 2.5 kpc) diameter region centered on the nuclear starburst. In principle, the (12)CO (3-2)/(1-0) emission line ratio provides a measure of temperature and optical depth for the (12)CO gas. The error weighted mean value of the (12)CO (3-2)/(1-0) emission line ratio measured for the seven starburst galaxy nuclei is -0.64 +/- 0.06. The (12)CO (3-2)/(1-0) emission line ratio measured for the starburst galaxy nuclei is significantly higher than the average value measured for molecular gas in the disk of the Galaxy, implying warmer temperatures for the molecular gas in starburst galaxy nuclei. On the other hand, the (12)CO (3-2)/(1-0) emission line ratio measured for the starburst galaxy nuclei is not as high as would be expected if the molecular gas were hot, greater than 20 K, and optically thin, tau much less than 1. The total mass of molecular gas contained within the central 1.2-2.8 kpc diameter region of the starburst galaxy nuclei ranges from 10(exp 8) to 10(exp 9) solar mass. While substantial, the molecular gas mass represents only a small percentage, approximately 9%-16%, of the dynamical mass in the same region.

  5. Exceptionally bright, compact starburst nucleus

    SciTech Connect

    Margon, B.; Anderson, S.F.; Mateo, M.; Fich, M.; Massey, P.

    1988-11-01

    Observations are reported of a remarkably bright (V about 13) starburst nucleus, 0833 + 652, which has been detected at radio, infrared, optical, ultraviolet, and X-ray wavelengths. Despite an observed flux at each of these wavelengths which is comparable to that of NGC 7714, often considered the 'prototypical' example of the starburst phenomenon, 0833 + 652 appears to be a previously uncataloged object. Its ease of detectability throughout the electromagnetic spectrum should make it useful for a variety of problems in the study of compact emission-line galaxies. 30 references.

  6. Toward Gas Chemistry in Low Metallicity Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Meier, David S.; Anderson, Crystal N.; Turner, Jean; Ott, Juergen; Beck, Sara C.

    2017-01-01

    Dense gas, which is intimately connected with star formation, is key to understanding star formation. Though challenging to study, dense gas in low metallicity starbursts is important given these system's often extreme star formation and their potential implications for high redshift analogs. High spatial resolution (~50 pc) ALMA observations of several key probes of gas chemistry, including HCN(1-0), HCO+(1-0), CS(2-1), CCH(1-0;3/2-1/2) and SiO(2-1), towards the nearby super star-cluster (SSC) forming, sub-solar metallicity galaxy NGC 5253 are discussed. Dense gas is observed to be extended well beyond the current compact starburst, reaching into the apparently infalling molecular streamer. The faintness of HCN, the standard dense gas tracer, is extreme both in an absolute sense relative to high metallicity starbursts of a similar intensity and in a relative sense, with the HCO+/HCN ratio being one of the most elevated observed. UV-irradiated molecular gas, traced by CCH, is also extended over the mapped region, not being strongly correlated with the SSC. Despite the accretion of molecular gas from the halo and the intense burst of star formation, chemical signatures of shocked gas, traced by SiO (and HNCO), are not obvious. By placing NGC 5253 in context with other local starbursts, like 30 Doradus in the Large Magellanic Clouds and the high metallicity proto-typical starburst NGC 253, it is suggested that a combination of gas excitation and abundance changes associated with the sub solar metallicity may explain these anomalous dense gas properties.

  7. DENSE MOLECULAR GAS EXCITATION IN NUCLEAR STARBURSTS AT HIGH REDSHIFT: HCN, HNC, AND HCO{sup +}(J = 6{yields}5) EMISSION IN THE z = 3.91 QUASAR HOST OF APM 08279+5255

    SciTech Connect

    Riechers, Dominik A.; Weiss, Axel; Walter, Fabian; Wagg, Jeff

    2010-12-10

    We report the detection of surprisingly strong HCN(J = 6{yields}5), HNC(J = 6{yields}5), and HCO{sup +}(J = 6{yields}5) emission in the host galaxy of the z = 3.91 quasar APM 08279+5255 through observations with the Combined Array for Research in Millimeter-wave Astronomy. HCN, HNC, and HCO{sup +} are typically used as star formation indicators, tracing dense molecular hydrogen gas [n(H{sub 2}) >10{sup 5} cm{sup -3}] within star-forming molecular clouds. However, the strength of their respective line emission in the J = 6{yields}5 transitions in APM 08279+5255 is extremely high, suggesting that they are excited by another mechanism besides collisions in the dense molecular gas phase alone. We derive J = 6{yields}5 line luminosities of L'{sub HCN} = (4.9 {+-} 0.6), L'{sub HNC} = (2.4 {+-} 0.7), and L{sup '}{sub HCO}{sup +}= (3.0{+-}0.6)x10{sup 10} {mu}{sup -1}{sub L} K km s{sup -1} pc{sup 2} (where {mu}{sub L} is the lensing magnification factor), corresponding to L' ratios of {approx}0.23-0.46 relative to CO(J = 1{yields}0). Such high line ratios would be unusual even in the respective ground-state (J = 1{yields}0) transitions, and indicate exceptional, collisionally and radiatively driven excitation conditions in the dense, star-forming molecular gas in APM 08279+5255. Through an expansion of our previous modeling of the HCN line excitation in this source, we show that the high rotational line fluxes are caused by substantial infrared pumping at moderate opacities in a {approx}220 K warm gas and dust component. This implies that standard M{sub dense}/L' conversion factors would substantially overpredict the dense molecular gas mass M{sub dense}. We also find a HCN(J = 6{yields}5)/HCN(J = 5{yields}4) L' ratio greater than 1 (1.36 {+-} 0.31)-however, our models show that the excitation is likely not 'super-thermal', but that the high line ratio is due to a rising optical depth between both transitions. These findings are consistent with the picture that the bulk of

  8. Initial conditions of formation of starburst clusters: constraints from stellar dynamics

    NASA Astrophysics Data System (ADS)

    Banerjee, Sambaran; Kroupa, Pavel

    2015-08-01

    Recent high resolution observations of dense regions of molecular clouds and massive gaseous clumps with instruments like Herschel and ALMA have revealed intricate and filamentary overdensity structures in them. Such progenitors of massive starburst clusters are in contrast with smooth, centrally-pronounced profiles of the latter. In this work, we intend to constrain massive, substructured stellar distributions that would evolve to cluster-like profiles at very young ages (~Myr), as seen in starburst clusters. Taking the well observed NGC3603 Young Cluster (NYC) as an example, we compute the infall and final merger of filament-like compact (0.1-0.3 pc) subclusters, totalling 10000 M_sun, from a range of spatial scales and modes of sub-clustering, using direct N-body calculations. These calculations infer an allowable span of approx. 2.5 pc from which the subclusters can fall in a gas potential and merge to form a single centrally-dense structure in near dynamical equilibrium, within the young age of NYC (1-2 Myr). However, these merged clusters are too compact and centrally overdense compared to typical young clusters. Our N-body calculations, beginning from such compact initial conditions, show that even stellar wind and supernova mass loss, dynamical heating from retaining black holes, external tidal field and heating due to tight O-star binaries together cannot expand these clusters to their observed sizes, even in 100 Myr. Hence an explosive gas dispersal phase seems essential for forming starburst and other young clusters observed in the Milky Way and in the Local Group which can expand the clusters to their observed sizes and concentrations; including that for NYC with approx. 30% clump star formation efficiency. However, some observed massive but highly extended (>10 pc) , >10 Myr old clusters better fit a slow (several Myr timescale) gas dispersal from parsec-scale initial profiles, which can be the future of embedded systems like W3 Main.

  9. Detection of the 158 Micrometers[CII] Transition at z=1.3: Evidence for a Galaxy-Wide Starburst

    NASA Technical Reports Server (NTRS)

    Hailey-Dunsheath, S.; Nikola, T.; Oberst, T. E.; Parshley, S. C.; Benford, D. J.; Staguhn, J. G.; Tucker, C. E.

    2010-01-01

    We report the detection of 158 micron [C II] fine-structure line emission from MIPS J142824.0+352619, a hyperluminous ( L(sub IR) approximates 10(exp 13) L (sub solar)) starburst galaxy at z = 1.3. The line is bright, corresponding to a fraction L(sub [Cu II] L(sub Fir) approximates 2 x 10(exp -3) of the far-IR (FIR) continuum. The [C II], CO, and FIR continuum emission may be modeled as arising from photodissociation regions (PDRs) that have a characteristic gas density of n approximates 10(exp 4.2) /cm(exp 3) , and that are illuminated by a far-UV radiation field approximately 10(exp 3.2) times more intense than the local interstellar radiation field. The mass in these PDRs accounts for approximately half of the molecular gas mass in this galaxy. The L(sub [CII])/L(sub FIR) ratio is higher than observed in local ultralummous infrared galaxies or in the few high-redshift QSOs detected in [C II], but the L(sub [CII])/L(sub FIR) and L(sub CO)/L(sub FIR) ratios are similar to the values seen in nearby starburst galaxies. This suggests that MIPS J142824.0+352619 is a scaled-up version of a starburst nucleus, with the burst extended over several kiloparsecs.

  10. Hard Gamma Ray Emission from the Starburst Galaxy NGC 253

    NASA Technical Reports Server (NTRS)

    Jackson, James M.; Marscher, Alan M.

    1996-01-01

    We have completed the study to search for hard gamma ray emission from the starburst galaxy NGC 253. Since supernovae are thought to provide the hard gamma ray emission from the Milky Way, starburst galaxies, with their extraordinarily high supernova rates, are prime targets to search for hard gamma ray emission. We conducted a careful search for hard gamma ray emission from NGC 253 using the archival data from the EGRET experiment aboard the CGRO. Because this starburst galaxy happens to lie near the South Galactic Pole, the Galactic gamma ray background is minimal. We found no significant hard gamma ray signal toward NGC 253, although a marginal signal of about 1.5 sigma was found. Because of the low Galactic background, we obtained a very sensitive upper limit to the emission of greater than 100 MeV gamma-rays of 8 x 10(exp -8) photons/sq cm s. Since we expected to detect hard gamma ray emission, we investigated the theory of gamma ray production in a dense molecular medium. We used a leaky-box model to simulate diffusive transport in a starburst region. Since starburst galaxies have high infrared radiation fields, we included the effects of self-Compton scattering, which are usually ignored. By modelling the expected gamma-ray and synchrotron spectra from NGC 253, we find that roughly 5 - 15% of the energy from supernovae is transferred to cosmic rays in the starburst. This result is consistent with supernova acceleration models, and is somewhat larger than the value derived for the Galaxy (3 - 10%). Our calculations match the EGRET and radio data very well with a supernova rate of 0.08/ yr, a magnetic field B approx. greater than 5 x 10(exp -5) G, a density n approx. less than 100/sq cm, a photon density U(sub ph) approx. 200 eV/sq cm, and an escape time scale tau(sub 0) approx. less than 10 Myr. The models also suggest that NGC 253 should be detectable with only a factor of 2 - 3 improvement in sensitivity. Our results are consistent with the standard picture

  11. Observations and starburst models of NGC 520

    NASA Astrophysics Data System (ADS)

    Bernloehr, K.

    1993-03-01

    CCD images in B, V, R, I, and in the light of the emission line H-alpha have been obtained as well as 11 long-slit spectra. Color maps and radial velocity maps show that the irregular galaxy NGC 520 consists of two interacting components which are very likely on a bound orbit and are going to merge. The more massive component is seen almost edge-on and has a warp of about 27. Its nuclear region coincides with the radio continuum source and shows an active starburst which, at visual wavelengths, is almost hidden behind the dust lane of the disk. The spectra of the less massive, although visually brighter, second component northwest of the main component indicate a post-starburst some 2-3 x 10 exp 8 years old. Numerical starburst models, which were fitted to the data of both components, indicate that both starbursts might be deficient in low-mass stars.

  12. Shaken, not stirred - the BCG starburst recipe

    NASA Astrophysics Data System (ADS)

    Bergvall, N.; Zackrisson, E.; Östlin, G.; Laurikainen, E.

    2003-06-01

    True starbursts are dramatic events that lead to a rapid exhaustion of the available gas supply and generate massive outflows of gas, strongly influencing the evolution of galaxies. To understand the early phases of galaxy evolution it is therefore crucial to identify the mechanisms that rule this process. In this study we present observations that show that interactions are inefficient to generate starbursts and that mergers appear to be a more plausible mechanism.

  13. The gas content in starburst galaxies

    NASA Technical Reports Server (NTRS)

    Mirabel, I. F.; Sanders, D. B.

    1987-01-01

    The results from two large and homogeneous surveys, one in H I, the other in CO, are used for a statistical review of the gaseous properties of bright infrared galaxies. A constant ratio between the thermal FIR radiation and nonthermal radio emission is a universal property of star formation in spiral galaxies. The current rate of star formation in starburst galaxies is found to be 3-20 times larger than in the Milky Way. Galaxies with the higher FIR luminosities and warmer dust, have the larger mass fractions of molecular to atomic interstellar gas, and in some instances, striking deficiencies of neutral hydrogen are found. A statistical blueshift of the optical systemic velocities relative to the radio systemic velocities, may be due to an outward motion of the optical line-emitting gas. From the high rates of star formation, and from the short times required for the depletion of the interstellar gas, it is concluded that the most luminous infrared galaxies represent a brief but important phase in the evolution of some galaxies, when two galaxies merge changing substantially their overall properties.

  14. Environments of Starburst Galaxies Diagnosed with the NVO

    NASA Astrophysics Data System (ADS)

    de Mello, D.; Sosey, M.

    2004-12-01

    We will present the analysis of the environment of starburst galaxies using the National Virtual Observatory. We have matched the sample of starburst galaxies by Wu et al. (2002) with the Sloan Digital Sky Survey (SDSS) and searched for companions in their neighborhood. We found: (i) three starbursts with no companion, (ii) four starbursts with clear interaction and in the process of merging, (iii) nine starbursts with at least one companion. We have compared the starburst sample with the sample of isolated galaxies by Karachentseva (1986) and with the SDSS merging galaxies by Allam et al. (2004). Using color selection criteria from the known sample of starburst galaxies, we have built a database of starburst candidates from the SDSS catalogue. This allowed us to do a more statistical comparison of starburst galaxies, their neighborhoods and possible environmental effects on their evolution. Direct links to the SDSS images and related photometry are provided for easy reference.

  15. X-ray Properties of the Central kpc of AGN and Starbursts: The Latest News from Chandra

    NASA Technical Reports Server (NTRS)

    Weaver, Kimberly A.; White, Nicholas E. (Technical Monitor)

    2001-01-01

    The X-ray properties of 15 nearby (v less than 3,000 km/s) galaxies that possess AGN (active galactic nuclei) and/or starbursts are discussed. Two-thirds have nuclear extended emission on scales from approx. 0.5 to approx. 1.5 kpc that is either clearly associated with a nuclear outflow or morphologically resembles an outflow. Galaxies that are AGN-dominated tend to have linear structures while starburst-dominated galaxies tend to have plume-like structures. Significant X-ray absorption is present in the starburst regions, indicating that a circumnuclear starburst is sufficient to block an AGN at optical wavelengths. Galaxies with starburst activity possess more X-ray point sources within their central kpc than non-starbursts. Many of these sources are more luminous than typical X-ray binaries. The Chandra results are discussed in terms of the starburst-AGN connection, a revised unified model for AGN, and possible evolutionary scenarios.

  16. From starburst to quiescence: testing active galactic nucleus feedback in rapidly quenching post-starburst galaxies

    SciTech Connect

    Yesuf, Hassen M.; Faber, S. M.; Trump, Jonathan R.; Koo, David C.; Fang, Jerome J.; Liu, F. S.; Wild, Vivienne; Hayward, Christopher C.

    2014-09-10

    Post-starbursts are galaxies in transition from the blue cloud to the red sequence. Although they are rare today, integrated over time they may be an important pathway to the red sequence. This work uses Sloan Digital Sky Survey, the Galaxy Evolution Explorer, and Wide-field Infrared Survey Explorer observations to identify the evolutionary sequence from starbursts to fully quenched post-starbursts (QPSBs) in the narrow mass range log M(M {sub ☉}) = 10.3-10.7, and identifies 'transiting' post-starbursts (TPSBs) which are intermediate between these two populations. In this mass range, ∼0.3% of galaxies are starbursts, ∼0.1% are QPSBs, and ∼0.5% are the transiting types in between. The TPSBs have stellar properties that are predicted for fast-quenching starbursts and morphological characteristics that are already typical of early-type galaxies. The active galactic nucleus (AGN) fraction, as estimated from optical line ratios, of these post-starbursts is about three times higher (≳ 36% ± 8%) than that of normal star forming galaxies of the same mass, but there is a significant delay between the starburst phase and the peak of nuclear optical AGN activity (median age difference of ≳ 200 ± 100 Myr), in agreement with previous studies. The time delay is inferred by comparing the broadband near-NUV-to-optical photometry with stellar population synthesis models. We also find that starbursts and post-starbursts are significantly more dust obscured than normal star forming galaxies in the same mass range. About 20% of the starbursts and 15% of the TPSBs can be classified as 'dust-obscured galaxies' (DOGs), with a near-UV-to-mid-IR flux ratio of ≳ 900, while only 0.8% of normal galaxies are DOGs. The time delay between the starburst phase and AGN activity suggests that AGNs do not play a primary role in the original quenching of starbursts but may be responsible for quenching later low-level star formation by removing gas and dust during the post-starburst

  17. DETECTION OF THE 158 {mu}m [C II] TRANSITION AT z = 1.3: EVIDENCE FOR A GALAXY-WIDE STARBURST

    SciTech Connect

    Hailey-Dunsheath, S.; Nikola, T.; Stacey, G. J.; Oberst, T. E.; Parshley, S. C.; Benford, D. J.; Staguhn, J. G.; Tucker, C. E.

    2010-05-01

    We report the detection of 158 {mu}m [C II] fine-structure line emission from MIPS J142824.0+352619, a hyperluminous (L {sub IR} {approx} 10{sup 13} L {sub sun}) starburst galaxy at z = 1.3. The line is bright, corresponding to a fraction L {sub [CII]}/L {sub FIR} {approx} 2 x 10{sup -3} of the far-IR (FIR) continuum. The [C II], CO, and FIR continuum emission may be modeled as arising from photodissociation regions (PDRs) that have a characteristic gas density of n {approx} 10{sup 4.2} cm{sup -3}, and that are illuminated by a far-UV radiation field {approx}10{sup 3.2} times more intense than the local interstellar radiation field. The mass in these PDRs accounts for approximately half of the molecular gas mass in this galaxy. The L {sub [CII]}/L {sub FIR} ratio is higher than observed in local ultraluminous infrared galaxies or in the few high-redshift QSOs detected in [C II], but the L {sub [CII]}/L {sub FIR} and L {sub CO}/L {sub FIR} ratios are similar to the values seen in nearby starburst galaxies. This suggests that MIPS J142824.0+352619 is a scaled-up version of a starburst nucleus, with the burst extended over several kiloparsecs.

  18. Molecular modeling of nucleic acid structure

    PubMed Central

    Galindo-Murillo, Rodrigo; Bergonzo, Christina

    2013-01-01

    This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure. PMID:18428873

  19. The Molecular Structure of Penicillin

    NASA Astrophysics Data System (ADS)

    Bentley, Ronald

    2004-10-01

    The chemical structure of penicillin was determined between 1942 and 1945 under conditions of secrecy established by the U.S. and U.K. governments. The evidence was not published in the open literature but as a monograph. This complex volume does not present a structure proof that can be readily comprehended by a student. In this article, a basic structural proof for the penicillin molecule is provided, emphasizing the chemical work. The stereochemistry of penicillin is also described, and various rearrangements are considered on the basis of the accepted β-lactam structure.

  20. Lyman alpha emission in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Kunth, Daniel

    1999-07-01

    We propose to perform a deep study of Ly-alpha emission and destruction in 3 star-forming galaxies. These objects have been already observed with the GHRS and exhibit a variety of situations, with Ly-alpha showing P Cyg profiles, secondary emissions or even a deep damped absorption line with no emission. They also span a range of intrinsic properties: IZW18 is a gas-rich, metal deficient dust free dwarf galaxy, Haro 2 has a simple morphology while IRAS 08339+6517 is a luminous IRAS starburst galaxy with more dust and complex Ly- alpha profile. The use of STIS will allow for the first time to study the geometrical/kinematical configuration of the ionized and neutral gas across the galaxies nuclear regions and pin point the effects of porosity and the kinematical structure of the ISM, that may play the key roles {in addition to dust} in the detectability of the line. This study will have important impact for cosmology since Ly-alpha emitters are nowaday found at high-re dshift. We strongly emphasize that since Ly-alpha is primarely a diagnostic of the ISM, a full understanding of how the ISM and Ly-alpha are related is a necessary step before we can hope to correlate Ly-alpha to the cosmic star-formation rate. Our results will be interpreted against the model of superbubble evolution developed with G. Tenorio Tagle.

  1. Chandra Images the Seething Cauldron of Starburst Galaxy

    NASA Astrophysics Data System (ADS)

    2000-01-01

    NASA's Chandra X-ray Observatory has imaged the core of the nearest starburst galaxy, Messier 82 (M82). The observatory has revealed a seething cauldron of exploding stars, neutron stars, black holes, 100 million degree gas, and a powerful galactic wind. The discovery will be presented by a team of scientists from Carnegie Mellon University, Pittsburgh, Penn., Pennsylvania State University, University Park, and the University of Michigan, Ann Arbor, on January 14 at the 195th national meeting of the American Astronomical Society. "In the disk of our Milky Way Galaxy, stars form and die in a relatively calm fashion like burning embers in a campfire," said Richard Griffiths, Professor of Astrophysics at Carnegie Mellon University. "But in a starburst galaxy, star birth and death are more like explosions in a fireworks factory." Short-lived massive stars in a starburst galaxy produce supernova explosions, which heat the interstellar gas to millions of degrees, and leave behind neutron stars and black holes. These explosions emit light in the X rays rather than in visible light. Because the superhot components inside starburst galaxies are complex and sometimes confusing, astronomers need an X-ray-detecting telescope with the highest focusing power (spatial resolution) to clearly discriminate the various structures. "NASA's Chandra X-ray Observatory is the perfect tool for studying starburst galaxies since it has the critical combination of high-resolution optics and good sensitivity to penetrating X rays," said Gordon Garmire, the Evan Pugh Professor of Astronomy and Astrophysics at Pennsylvania State University, and head of the team that conceived and built Chandra's Advanced CCD Imaging Spectrograph (ACIS) X-ray camera, which acquired the data. Many intricate structures missed by earlier satellite observatories are now visible in the ACIS image, including more than twenty powerful X-ray binary systems that contain a normal star in a close orbit around a neutron star

  2. Extended HCN and HCO+ Emission in the Starburst Galaxy M82

    NASA Astrophysics Data System (ADS)

    Salas, P.; Galaz, G.; Salter, D.; Herrera-Camus, R.; Bolatto, A. D.; Kepley, A.

    2014-12-01

    We mapped 3 mm continuum and line emission from the starburst galaxy M82 using the Combined Array for Research in Millimeter-wave Astronomy. We targeted the HCN, HCO+, HNC, CS, and HC3N lines, but here we focus on the HCN and HCO+ emission. The map covers a field of 1.'2 with an ≈5'' resolution. The HCN and HCO+ observations are short spacings corrected. The molecular gas in M82 had been previously found to be distributed in a molecular disk, coincident with the central starburst, and a galactic scale outflow which originates in the central starburst. With the new short spacings-corrected maps we derive some of the properties of the dense molecular gas in the base of the outflow. From the HCN and HCO+ J = (1-0) line emission, and under the assumptions of the gas being optically thin and in local thermodynamic equilibrium, we place lower limits on the amount of dense molecular gas in the base of the outflow. The lower limits are 7 × 106 M ⊙ and 21 × 106 M ⊙, or >~ 2% of the total molecular mass in the outflow. The kinematics and spatial distribution of the dense gas outside the central starburst suggests that it is being expelled through chimneys. Assuming a constant outflow velocity, the derived outflow rate of dense molecular gas is >=0.3 M ⊙ yr-1, which would lower the starburst lifetime by >=5%. The energy required to expel this mass of dense gas is (1-10) × 1052 erg.

  3. EXTENDED HCN AND HCO{sup +} EMISSION IN THE STARBURST GALAXY M82

    SciTech Connect

    Salas, P.; Galaz, G.; Salter, D.; Herrera-Camus, R.; Bolatto, A. D.; Kepley, A.

    2014-12-20

    We mapped 3 mm continuum and line emission from the starburst galaxy M82 using the Combined Array for Research in Millimeter-wave Astronomy. We targeted the HCN, HCO{sup +}, HNC, CS, and HC{sub 3}N lines, but here we focus on the HCN and HCO{sup +} emission. The map covers a field of 1.'2 with an ≈5'' resolution. The HCN and HCO{sup +} observations are short spacings corrected. The molecular gas in M82 had been previously found to be distributed in a molecular disk, coincident with the central starburst, and a galactic scale outflow which originates in the central starburst. With the new short spacings-corrected maps we derive some of the properties of the dense molecular gas in the base of the outflow. From the HCN and HCO{sup +} J = (1-0) line emission, and under the assumptions of the gas being optically thin and in local thermodynamic equilibrium, we place lower limits on the amount of dense molecular gas in the base of the outflow. The lower limits are 7 × 10{sup 6} M {sub ☉} and 21 × 10{sup 6} M {sub ☉}, or ≳ 2% of the total molecular mass in the outflow. The kinematics and spatial distribution of the dense gas outside the central starburst suggests that it is being expelled through chimneys. Assuming a constant outflow velocity, the derived outflow rate of dense molecular gas is ≥0.3 M {sub ☉} yr{sup –1}, which would lower the starburst lifetime by ≥5%. The energy required to expel this mass of dense gas is (1-10) × 10{sup 52} erg.

  4. The Molecular Structure of Penicillin

    ERIC Educational Resources Information Center

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  5. Structured Molecular Gas Reveals Galactic Spiral Arms

    NASA Astrophysics Data System (ADS)

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory 13CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  6. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    SciTech Connect

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  7. THE NATURE OF STARBURSTS. I. THE STAR FORMATION HISTORIES OF EIGHTEEN NEARBY STARBURST DWARF GALAXIES

    SciTech Connect

    McQuinn, Kristen B. W.; Skillman, Evan D.; Stark, David; Weisz, Daniel; Cannon, John M.; Dalcanton, Julianne; Williams, Benjamin; Dolphin, Andrew; Hidalgo-RodrIguez, Sebastian

    2010-09-20

    We use archival Hubble Space Telescope observations of resolved stellar populations to derive the star formation histories (SFHs) of 18 nearby starburst dwarf galaxies. In this first paper, we present the observations, color-magnitude diagrams (CMDs), and the SFHs of the 18 starburst galaxies, based on a homogeneous approach to the data reduction, differential extinction, and treatment of photometric completeness. We adopt a star formation rate (SFR) threshold normalized to the average SFR of the individual system as a metric for classifying starbursts in SFHs derived from resolved stellar populations. This choice facilitates finding not only the currently bursting galaxies but also 'fossil' bursts increasing the sample size of starburst galaxies in the nearby (D < 8 Mpc) universe. Thirteen of the eighteen galaxies are experiencing ongoing bursts and five galaxies show fossil bursts. From our reconstructed SFHs, it is evident that the elevated SFRs of a burst are sustained for hundreds of Myr with variations on small timescales. A long >100 Myr temporal baseline is thus fundamental to any starburst definition or identification method. The longer lived bursts rule out rapid 'self-quenching' of starbursts on global scales. The bursting galaxies' gas consumption timescales are shorter than the Hubble time for all but one galaxy confirming the short-lived nature of starbursts based on fuel limitations. Additionally, we find that the strength of the H{alpha} emission usually correlates with the CMD-based SFR during the last 4-10 Myr. However, in four cases, the H{alpha} emission is significantly less than what is expected for models of starbursts; the discrepancy is due to the SFR changing on timescales of a few Myr. The inherently short timescale of the H{alpha} emission limits identifying galaxies as starbursts based on the current characteristics which may or may not be representative of the recent SFH of a galaxy.

  8. Young star clusters in circumnuclear starburst rings

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Ma, Chao; Jia, Siyao; Ho, Luis C.; Anders, Peter

    2017-03-01

    We analyse the cluster luminosity functions (CLFs) of the youngest star clusters in two galaxies exhibiting prominent circumnuclear starburst rings. We focus specifically on NGC 1512 and NGC 6951, for which we have access to Hα data that allow us to unambiguously identify the youngest sample clusters. To place our results on a firm statistical footing, we first explore in detail a number of important technical issues affecting the process from converting the observational data into the spectral energy distributions of the objects in our final catalogues. The CLFs of the young clusters in both galaxies exhibit approximate power-law behaviour down to the 90 per cent observational completeness limits, thus showing that star cluster formation in the violent environments of starburst rings appears to proceed similarly as that elsewhere in the local Universe. We discuss this result in the context of the density of the interstellar medium in our starburst-ring galaxies.

  9. GIANT Hα NEBULA SURROUNDING THE STARBURST MERGER NGC 6240

    SciTech Connect

    Yoshida, Michitoshi; Yagi, Masafumi; Komiyama, Yutaka; Kashikawa, Nobunari; Ohyama, Youichi; Okamura, Sadanori

    2016-03-20

    We revealed the detailed structure of a vastly extended Hα-emitting nebula (“Hα nebula”) surrounding the starburst/merging galaxy NGC 6240 by deep narrow-band imaging observations with the Subaru Suprime-Cam. The extent of the nebula is ∼90 kpc in diameter and the total Hα luminosity amounts to L{sub Hα} ≈ 1.6 × 10{sup 42} erg s{sup −1}. The volume filling factor and the mass of the warm ionized gas are ∼10{sup −4}–10{sup −5} and ∼5 × 10{sup 8} M{sub ⊙}, respectively. The nebula has a complicated structure, which includes numerous filaments, loops, bubbles, and knots. We found that there is a tight spatial correlation between the Hα nebula and the extended soft-X-ray-emitting gas, both in large and small scales. The overall morphology of the nebula is dominated by filamentary structures radially extending from the center of the galaxy. A large-scale bipolar bubble extends along the minor axis of the main stellar disk. The morphology strongly suggests that the nebula was formed by intense outflows—superwinds—driven by starbursts. We also found three bright knots embedded in a looped filament of ionized gas that show head-tail morphologies in both emission-line and continuum, suggesting close interactions between the outflows and star-forming regions. Based on the morphology and surface brightness distribution of the Hα nebula, we propose the scenario that three major episodes of starburst/superwind activities, which were initiated ∼10{sup 2} Myr ago, formed the extended ionized gas nebula of NGC 6240.

  10. Giant Hα Nebula Surrounding the Starburst Merger NGC 6240

    NASA Astrophysics Data System (ADS)

    Yoshida, Michitoshi; Yagi, Masafumi; Ohyama, Youichi; Komiyama, Yutaka; Kashikawa, Nobunari; Tanaka, Hisashi; Okamura, Sadanori

    2016-03-01

    We revealed the detailed structure of a vastly extended Hα-emitting nebula (“Hα nebula”) surrounding the starburst/merging galaxy NGC 6240 by deep narrow-band imaging observations with the Subaru Suprime-Cam. The extent of the nebula is ˜90 kpc in diameter and the total Hα luminosity amounts to LHα ≈ 1.6 × 1042 erg s-1. The volume filling factor and the mass of the warm ionized gas are ˜10-4-10-5 and ˜5 × 108 M⊙, respectively. The nebula has a complicated structure, which includes numerous filaments, loops, bubbles, and knots. We found that there is a tight spatial correlation between the Hα nebula and the extended soft-X-ray-emitting gas, both in large and small scales. The overall morphology of the nebula is dominated by filamentary structures radially extending from the center of the galaxy. A large-scale bipolar bubble extends along the minor axis of the main stellar disk. The morphology strongly suggests that the nebula was formed by intense outflows—superwinds—driven by starbursts. We also found three bright knots embedded in a looped filament of ionized gas that show head-tail morphologies in both emission-line and continuum, suggesting close interactions between the outflows and star-forming regions. Based on the morphology and surface brightness distribution of the Hα nebula, we propose the scenario that three major episodes of starburst/superwind activities, which were initiated ˜102 Myr ago, formed the extended ionized gas nebula of NGC 6240. Based on data collected at the Subaru Telescope, which is operated by the National Astronomical Observatory of Japan.

  11. Detection of the 158 Micrometers[CII] Transition at z=1.3: Evidence for a Galaxy-Wide Starburst

    NASA Technical Reports Server (NTRS)

    Hailey-Dunsheath, S.; Nikola, T.; Stacey, G. J.; Oberst, T. E.; Parshley, S. C.; Benford, D. J.; Staguhn, J. G.; Tucker, C. E.

    2010-01-01

    We report the detection of 158 micrometer [C II] fine-structure line emission from MIPS J 142824.0+3526l9, a hyperluminous (L(sub IR) approx. 10(exp 13) Solar Luminosity starburst galaxy at z = 1.3. The line is bright, corresponding to a fraction L[C II]/L(sub FIR) approx. equals 2 x l0(exp -3) of the far-IR(FIR) continuum. The [C II], CO, and FIR continuum emission may be modeled as arising from photodissociation regions (PDRs) that have a characteristic gas density of n approx. 10(exp 4.2)/cu cm., and that are illuminated by a far-UV radiation field approx. 10(exp 3.2) times more intense than the local interstellar radiation field. The mass in these PDRs accounts for approximately half of the molecular gas mass in this galaxy. The L[C II]/L(sub F1R) ratio is higher than observed in local ultraluminous infrared galaxies or in the few high-redshift QSOs detected in [C II], but the L[CII]/L(sub FIR) and L(sub CO)/L(sub FIR) ratios are similar to the values seen in nearby starburst galaxies

  12. What powers the starburst activity of NGC 1068? Star-driven gravitational instabilities caught in the act

    NASA Astrophysics Data System (ADS)

    Romeo, Alessandro B.; Fathi, Kambiz

    2016-08-01

    We explore the role that gravitational instability plays in NGC 1068, a nearby Seyfert galaxy that exhibits unusually vigorous starburst activity. For this purpose, we use the Romeo-Falstad disc instability diagnostics and data from the BIMA Survey of Nearby Galaxies, the Sloan Digital Sky Survey and the Spectrographic Areal Unit for Research on Optical Nebulae. Our analysis illustrates that NGC 1068 is a gravitationally unstable `monster'. Its starburst disc is subject to unusually powerful instabilities. Several processes, including feedback from the active galactic nucleus and starburst activity, try to quench such instabilities from inside out by depressing the surface density of molecular gas across the central kpc, but they do not succeed. Gravitational instability `wins' because it is driven by the stars via their much higher surface density. In this process, stars and molecular gas are strongly coupled, and it is such a coupling that ultimately triggers local gravitational collapse/fragmentation in the molecular gas.

  13. Structure and kinematics of molecular jets

    NASA Astrophysics Data System (ADS)

    Snell, R. L.

    1986-04-01

    Observational studies of the structure and kinematics of the supersonic molecular gas in star-forming regions are reviewed. These studies have suggested that the bulk of the high-velocity gas may be ambient-cloud material swept up by a collimated stellar wind. The actual structures of these outflows, however, are poorly understood. One source that may provide a better understanding of molecular outflows is that in the nearby dark cloud LDN 1551. New observations of this outflow are presented and discussed in context of the models proposed by Snell and Schloerb.

  14. On the emergence of molecular structure

    SciTech Connect

    Matyus, Edit; Reiher, Markus; Hutter, Juerg; Mueller-Herold, Ulrich

    2011-05-15

    The structure of (a{sup {+-}},a{sup {+-}},b{sup {+-}})-type Coulombic systems is characterized by the effective ground-state density of the a-type particles, computed via nonrelativistic quantum mechanics without introduction of the Born-Oppenheimer approximation. A structural transition is observed when varying the relative mass of the a- and b-type particles, e.g., between atomic H{sup -} and molecular H{sub 2}{sup +}. The particle-density profile indicates a molecular-type behavior for the positronium ion, Ps{sup -}.

  15. Molecular docking to ensembles of protein structures.

    PubMed

    Knegtel, R M; Kuntz, I D; Oshiro, C M

    1997-02-21

    Until recently, applications of molecular docking assumed that the macromolecular receptor exists in a single, rigid conformation. However, structural studies involving different ligands bound to the same target biomolecule frequently reveal modest but significant conformational changes in the target. In this paper, two related methods for molecular docking are described that utilize information on conformational variability from ensembles of experimental receptor structures. One method combines the information into an "energy-weighted average" of the interaction energy between a ligand and each receptor structure. The other method performs the averaging on a structural level, producing a "geometry-weighted average" of the inter-molecular force field score used in DOCK 3.5. Both methods have been applied in docking small molecules to ensembles of crystal and solution structures, and we show that experimentally determined binding orientations and computed energies of known ligands can be reproduced accurately. The use of composite grids, when conformationally different protein structures are available, yields an improvement in computational speed for database searches in proportion to the number of structures.

  16. [Ne V] Emission in Optically Classified Starbursts

    NASA Astrophysics Data System (ADS)

    Abel, N. P.; Satyapal, S.

    2008-05-01

    Detecting active galactic nuclei (AGNs) in galaxies dominated by powerful nuclear star formation and extinction effects poses a unique challenge. Due to the longer wavelength emission and the ionization potential of Ne4+, infrared [Ne V] emission lines are thought to be excellent AGN diagnostics. However, stellar evolution models predict that Wolf-Rayet stars in young stellar clusters emit significant numbers of photons capable of creating Ne4+. Recent observations of [Ne V] emission in optically classified starburst galaxies require us to investigate whether [Ne V] can arise from star formation activity and not an AGN. In this work, we calculate the optical and IR spectrum of gas exposed to a young starburst and AGN SED. We find: (1) a range of parameters where [Ne V] emission can be explained solely by star formation and (2) a range of relative AGN to starburst luminosities that reproduces the [Ne V] observations, yet leaves the optical spectrum looking like a starburst. We also find that infrared emission-line diagnostics are much more sensitive to the AGNs than optical diagnostics, particularly for weak AGNs. We apply our model to the optically classified, yet [Ne V] emitting, starburst galaxy NGC 3621. We find, when taking the infrared and optical spectrum into account, ~30%-50% of the galaxy's total luminosity is due to an AGN. Our calculations show that [Ne V] emission is almost always the result of AGN activity. The models presented in this work can be used to determine the AGN contribution to a galaxy's power output.

  17. Students' Understanding of Molecular Structure Representations

    ERIC Educational Resources Information Center

    Ferk, Vesna; Vrtacnik, Margareta; Blejec, Andrej; Gril, Alenka

    2003-01-01

    The purpose of the investigation was to determine the meanings attached by students to the different kinds of molecular structure representations used in chemistry teaching. The students (n = 124) were from primary (aged 13-14 years) and secondary (aged 17-18 years) schools and a university (aged 21-25 years). A computerised "Chemical…

  18. Molecular Association and Structure of Hydrogen Peroxide.

    ERIC Educational Resources Information Center

    Giguere, Paul A.

    1983-01-01

    The statement is sometimes made in textbooks that liquid hydrogen peroxide is more strongly associated than water, evidenced by its higher boiling point and greater heat of vaporization. Discusses these and an additional factor (the nearly double molecular mass of the peroxide), focusing on hydrogen bonds and structure of the molecule. (JN)

  19. Structural effects in molecular metal halides.

    PubMed

    Hargittai, Magdolna

    2009-03-17

    Metal halides are a relatively large class of inorganic compounds that participate in many industrial processes, from halogen metallurgy to the production of semiconductors. Because most metal halides are ionic crystals at ambient conditions, the term "molecular metal halides" usually refers to vapor-phase species. These gas-phase molecules have a special place in basic research because they exhibit the widest range of chemical bonding from the purely ionic to mostly covalent bonding through to weakly interacting systems. Although our focus is basic research, knowledge of the structural and thermodynamic properties of gas-phase metal halides is also important in industrial processes. In this Account, we review our most recent work on metal halide molecular structures. Our studies are based on electron diffraction and vibrational spectroscopy, and increasingly, we have augmented our experimental work with quantum chemical computations. Using both experimental and computational techniques has enabled us to determine intriguing structural effects with better accuracy than using either technique alone. We loosely group our discussion based on structural effects including "floppiness", relativistic effects, vibronic interactions, and finally, undiscovered molecules with computational thermodynamic stability. Floppiness, or serious "nonrigidity", is a typical characteristic of metal halides and makes their study challenging for both experimentalists and theoreticians. Relativistic effects are mostly responsible for the unique structure of gold and mercury halides. These molecules have shorter-than-expected bonds and often have unusual geometrical configurations. The gold monohalide and mercury dihalide dimers and the molecular-type crystal structure of HgCl(2) are examples. We also examined spin-orbit coupling and the possible effect of the 4f electrons on the structure of lanthanide trihalides. Unexpectedly, we found that the geometry of their dimers depends on the f

  20. 2004 Reversible Associations in Structure & Molecular Biology

    SciTech Connect

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  1. Environments of Starburst Galaxies Diagnosed with the NVO

    NASA Astrophysics Data System (ADS)

    Nieto-Santisteban, M. A.; Sosey, M.; de Mello, D.

    2004-12-01

    We present an analysis of the environment of starburst galaxies using the National Virtual Observatory. We have matched the sample of starburst galaxies by Wu et al. (2002) with the Sloan Digital Sky Survey (SDSS) and searched for companions in their neighborhood. We also have compared the starburst sample with the sample of isolated galaxies by Karachentseva (1986) and with the SDSS merging galaxies by Allam et al. (2004). Using color selection criteria from the known sample of starburst galaxies, we have built a database of starburst candidates from the SDSS catalogue. This allowed us to do a more statistical comparison of starburst galaxies, their neighborhoods and possible environmental effects on their evolution. We see the NVO environment as an extrememly useful tool for astronomical research. As such, this poster also details the effective ways in which we were able to access both the SDSS catalogue as well as other internet resources, encorporating the entire project into a very useful internet website.

  2. Compact starbursts in ultraluminous infrared galaxies

    NASA Technical Reports Server (NTRS)

    Condon, J. J.; Huang, Z.-P.; Yin, Q. F.; Thuan, T. X.

    1991-01-01

    The 40 ultraluminous galaxies in the IRAS Bright Galaxy Sample of sources stronger than S = 5.24 Jy at lambda = 60 microns were mapped with approximately 0.25 arcsec resolution at 8.44 GHz. Twenty-five contain diffuse radio sources obeying the FIR-radio correlation; these are almost certainly starburst galaxies. Fourteen other galaxies have nearly blackbody FIR spectra with color temperatures between 60 and 80 K so their (unmeasured) FIR angular sizes must exceed approximately 0.25 arcsec, yet they contain compact (but usually resolved) radio sources smaller than this limit. The unique radio and FIR properties of these galaxies can be modeled by ultraluminous nuclear starbursts so dense that they 67 are optically thick to free-free absorption at about 1.49 GHz and dust absorption at about 25 microns. Only one galaxy (UGC 08058 = Mrk 231) is a dominated by a variable radio source too compact to be an ultraluminous starburst; it must be powered by a 'monster'.

  3. THE IMPACT OF STARBURSTS ON THE CIRCUMGALACTIC MEDIUM

    SciTech Connect

    Borthakur, Sanchayeeta; Heckman, Timothy; Strickland, David; Wild, Vivienne; Schiminovich, David

    2013-05-01

    We present a study exploring the impact of a starburst on the properties of the surrounding circumgalactic medium (CGM): gas located beyond the galaxy's stellar body and extending out to the virial radius ({approx}200 kpc). We obtained ultraviolet spectroscopic data from the Cosmic Origins Spectrograph (COS) probing the CGM of 20 low-redshift foreground galaxies using background QSOs. Our sample consists of starburst and control galaxies. The latter comprises normal star-forming and passive galaxies with similar stellar masses and impact parameters as the starbursts. We used optical spectra from the Sloan Digital Sky Survey to estimate the properties of the starbursts, inferring average ages of {approx}200 Myr and burst fractions involving {approx}10% of their stellar mass. The COS data reveal highly ionized gas traced by C IV in 80%(4/5) of the starburst and in 17%(2/12) of the control sample. The two control galaxies with C IV absorbers differed from the four starbursts in showing multiple low-ionization transitions and strong saturated Ly{alpha} lines. They therefore appear to be physically different systems. We show that the C IV absorbers in the starburst CGM represent a significant baryon repository. The high detection rate of this highly ionized material in the starbursts suggests that starburst-driven winds can affect the CGM out to radii as large as 200 kpc. This is plausible given the inferred properties of the starbursts and the known properties of starburst-driven winds. This would represent the first direct observational evidence of local starbursts impacting the bulk of their gaseous halos, and as such provides new evidence of the importance of this kind of feedback in the evolution of galaxies.

  4. THE NATURE OF STARBURSTS. II. THE DURATION OF STARBURSTS IN DWARF GALAXIES

    SciTech Connect

    McQuinn, Kristen B. W.; Skillman, Evan D.; Stark, David; Weisz, Daniel; Cannon, John M.; Dalcanton, Julianne; Williams, Benjamin; Dolphin, Andrew; Hidalgo-RodrIguez, Sebastian

    2010-11-20

    The starburst phenomenon can shape the evolution of the host galaxy and the surrounding intergalactic medium. The extent of the evolutionary impact is partly determined by the duration of the starburst, which has a direct correlation with both the amount of stellar feedback and the development of galactic winds, particularly for smaller mass dwarf systems. We measure the duration of starbursts in twenty nearby, ongoing, and 'fossil' starbursts in dwarf galaxies based on the recent star formation histories derived from resolved stellar population data obtained with the Hubble Space Telescope. Contrary to the shorter times of 3-10 Myr often cited, the starburst durations we measure range from 450to650 Myr in fifteen of the dwarf galaxies and up to 1.3 Gyr in four galaxies; these longer durations are comparable to or longer than the dynamical timescales for each system. The same feedback from massive stars that may quench the flickering star formation does not disrupt the overall burst event in our sample of galaxies. While five galaxies present fossil bursts, fifteen galaxies show ongoing bursts and thus the final durations may be longer than we report here for these systems. One galaxy shows a burst that has been ongoing for only 20 Myr; we are likely seeing the beginning of a burst event in this system. Using the duration of the starbursts, we calculate that the bursts deposited 10{sup 53.9}-10{sup 57.2} erg of energy into the interstellar medium through stellar winds and supernovae, and produced 3%-26% of the host galaxy's mass.

  5. Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure

    DTIC Science & Technology

    2014-08-30

    properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to

  6. FAR-INFRARED PROPERTIES OF SPITZER-SELECTED LUMINOUS STARBURSTS

    SciTech Connect

    Kovacs, A.; Omont, A.; Fiolet, N.; Beelen, A.; Dole, H.; Lagache, G.; Lonsdale, C.; Polletta, M.; Greve, T. R.; Borys, C.; Dowell, C. D.; Bell, T. A.; Cox, P.; De Breuck, C.; Farrah, D.; Menten, K. M.; Owen, F.

    2010-07-01

    We present SHARC-2 350 {mu}m data on 20 luminous z {approx} 2 starbursts with S{sub 1.2{sub mm}} > 2 mJy from the Spitzer-selected samples of Lonsdale et al. and Fiolet et al. All the sources were detected, with S{sub 350{sub {mu}m}} > 25 mJy for 18 of them. With the data, we determine precise dust temperatures and luminosities for these galaxies using both single-temperature fits and models with power-law mass-temperature distributions. We derive appropriate formulae to use when optical depths are non-negligible. Our models provide an excellent fit to the 6 {mu}m-2 mm measurements of local starbursts. We find characteristic single-component temperatures T{sub 1} {approx_equal} 35.5 {+-} 2.2 K and integrated infrared (IR) luminosities around 10{sup 12.9{+-}0.1} L{sub sun} for the SWIRE-selected sources. Molecular gas masses are estimated at {approx_equal}4 x 10{sup 10} M{sub sun}, assuming {kappa}{sub 850{sub {mu}m}} = 0.15 m{sup 2} kg{sup -1} and a submillimeter-selected galaxy (SMG)-like gas-to-dust mass ratio. The best-fit models imply {approx_gt}2 kpc emission scales. We also note a tight correlation between rest-frame 1.4 GHz radio and IR luminosities confirming star formation as the predominant power source. The far-IR properties of our sample are indistinguishable from the purely submillimeter-selected populations from current surveys. We therefore conclude that our original selection criteria, based on mid-IR colors and 24 {mu}m flux densities, provides an effective means for the study of SMGs at z {approx} 1.5-2.5.

  7. Anatomy of Starbursts in Extragalactic Giant HII Regions

    NASA Astrophysics Data System (ADS)

    Evans, Jessica Marie; Chu, You-Hua

    2013-06-01

    Extragalactic giant HII regions (EGHRs) are sites of active, concentrated star formation, and thus provide excellent labs to analyze the starburst phenomenon. Although they have been known for a long time, ground-based observations cannot resolve the physical structures and stellar content of EGHRs. The high resolution and sensitivity of Hubble Space Telescope (HST) are ideal for detailed studies of EGHRs. We have searched the Hubble Legacy Archives (HLA) and found > 10 nearby galaxies, within 20 Mpc, with H-α and continuum images. To determine the best methods for analyzing these data, we perform an in-depth analysis of the EGHRs in M51. M51 is a face-on spiral galaxy 8.4 Mpc away, with well-resolved multi-wavelength observations in the HLA. We sample the 20 most luminous HII regions in M51, and the top three in several other galaxies, many of which are bonafide EGHRs with an H-α luminosity > 10^{39} ergs s^{-1}. We use the H-α image to study the distribution and physical structure of the gas in each HII region and determine its H-α luminosity and required ionizing flux. We use the continuum images to determine whether super stellar clusters (SSCs) are found in these HII regions, and use photometric measurements to determine the mass and age spread of the resolved stellar population. These are then compared with the interstellar structures. The results help us provide the groundwork for studying EGHRs in multiple galaxies and elucidate the starburst phenomenon by investigating questions such as: What role does environment play in the formation of EGHRs? How do EGHRs evolve? How does star formation proceed in an EGHR?

  8. The formation of NGC 3603 young starburst cluster: `prompt' hierarchical assembly or monolithic starburst?

    NASA Astrophysics Data System (ADS)

    Banerjee, Sambaran; Kroupa, Pavel

    2015-02-01

    The formation of very young massive clusters or `starburst' clusters is currently one of the most widely debated topic in astronomy. The classical notion dictates that a star cluster is formed in situ in a dense molecular gas clump. The stellar radiative and mechanical feedback to the residual gas energizes the latter until it escapes the system. The newly born gas-free young cluster eventually readjusts with the corresponding mass-loss. Based on the observed substructured morphologies of many young stellar associations, it is alternatively suggested that even the smooth-profiled massive clusters are also assembled from migrating less massive subclusters. A very young (age ≈ 1 Myr), massive (>104 M⊙) star cluster like the Galactic NGC 3603 young cluster (HD 97950) is an appropriate testbed for distinguishing between the above `monolithic' and `hierarchical' formation scenarios. A recent study by Banerjee & Kroupa demonstrates that the monolithic scenario remarkably reproduces the HD 97950 cluster. In particular, its shape, internal motion and the mass distribution of stars are found to follow naturally and consistently from a single model calculation undergoing ≈70 per cent by mass gas dispersal. In this work, we explore the possibility of the formation of the above cluster via hierarchical assembly of subclusters. These subclusters are initially distributed over a wide range of spatial volumes and have various modes of subclustering in both absence and presence of a background gas potential. Unlike the above monolithic initial system that reproduces HD 97950 very well, the same is found to be prohibitive with hierarchical assembly alone (with/without a gas potential). Only those systems which assemble promptly into a single cluster (in ≲1 Myr) from a close separation (all within ≲2 pc) could match the observed density profile of HD 97950 after a similar gas removal. These results therefore suggest that the NGC 3603 young cluster has formed essentially

  9. Starburst Driven Superbubbles Radiating to 10 K

    NASA Astrophysics Data System (ADS)

    Tanner, Ryan; Cecil, Gerald; Heitsch, Fabian

    2016-01-01

    Starburst driven superbubbles can produce large scale galactic outflows. Whether any given starburst can create an outflow depends on several variables including the rate at which energy and mass are injected into the interstellar medium (ISM), the radiative cooling prescription used, and the overall density distribution of the ISM. We investigate the effect that two different temperature floors in our radiative cooling prescription have on wind kinematics and content. We find that cooling to 10 K instead of to 104 K increases the mass fraction of cold neutral and hot X-ray gas in the galactic wind while halving that in warm Hα. For sufficiently powerful starbursts our cooling prescription does not affect the terminal velocity of gas within the superbubble. Filaments embedded in the hot galactic wind contain warm and cold gas which moves slower than the surrounding wind, with the coldest gas hardly moving with respect to the galaxy. Optically bright filaments form at the edge of merging superbubbles and if anchored to a star forming complex will persist and grow to > 400 pc in length. These filaments are the main source of warm and cold gas being transported into the galactic halo. Using synthetic absorption profiles we measure the velocity of the warm and hot gas phases and find vwarm ∝ vhot0.5. We also find that vhot ∝ SFR0.5, which implies vwarm ∝ SFR0.25. Warm and cold gas embedded in the galactic wind show asymmetric absorption profiles consistent with observations and theoretical predictions. These asymmetries can be used to infer the kinematics of the filaments and associated dense cores.

  10. High resolution sub-millimetre mapping of starburst galaxies: Comparison with CO emission

    NASA Technical Reports Server (NTRS)

    Smith, P. A.; Brand, P. W. J. L.; Puxley, Phil J.; Mountain, C. M.; Nakai, Naomasa

    1990-01-01

    Researchers present first results from a program of submillimeter continuum mapping of starburst galaxies, and comparison of their dust and CO emission. This project was prompted by surprising results from the first target, the nearby starburst M82, which shows in the dust continuum a morphology quite unlike that of its CO emission, in contrast to what might be expected if both CO and dust are accurately tracing the molecular hydrogen. Possible explanations for this striking difference are discussed. In the light of these results, the program has been extended to include sub-mm mapping of the nearby, vigorously star forming spirals, M83 and Maffei 2. The latter were also observed extensively in CO, in order to study excitation conditions in its central regions. The James Clerk Maxwell Telescope was used in these studies.

  11. An infrared study of starbursts in the interacting galaxy pair Arp 299 (NGC 3690+IC 694)

    SciTech Connect

    Nakagawa, Takao; Nagata, Tetsuya; Geballe, T.R.; Okuda, Haruyuki; Shibai, Hiroshi; Tokyo Univ.; Kyoto Univ.; Joint Astronomy Center, Hilo, HI; Institute of Space and Astronautical Science, Sagamihara )

    1989-05-01

    Extensive infrared observations have been obtained of the three active regions in Arp 299. Multiaperture JHK photometry reveals that the colors of the three regions are totally different from each other, and that there are very red nuclei smaller than 4 arcsec in two of them. Multiaperture spectroscopy of the Br-gamma and the shock-excited H2 lines shows that both the atomic and molecular lines are spatially extended, indicating that Arp 299 is undergoing an active episode of star formation not only in its nuclei but also well outside of them. Although there is some evidence that suggests the presence of a compact, active galactic nucleus, a simple starburst model can explain the bolometric luminosities, production rates of ionizing photons, and H24 line luminosities of each active region in Arp 299. However, each starburst cannot last longer than 10 to the 8th yr. 56 refs.

  12. Investigating Starburst Galaxy Emission Line Equivalent Widths

    NASA Astrophysics Data System (ADS)

    Meskhidze, Helen; Richardson, Chris T.

    2016-01-01

    Modeling star forming galaxies with spectral synthesis codes allows us to study the gas conditions and excitation mechanisms that are necessary to reproduce high ionization emission lines in both local and high-z galaxies. Our study uses the locally optimally-emitting clouds model to develop an atlas of starburst galaxy emission line equivalent widths. Specifically, we address the following question: What physical conditions are necessary to produce strong high ionization emission lines assuming photoionization via starlight? Here we present the results of our photoionization simulations: an atlas spanning 15 orders of magnitude in ionizing flux and 10 orders of magnitude in hydrogen density that tracks over 150 emission lines ranging from the UV to the near IR. Each simulation grid contains ~1.5x104 photoionization models calculated by supplying a spectral energy distribution, grain content, and chemical abundances. Specifically, we will be discussing the effects on the emission line equivalent widths of varying the metallicity of the cloud, Z = 0.2 Z⊙ to Z = 5.0 Z⊙, and varying the star-formation history, using the instantaneous and continuous evolution tracks and the newly released Starburst99 Geneva rotation tracks.

  13. Algorithmic dimensionality reduction for molecular structure analysis.

    PubMed

    Brown, W Michael; Martin, Shawn; Pollock, Sara N; Coutsias, Evangelos A; Watson, Jean-Paul

    2008-08-14

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation--a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

  14. Molecular structure of the collagen triple helix.

    PubMed

    Brodsky, Barbara; Persikov, Anton V

    2005-01-01

    The molecular conformation of the collagen triple helix confers strict amino acid sequence constraints, requiring a (Gly-X-Y)(n) repeating pattern and a high content of imino acids. The increasing family of collagens and proteins with collagenous domains shows the collagen triple helix to be a basic motif adaptable to a range of proteins and functions. Its rodlike domain has the potential for various modes of self-association and the capacity to bind receptors, other proteins, GAGs, and nucleic acids. High-resolution crystal structures obtained for collagen model peptides confirm the supercoiled triple helix conformation, and provide new information on hydrogen bonding patterns, hydration, sidechain interactions, and ligand binding. For several peptides, the helix twist was found to be sequence dependent, and such variation in helix twist may serve as recognition features or to orient the triple helix for binding. Mutations in the collagen triple-helix domain lead to a variety of human disorders. The most common mutations are single-base substitutions that lead to the replacement of one Gly residue, breaking the Gly-X-Y repeating pattern. A single Gly substitution destabilizes the triple helix through a local disruption in hydrogen bonding and produces a discontinuity in the register of the helix. Molecular information about the collagen triple helix and the effect of mutations will lead to a better understanding of function and pathology.

  15. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  16. Direct Measurement of the Supernova Rate in Starburst Galaxies

    NASA Technical Reports Server (NTRS)

    Bregman, J. D.; Temi, P.; Rank, D.

    2000-01-01

    Supernovae play a key role in the dynamics, structure, and chemical evolution of galaxies. The massive stars that end their lives as supernovae live for short enough times that many are still associated with dusty star formation regions when they explode, making them difficult to observe at visible wavelengths. In active star forming regions (galactic nuclei and starburst regions), dust extinction is especially severe. Thus, determining the supernova rate in active star forming regions of galaxies, where the supernova rate can be one or two orders of magnitude higher than the average, has proven to be difficult. From observations of SN1987A, we know that the [NiII] 6.63 micrometer emission line was the strongest line in the infrared spectrum for a period of a year and half after th explosion. Since dust extinction is much less at 6.63 micrometers than at visible wavelengths (A(sub 6.63)/A(sub V) = 0.025), the [NiII] line can be used as a sensitive probe for the detection of recent supernovae. We have observed a sample of starburst galaxies at 6.63 micrometers using ISOCAM to search for the [NiII] emission line characteristic of recent supernovae. We did not detect any [NiII] line emission brighter than a 5-sigma limit of 5 mJy. We can set upper limits to the supernova rate in our sample, scaled ot the rate in M82, of less than 0.3 per year at the 90% confidence level using Bayesian methods. Assuming that a supernova would have a [NiII] line with the same luminosity as observed in SN1987A, we find less than 0.09 and 0.15 per year at the 50% and 67% confidence levels. These rates are somewhat less if a more normal type II supernovae has a [NiII] line luminosity greater than the line in SN1987A.

  17. Direct Measurement of the Supernova Rate in Starburst Galaxies

    NASA Technical Reports Server (NTRS)

    Bregman, Jesse D.; Temi, Pasquale; Rank, David; DeVincenzi, Donald L. (Technical Monitor)

    1999-01-01

    Supernovae play a key role in the dynamics, structure, and chemical evolution of galaxies. The massive stars that end their lives as supernovae live for short times. Many are still associated with dusty star formation regions when they explode, making them difficult to observe at visible wavelengths. In active star forming regions (galactic nuclei and starburst regions), dust extintion is especially severe. Thus, determining the supernova rate in the active star forming regions of galaxies, where the supernova rate can be one or two orders of magnitude higher than the average, has proven to be difficult. From observations of SN1987A, we know that the [NiII] 6.63 micron emission line was the strongest line in the infrared spectrum for a period of a year and a half after the explosion. Since dust extintion is much less at 6.63 pm than at visible wavelengths (A(sub 6.63)/A(sub V) = 0.025), the NiII line can be used as a sensitive probe for the detection of recent supernovae. We have observed a sample of starburst galaxies at 6.63 micron using ISOCAM to search for the NiII emission line characteristic of recent supernovae. We did not detect any NiII line emission brighter than a 5sigma limit of 5 mJy. We can set upper limits to the supernova rate in our sample, scaled to the rate in M82, of less than 0.3 per year at the 90% confidence level using Bayesian methods. Assuming that a supernova would have a NiII with the same luminosity as observed in SN1987A, we find less than 0.09 and 0.15 per year at the 50% and 67% confidence levels. These rates are somewhat less if a more normal type II supernovae has a NiII line luminosity greater than the line in SN1987A.

  18. Uncovering the Beast: The Galactic Starburst Region W49A

    NASA Astrophysics Data System (ADS)

    Homeier, N.; Alves, J.

    2002-12-01

    We present J, H, and Ks images of an unbiased 5‧ x 5‧ (16 pc x 16 pc) survey of the densest region of the W49 giant molecular cloud. The observations reveal a massive stellar cluster (Cluster 1) about 3 pc East of the well-known Welch ring of ultra-compact H II regions, as well as three smaller clusters associated with compact sources of radio emission. Cluster 1 powers a 6 pc diameter giant H II region seen at both the NIR and radio continuum, and has more than 30 visual magnitudes of internal imhomogeneous extinction, implying that it is still deeply embedded in its parent molecular cloud. The census of massive stars in W49A agrees or slightly overabundant when compared with the number of Lyman continuum photons derived from radio observations. We argue that although the formation of the Welch ring could have been triggered by Cluster 1, the entire W49A starburst region seems to have been multi-seeded instead of resulting from a coherent trigger.

  19. Speculations on the molecular structure of eumelanin.

    PubMed

    Swift, J A

    2009-04-01

    Eumelanin is the polymeric black pigment commonly found in hair and skin. Its chemical intractability, to all but vigorous oxidizing agents, has hindered satisfactory understanding of its molecular structure. It is well-established that the immediate precursor to polymerization, indole-5,6-quinone (IQ), is biosynthesized from the amino acid tyrosine. Current views are that the polymer consists of single bond connections between random indole and degraded indole units. In this paper, an alternative chemical scheme for the polymerization of IQ is proposed based upon the original suggestion by Horner in 1949 that a Diels-Alder (D-A) reaction might be involved. The proposed basic chemical scheme for eumelanin formation is that D-A addition occurs specifically between the 2- and 3-positions of one IQ molecule and the 7- and 4- positions respectively of a second IQ molecule, that the ensuing diketo bridge is oxidized to carboxyl groups and that, by decarboxylation and aromatization, a fused indole dimer is produced. It is envisaged that, by further D-A addition of more IQ molecules, oligomers of greater molecular mass are produced. Calculations based on published bond lengths and angles for the indole nucleus show that oligomeric units containing a total of up to 11 fused indoles could be packed into a flat circular disc of 20 A diameter. The discs of the extensively conjugated polymer are envisaged to be stacked above each other by pi-pi interaction and with a spacing of 3.4 A to produce cylindrical units, the mass density of which is calculated to be 1.54 gm cm(-3); approximating with actual physical measurements. The size and shape of the predicted cylinders are in concordance with those observed in atomic force microscope investigations of eumelanin proto-particles. The model is also in agreement with published experimental data that 2/3rds of the carbon dioxide liberated during eumelanin formation derives from positions 5- and 6- of the IQ molecule.

  20. The Circumnuclear Starburst Ring in NGC 1097

    NASA Astrophysics Data System (ADS)

    Thackeray-Lacko, Beverly; Stierwalt, Sabrina; Sheth, Kartik

    2016-01-01

    The circumnuclear ring in galaxy NGC 1097 is bursting with star formation at a rate of five solar masses per year as previously measured through Hα emission. The rate of star formation drops by a factor of one thousand outside the circumnuclear ring. We characterize the behavior of the dust in this region by measuring the spectral energy distribution focused exclusively on the circumnuclear ring using a selective variety of high resolution science images spanning wavelengths from ultraviolet to infrared, and adding proprietary high resolution radio data from Atacoma Large Millimeter Array (ALMA) in Chile. High resolution radio data obtained from ALMA allows us to constrain the shape of the spectral energy distribution curve specifically at longer wavelengths, and therefore the rate of star formation within the circumnuclear ring. Comparing the spectral energy distribution of the entire galaxy with that of the circumnuclear ring indicates how starburst activity influences the galactic spectral energy distribution.

  1. Molecular structures and intramolecular dynamics of pentahalides

    NASA Astrophysics Data System (ADS)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  2. Filamentary structure in the Orion molecular cloud

    NASA Technical Reports Server (NTRS)

    Bally, J.; Langer, W. D.; Bally, J.; Langer, W. D.; Bally, J.; Langer, W. D.

    1986-01-01

    A large scale 13CO map (containing 33,000 spectra) of the giant molecular cloud located in the southern part of Orion is presented which contains the Orion Nebula, NGC1977, and the LI641 dark cloud complex. The overall structure of the cloud is filamentary, with individual features having a length up to 40 times their width. This morphology may result from the effects of star formation in the region or embedded magnetic fields in the cloud. We suggest a simple picture for the evolution of the Orion-A cloud and the formation of the major filament. A rotating proto-cloud (counter rotating with respect to the galaxy) contians a b-field aligned with the galaxtic plane. The northern protion of this cloud collapsed first, perhaps triggered by the pressure of the Ori I OB association. The magnetic field combined with the anisotropic pressure produced by the OB-association breaks the symmetry of the pancake instability, a filament rather than a disc is produced. The growth of instabilities in the filament formed sub-condensations which are recent sites of star formation.

  3. The Determination of Molecular Structure from Rotational Spectra

    DOE R&D Accomplishments Database

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  4. Molecular cloning of chicken aggrecan. Structural analyses.

    PubMed Central

    Chandrasekaran, L; Tanzer, M L

    1992-01-01

    The large, aggregating chondroitin sulphate proteoglycan of cartilage, aggrecan, has served as a generic model of proteoglycan structure. Molecular cloning of aggrecans has further defined their amino acid sequences and domain structures. In this study, we have obtained the complete coding sequence of chicken sternal cartilage aggrecan by a combination of cDNA and genomic DNA sequencing. The composite sequence is 6117 bp in length, encoding 1951 amino acids. Comparison of chicken aggrecan protein primary structure with rat, human and bovine aggrecans has disclosed both similarities and differences. The domains which are most highly conserved at 70-80% identity are the N-terminal domains G1 and G2 and the C-terminal domain G3. The chondroitin sulphate domain of chicken aggrecan is smaller than that of rat and human aggrecans and has very distinctive repeat sequences. It has two separate sections, one comprising 12 consecutive Ser-Gly-Glu repeats of 20 amino acids each, adjacent to the other which has 23 discontinuous Ser-Gly-Glu repeats of 10 amino acids each; this latter region, N-terminal to the former one, appears to be unique to chicken aggrecan. The two regions contain a total of 94 potential chondroitin sulphate attachment sites. Genomic comparison shows that, although chicken exons 11-14 are identical in size to the rat and human exons, chicken exon 10 is the smallest of the three species. This is also reflected in the size of its chondroitin sulphate coding region and in the total number of Ser-Gly pairs. The putative keratan sulphate domain shows 31-45% identity with the other species and lacks the repetitive sequences seen in the others. In summary, while the linear arrangement of specific domains of chicken aggrecan is identical to that in the aggrecans of other species, and while there is considerable identity of three separate domains, chicken aggrecan demonstrates unique features, notably in its chondroitin sulphate domain and its keratan sulphate

  5. STARBURST-DRIVEN GALACTIC WINDS: FILAMENT FORMATION AND EMISSION PROCESSES

    SciTech Connect

    Cooper, Jackie L.; Bicknell, Geoffrey V.; Sutherland, Ralph S.; Bland-Hawthorn, Joss

    2009-09-20

    We have performed a series of three-dimensional simulations of the interaction of a supersonic wind with a nonspherical radiative cloud. These simulations are motivated by our recent three-dimensional model of a starburst-driven galactic wind interacting with an inhomogeneous disk, which shows that an optically emitting filament can be formed by the breakup and acceleration of a cloud into a supersonic wind. In this study, we consider the evolution of a cloud with two different geometries (fractal and spherical) and investigate the importance of radiative cooling on the cloud's survival. We have also undertaken a comprehensive resolution study in order to ascertain the effect of the assumed numerical resolution on the results. We find that the ability of the cloud to radiate heat is crucial for its survival, with a radiative cloud experiencing a lower degree of acceleration and having a higher relative Mach number to the flow than in the adiabatic case. This diminishes the destructive effect of the Kelvin-Helmholtz instability on the cloud. While an adiabatic cloud is destroyed over a short period of time, a radiative cloud is broken up via the Kelvin-Helmholtz instability into numerous small, dense cloudlets, which are drawn into the flow to form a filamentary structure. The degree of fragmentation is highly dependent on the resolution of the simulation, with the number of cloudlets formed increasing as the Kelvin-Helmholtz instability is better resolved. Nevertheless, there is a clear qualitative trend, with the filamentary structure still persistent at high resolution. The geometry of the cloud affects the speed at which the cloud fragments; a wind more rapidly breaks up the cloud in regions of least density. A cloud with a more inhomogeneous density distribution fragments faster than a cloud with a more uniform structure (e.g., a sphere). We confirm the mechanism behind the formation of the Halpha emitting filaments found in our global simulations of a

  6. The Ubiquity of Coeval Starbursts in Massive Galaxy Cluster Progenitors

    NASA Astrophysics Data System (ADS)

    Casey, Caitlin M.

    2016-06-01

    The universe’s largest galaxy clusters likely built the majority of their massive >1011 M {}⊙ galaxies in simultaneous, short-lived bursts of activity well before virialization. This conclusion is reached based on emerging data sets for z\\gt 2 proto-clusters and the characteristics of their member galaxies, in particular, rare starbursts and ultraluminous active galactic nuclei (AGN). The most challenging observational hurdle in identifying such structures is their very large volumes, ˜104 comoving Mpc3 at z\\gt 2, subtending areas of approximately half a degree on the sky. Thus, the contrast afforded by an overabundance of very rare galaxies in comparison to the background can more easily distinguish overdense structures from the surrounding, normal density field. Five 2≲ z≲ 3 proto-clusters from the literature are discussed in detail and are found to contain up to 12 dusty starbursts or luminous AGN galaxies each, a phenomenon that is unlikely to occur by chance even in overdense environments. These are contrasted with three higher-redshift (4≲ z≲ 5.5) dusty star-forming galaxy (DSFG) groups, whose evolutionary fate is less clear. Measurements of DSFGs’ gas depletion times suggest that they are indeed short-lived on ˜100 Myr timescales, and accordingly the probability of finding a structure containing more than 8 such systems is ˜0.2%, unless their “triggering” is correlated on very large spatial scales, ˜10 Mpc across. The volume density of DSFG-rich proto-clusters is found to be comparable to all of the >1015 M {}⊙ galaxy clusters in the nearby universe, which is a factor of five larger than expected in some simulations. Some tension still exists between measurements of the volume density of DSFG-rich proto-clusters and the expectation that they are generated via short-lived episodes, as the latter suggests that only a fraction (\\lt \\tfrac{1}{2}) of all proto-clusters should be rich with DSFGs. However, improved observations of proto

  7. Structure and dynamics of layered molecular assemblies

    NASA Astrophysics Data System (ADS)

    Horne, Jennifer Conrad

    This dissertation focuses on the goal of understanding and controlling layered material properties from a molecular perspective. With this understanding, materials can be synthetically tailored to exhibit predetermined bulk properties. This investigation describes the optical response of a family of metal-phosphonate (MP) monolayers and multilayers, materials that are potentially useful because the films are easy to synthesize and are chemically and thermally stable. MP films have shown potential in a variety of chemical sensing and optical applications, and in this dissertation, the suitability of MP films for optical information storage is explored For this application, the extent of photonic energy transport within and between optically active layers is an important factor in determining the stability and specificity of optical modifications made to a material. Intralayer and interlayer energy transport processes can be studied selectively in MP films because the composition, and thus the properties, of each layer are controlled synthetically. It was determined by fluorescence relaxation dynamics in conjunction with atomic force microscopy (AFM) that the substrate and layer morphologies are key factors in determining the layer optical and physical properties. The initial MP layers in a multilayer are structurally heterogeneous, characterized by randomly distributed islands that are ~50 A in diameter. The population dynamics measured for these layers are non-exponential, chromophore concentration-independent, and identical for two different chromophores. The data is explained in the context of an excitation hopping model in a system where the surface is characterized by islands of aggregated chromophores as well as non-aggregated monomers. Within a MP monolayer, the dynamics are dominated by intra-island excitation hopping. Forster (dipolar) energy transfer between the energetically overlapped chromophores does not play a significant role in determining the

  8. The Green Bank Telescope Maps the Dense, Star-forming Gas in the Nearby Starburst Galaxy M82

    NASA Astrophysics Data System (ADS)

    Kepley, Amanda A.; Leroy, Adam K.; Frayer, David; Usero, Antonio; Marvil, Josh; Walter, Fabian

    2014-01-01

    Observations of the Milky Way and nearby galaxies show that dense molecular gas correlates with recent star formation, suggesting that the formation of this gas phase may help regulate star formation. A key test of this idea requires wide-area, high-resolution maps of dense molecular gas in galaxies to explore how local physical conditions drive dense gas formation, but these observations have been limited because of the faintness of dense gas tracers like HCN and HCO+. Here we demonstrate the power of the Robert C. Byrd Green Bank Telescope (GBT)—the largest single-dish millimeter radio telescope—for mapping dense gas in galaxies by presenting the most sensitive maps yet of HCN and HCO+ in the starburst galaxy M82. The HCN and HCO+ in the disk of this galaxy correlates with both recent star formation and more diffuse molecular gas and shows kinematics consistent with a rotating torus. The HCO+ emission extending to the north and south of the disk is coincident with the outflow previously identified in CO and traces the eastern edge of the hot outflowing gas. The central starburst region has a higher ratio of star formation to dense gas than the outer regions, pointing to the starburst as a key driver of this relationship. These results establish that the GBT can efficiently map the dense molecular gas at 90 GHz in nearby galaxies, a capability that will increase further with the 16 element feed array under construction.

  9. Molecular clouds and galactic spiral structure

    NASA Technical Reports Server (NTRS)

    Dame, T. M.

    1984-01-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide.

  10. A survey of quantitative descriptions of molecular structure.

    PubMed

    Guha, Rajarshi; Willighagen, Egon

    2012-01-01

    Numerical characterization of molecular structure is a first step in many computational analysis of chemical structure data. These numerical representations, termed descriptors, come in many forms, ranging from simple atom counts and invariants of the molecular graph to distribution of properties, such as charge, across a molecular surface. In this article we first present a broad categorization of descriptors and then describe applications and toolkits that can be employed to evaluate them. We highlight a number of issues surrounding molecular descriptor calculations such as versioning and reproducibility and describe how some toolkits have attempted to address these problems.

  11. Structures of High Density Molecular Fluids

    SciTech Connect

    Baer, B; Cynn, H; Iota, V; Yoo, C-S

    2002-02-01

    The goal of this proposal is to develop an in-situ probe for high density molecular fluids. We will, therefore, use Coherent Anti-Stokes Raman Spectroscopy (CARS) applied to laser heated samples in a diamond-anvil cell (DAC) to investigate molecular fluids at simultaneous conditions of high temperatures (T > 2000K) and high pressures (P > 10 GPa.) Temperatures sufficient to populate vibrational levels above the ground state will allow the vibrational potential to be mapped by CARS. A system capable of heating and probing these samples will be constructed. Furthermore, the techniques that enable a sample to be sufficiently heated and probed while held at static high pressure in a diamond-anvil-cell will be developed. This will be an in-situ investigation of simple molecules under conditions relevant to the study of detonation chemistry and the Jovain planet interiors using state of the art non-linear spectroscopy, diamond-anvil-cells, and laser heating technology.

  12. Colour Chemistry, Part I, Principles, Colour, and Molecular Structure

    ERIC Educational Resources Information Center

    Hallas, G.

    1975-01-01

    Discusses various topics in color chemistry, including the electromagnetic spectrum, the absorption and reflection of light, additive and subtractive color mixing, and the molecular structure of simple colored substances. (MLH)

  13. Circumnuclear ionized gas in starburst nuclei

    NASA Technical Reports Server (NTRS)

    Taniguchi, Yoshiaki

    1990-01-01

    In order to study kinematical properties of starburst nuclei (SBNs), researchers made high-resolution spectroscopy of fifteen SBNs in the H alpha region using an intensified Reticon system attached to the coude focus of the 188-cm reflector at the Okayama Astrophysical Observatory. The instrumental resolution is 21 km s(-1) Full Width Half Maximum (FWHM) at lambda sub H alpha. As for the archetypical SBN, Mrk 538 (=NGC 7714), researchers present high-resolution emission line profiles of several species of ions such as (OIII), (NII), (SII), and (OII). Main results and conclusions are summarized. It has been known that emission-line profiles of SBNs are symmetrical and narrow. However, this high-resolution spectroscopy shows that the observed emission-line profiles of the SBNs have the following asymmetrical patterns; blueward, redward, and double-peaked. It is known that such features have been observed for narrow line regions (NLRs) of active galactic nuclei (AGNs). There is no remarkable correlation between the asymmetry index and the reddening indicator such as a Balmer decrement. Thus the line asymmetry is not attributed to inhomogeneous obscuration in the emitting regions. The observed FWHMs of the H alpha emission lines cover a range from 85 km s(-1) to 318 km s(-1) and are slightly larger than those of (NII) lambda 6584A emission except for the double-peaked SBNs. The FWHMs of H alpha emission show a good correlation with sin i (i is an inclination angle of galaxy). This correlation means that the FWHMs of the SBNs suffer significantly from rotational broadening. Mrk 52 is an anomalous SBN because it has narrow emission line widths for its high inclination angle (cf. Taniguchi 1987). From the above correlation, it is estimated that the intrinsic (i.e., rotation free) FWHMs of H alpha emission are about 50 km s(-1).

  14. Circumnuclear ionized gas in starburst nuclei

    NASA Astrophysics Data System (ADS)

    Taniguchi, Yoshiaki

    1990-07-01

    In order to study kinematical properties of starburst nuclei (SBNs), researchers made high-resolution spectroscopy of fifteen SBNs in the H alpha region using an intensified Reticon system attached to the coude focus of the 188-cm reflector at the Okayama Astrophysical Observatory. The instrumental resolution is 21 km s(-1) Full Width Half Maximum (FWHM) at lambdaH alpha. As for the archetypical SBN, Mrk 538 (=NGC 7714), researchers present high-resolution emission line profiles of several species of ions such as (OIII), (NII), (SII), and (OII). Main results and conclusions are summarized. It has been known that emission-line profiles of SBNs are symmetrical and narrow. However, this high-resolution spectroscopy shows that the observed emission-line profiles of the SBNs have the following asymmetrical patterns; blueward, redward, and double-peaked. It is known that such features have been observed for narrow line regions (NLRs) of active galactic nuclei (AGNs). There is no remarkable correlation between the asymmetry index and the reddening indicator such as a Balmer decrement. Thus the line asymmetry is not attributed to inhomogeneous obscuration in the emitting regions. The observed FWHMs of the H alpha emission lines cover a range from 85 km s(-1) to 318 km s(-1) and are slightly larger than those of (NII) lambda 6584A emission except for the double-peaked SBNs. The FWHMs of H alpha emission show a good correlation with sin i (i is an inclination angle of galaxy). This correlation means that the FWHMs of the SBNs suffer significantly from rotational broadening. Mrk 52 is an anomalous SBN because it has narrow emission line widths for its high inclination angle (cf. Taniguchi 1987). From the above correlation, it is estimated that the intrinsic (i.e., rotation free) FWHMs of H alpha emission are about 50 km s(-1).

  15. Cyanoacetylene in IC 342: An Evolving Dense Gas Component with Starburst Age

    NASA Astrophysics Data System (ADS)

    Meier, David S.; Turner, Jean L.; Schinnerer, Eva

    2011-07-01

    We present the first images of the J = 5-4 and J = 16-15 lines of the dense gas tracer, cyanoacetylene, HC3N, in an external galaxy. The central 200 pc of the nearby star-forming spiral galaxy, IC 342, was mapped using the Very Large Array and the Plateau de Bure Interferometer. HC3N(5-4) line emission is found across the nuclear mini-spiral, but is very weak toward the starburst site, the location of the strongest mid-IR and radio emission. The J = 16-15 and 10-9 lines are also faint near the large H II region complex, but are brighter relative to the 5-4 line, consistent with higher excitation. The brightest HC3N emission is located in the northern arm of the nuclear mini-spiral, 100 pc away from the radio/IR source to the southwest of the nucleus. This location appears less affected by ultraviolet radiation and may represent a more embedded, earlier stage of star formation. HC3N excitation temperatures are consistent with those determined from C18O; the gas is dense 104 - 105 cm-3 and cool, Tk < 40 K. So as to not violate limits on the total H2 mass determined from C18O, at least two dense components are required to model IC 342's giant molecular clouds. These observations suggest that HC3N(5-4) is an excellent probe of the dense, quiescent gas in galaxies. The high excitation combined with faint emission toward the dense molecular gas at the starburst indicates that it currently lacks large masses of very dense gas. We propose a scenario where the starburst is being caught in the act of dispersing or destroying its dense gas in the presence of the large H II region. This explains the high star formation efficiency seen in the dense component. The little remaining dense gas appears to be in pressure equilibrium with the starburst H II region. Based on observations carried out with the IRAM Plateau de Bure Interferometer. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).

  16. Detection of gamma rays from a starburst galaxy.

    PubMed

    Acero, F; Aharonian, F; Akhperjanian, A G; Anton, G; Barres de Almeida, U; Bazer-Bachi, A R; Becherini, Y; Behera, B; Bernlöhr, K; Bochow, A; Boisson, C; Bolmont, J; Borrel, V; Brucker, J; Brun, F; Brun, P; Bühler, R; Bulik, T; Büsching, I; Boutelier, T; Chadwick, P M; Charbonnier, A; Chaves, R C G; Cheesebrough, A; Chounet, L-M; Clapson, A C; Coignet, G; Dalton, M; Daniel, M K; Davids, I D; Degrange, B; Deil, C; Dickinson, H J; Djannati-Ataï, A; Domainko, W; Drury, L O'C; Dubois, F; Dubus, G; Dyks, J; Dyrda, M; Egberts, K; Emmanoulopoulos, D; Espigat, P; Farnier, C; Fegan, S; Feinstein, F; Fiasson, A; Förster, A; Fontaine, G; Füssling, M; Gabici, S; Gallant, Y A; Gérard, L; Gerbig, D; Giebels, B; Glicenstein, J F; Glück, B; Goret, P; Göring, D; Hauser, D; Hauser, M; Heinz, S; Heinzelmann, G; Henri, G; Hermann, G; Hinton, J A; Hoffmann, A; Hofmann, W; Hofverberg, P; Hoppe, S; Horns, D; Jacholkowska, A; de Jager, O C; Jahn, C; Jung, I; Katarzyński, K; Katz, U; Kaufmann, S; Kerschhaggl, M; Khangulyan, D; Khélifi, B; Keogh, D; Klochkov, D; Kluźniak, W; Kneiske, T; Komin, Nu; Kosack, K; Kossakowski, R; Lamanna, G; Lenain, J-P; Lohse, T; Marandon, V; Martineau-Huynh, O; Marcowith, A; Masbou, J; Maurin, D; McComb, T J L; Medina, M C; Méhault, J; Moderski, R; Moulin, E; Naumann-Godo, M; de Naurois, M; Nedbal, D; Nekrassov, D; Nicholas, B; Niemiec, J; Nolan, S J; Ohm, S; Olive, J-F; de Oña Wilhelmi, E; Orford, K J; Ostrowski, M; Panter, M; Paz Arribas, M; Pedaletti, G; Pelletier, G; Petrucci, P-O; Pita, S; Pühlhofer, G; Punch, M; Quirrenbach, A; Raubenheimer, B C; Raue, M; Rayner, S M; Reimer, O; Renaud, M; Rieger, F; Ripken, J; Rob, L; Rosier-Lees, S; Rowell, G; Rudak, B; Rulten, C B; Ruppel, J; Sahakian, V; Santangelo, A; Schlickeiser, R; Schöck, F M; Schwanke, U; Schwarzburg, S; Schwemmer, S; Shalchi, A; Sikora, M; Skilton, J L; Sol, H; Stawarz, Ł; Steenkamp, R; Stegmann, C; Stinzing, F; Superina, G; Szostek, A; Tam, P H; Tavernet, J-P; Terrier, R; Tibolla, O; Tluczykont, M; van Eldik, C; Vasileiadis, G; Venter, C; Venter, L; Vialle, J P; Vincent, P; Vivier, M; Völk, H J; Volpe, F; Wagner, S J; Ward, M; Zdziarski, A A; Zech, A

    2009-11-20

    Starburst galaxies exhibit in their central regions a highly increased rate of supernovae, the remnants of which are thought to accelerate energetic cosmic rays up to energies of approximately 10(15) electron volts. We report the detection of gamma rays--tracers of such cosmic rays--from the starburst galaxy NGC 253 using the High Energy Stereoscopic System (H.E.S.S.) array of imaging atmospheric Cherenkov telescopes. The gamma-ray flux above 220 billion electron volts is F = (5.5 +/- 1.0(stat) +/- 2.8(sys)) x 10(-13) cm(-2) s(-1), implying a cosmic-ray density about three orders of magnitude larger than that in the center of the Milky Way. The fraction of cosmic-ray energy channeled into gamma rays in this starburst environment is five times as large as that in our Galaxy.

  17. Upper limits to the water abundance in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Wilson, C. D.; Booth, R. S.; Olofsson, A. O. H.; Olberg, M.; Persson, C. M.; Sandqvist, Aa.; Hjalmarson, Â.; Buat, V.; Encrenaz, P. J.; Fich, M.; Frisk, U.; Gerin, M.; Rydback, G.; Wiklind, T.

    2007-07-01

    Aims:We have searched for emission from the 557 GHz ortho-water line in the interstellar medium of six nearby starburst galaxies. Methods: We used the Odin satellite to observe the 110{-}101 transition of o-H2O in the galaxies NGC 253, IC 342, M 82, NGC 4258, CenA, and M 51. None of the galaxies in our sample was detected. Results: We derive three sigma upper limits to the H2O abundance relative to H2 ranging from 2×10-9 to 1×10-8. The best of these upper limits are comparable to the measured abundance of H2O in the Galactic star forming region W3. However, if only 10% of the molecular gas is in very dense cores, then the water abundance limits in the cores themselves would be larger by a factor of 10 i.e. 2×10-8 to 1×10-7. Conclusions: These observations suggest that detections of H2O emission in galaxies with the upcoming Herschel Space Observatory are likely to require on-source integration times of an hour or more except in the very brightest extragalactic targets such as M 82 and NGC 253. Based on observations with Odin, a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes) and Centre National d'Etude Spatiale (CNES). The Swedish Space Corporation has been the industrial prime contractor and also is operating the satellite.

  18. Star formation in the starburst cluster in NGC 3603

    NASA Astrophysics Data System (ADS)

    Correnti, Matteo; Paresce, Francesco; Aversa, Rossella; Beccari, Giacomo; De Marchi, Guido; Di Criscienzo, Marcella; Pang, Xiaoying; Spezzi, Loredana; Valenti, Elena; Ventura, Paolo

    2012-08-01

    We have used new, deep, visible and near infrared observations of the compact starburst cluster in the giant HII region NGC 3603 and its surroundings with the WFC3 on HST and HAWK-I on the VLT to study in detail the physical properties of its intermediate mass (˜1-3 M⊙) stellar population. We show that after correction for differential extinction and actively accreting stars, and the study of field star contamination, strong evidence remains for a continuous spread in the ages of pre-main sequence stars in the range ˜2 to ˜30 Myr within the temporal resolution available. Existing differences among presently available theoretical models account for the largest possible variation in shape of the measured age histograms within these limits. We also find that this isochronal age spread in the near infrared and visible Colour-Magnitude Diagrams cannot be reproduced by any other presently known source of astrophysical or instrumental scatter that could mimic the luminosity spread seen in our observations except, possibly, episodic accretion. The measured age spread and the stellar spatial distribution in the cluster are consistent with the hypothesis that star formation started at least 20-30 Myrs ago progressing slowly but continuously up to at least a few million years ago. All the stars in the considered mass range are distributed in a flattened oblate spheroidal pattern with the major axis oriented in an approximate South-East-North-West direction, and with the length of the equatorial axis decreasing with increasing age. This asymmetry is most likely due to the fact that star formation occurred along a filament of gas and dust in the natal molecular cloud oriented locally in this direction.

  19. Feedback from starbursts: 30 Dorado as a case study

    NASA Astrophysics Data System (ADS)

    Wang, Q. Daniel; lim, Seunghwan

    2016-01-01

    Stellar feedback remains a key uncertain aspect in galaxy formation and evolution theories. In addition to the mechanical energy injection from fast stellar winds and supernovae of massive stars, their radiative transfer feedback (via direct and indirect/dust-processed radiation pressures and photo-ionization) has also been proposed to play a significant role in dispersing dense dusty gas and possibly in driving outflows from starburst regions. To test the relative efficiency of these two forms of the stellar feedback, we study the energetics of the Tarantula Nebula (30 Doradus) in the Large Magellanic Cloud. The nebula consists of various blisters of diffuse hot plasma enveloped by cool gas. Based on the X-ray spectroscopy of the nebula, using a 100 ks Suzaku X-ray observation, we estimate the thermal energy of the enclosed plasma, accounting for its temperature distribution and foreground absorption variation. The estimated thermal energy is far short of the expected fraction of the mechanical energy input from the central young stellar association (NGC 2070) of the nebula, according to the classic superbubble solution, indicating a substantial loss of energy via probably hot electron-dust interaction and cosmic-ray acceleration, as well as the cool shell formation. We further characterize the kinetic energy of dense dusty gas, using a recently published dust mass map and the velocity dispersion inferred from molecular and HI gases in the nebula. However, this component of the kinetic energy appears to be dominated by the turbulent and bulk motions of HII gas. The total kinetic energy of the nebula is consistent with the expected fraction of the mechanical energy input. Therefore, the radiation transfer feedback does not seem to play a significant role in the expansion of 30 Doradus.

  20. Instructional Approach to Molecular Electronic Structure Theory

    ERIC Educational Resources Information Center

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  1. Hygrothermal aging effects on buried molecular structures at epoxy interfaces.

    PubMed

    Myers, John N; Zhang, Chi; Lee, Kang-Wook; Williamson, Jaimal; Chen, Zhan

    2014-01-14

    Interfacial properties such as adhesion are determined by interfacial molecular structures. Adhesive interfaces in microelectronic packages that include organic polymers such as epoxy are susceptible to delamination during accelerated stress testing. Infrared-visible sum frequency generation vibrational spectroscopy (SFG) and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) were used to study molecular structures at buried epoxy interfaces during hygrothermal aging to relate molecular structural changes at buried interfaces to decreases in macroscopic adhesion strength. SFG peaks associated with strongly hydrogen bonded water were detected at hydrophilic epoxy interfaces. Ordered interfacial water was also correlated to large decreases in interfacial adhesion strength that occurred as a result of hygrothermal aging, which suggests that water diffused to the interface and replaced original hydrogen bond networks. No water peaks were observed at hydrophobic epoxy interfaces, which was correlated with a much smaller decrease in adhesion strength from the same aging process. ATR-FTIR water signals observed in the epoxy bulk were mainly contributed by relatively weakly hydrogen bonded water molecules, which suggests that the bulk and interfacial water structure was different. Changes in interfacial methyl structures were observed regardless of the interfacial hydrophobicity which could be due to water acting as a plasticizer that restructured both the bulk and interfacial molecular structure. This research demonstrates that SFG studies of molecular structural changes at buried epoxy interfaces during hygrothermal aging can contribute to the understanding of moisture-induced failure mechanisms in electronic packages that contain organic adhesives.

  2. Induced starburst and nuclear activity: Faith, facts, and theory

    NASA Technical Reports Server (NTRS)

    Shlosman, Isaac

    1990-01-01

    The problem of the origin of starburst and nuclear (nonstellar) activity in galaxies is reviewed. A physical understanding of the mechanism(s) that induce both types of activity requires one to address the following issues: (1) what is the source of fuel that powers starbursts and active galactic nuclei; and (2) how is it channeled towards the central regions of host galaxies? As a possible clue, the author examines the role of non-axisymmetric perturbations of galactic disks and analyzes their potential triggers. Global gravitational instabilities in the gas on scales approx. 100 pc appear to be crucial for fueling the active galactic nuclei.

  3. Clumpy and Extended Starbursts in the Brightest Unlensed Submillimeter Galaxies

    NASA Astrophysics Data System (ADS)

    Iono, Daisuke; Yun, Min S.; Aretxaga, Itziar; Hatsukade, Bunyo; Hughes, David; Ikarashi, Soh; Izumi, Takuma; Kawabe, Ryohei; Kohno, Kotaro; Lee, Minju; Matsuda, Yuichi; Nakanishi, Kouichiro; Saito, Toshiki; Tamura, Yoichi; Ueda, Junko; Umehata, Hideki; Wilson, Grant; Michiyama, Tomonari; Ando, Misaki

    2016-09-01

    The central structure in three of the brightest unlensed z = 3-4 submillimeter galaxies is investigated through 0.″015-0.″05 (120-360 pc) 860 μm continuum images obtained using the Atacama Large Millimeter/submillimeter Array (ALMA). The distribution in the central kiloparsec in AzTEC1 and AzTEC8 is extremely complex, and they are composed of multiple ˜200 pc clumps. AzTEC4 consists of two sources that are separated by ˜1.5 kpc, indicating a mid-stage merger. The peak star formation rate densities in the central clumps are ˜300-3000 M ⊙ yr-1 kpc-2, suggesting regions with extreme star formation near the Eddington limit. By comparing the flux obtained by ALMA and Submillimeter Array, we find that 68%-90% of the emission is extended (≳1 kpc) in AzTEC4 and 8. For AzTEC1, we identify at least 11 additional compact (˜200 pc) clumps in the extended 3-4 kpc region. Overall, the data presented here suggest that the luminosity surface densities observed at ≲150 pc scales are roughly similar to that observed in local ULIRGs, as in the eastern nucleus of Arp 220. Between 10% and 30% of the 860 μm continuum is concentrated in clumpy structures in the central kiloparsec, while the remaining flux is distributed over ≳1 kpc regions, some of which could also be clumpy. These sources can be explained by a rapid inflow of gas such as a merger of gas-rich galaxies, surrounded by extended and clumpy starbursts. However, the cold mode accretion model is not ruled out.

  4. ALMA MULTI-LINE IMAGING OF THE NEARBY STARBURST NGC 253

    SciTech Connect

    Meier, David S.; Walter, Fabian; Zschaechner, Laura K.; Bolatto, Alberto D.; Veilleux, Sylvain; Warren, Steven R.; Leroy, Adam K.; Ott, Jürgen; Rosolowsky, Erik; Weiß, Axel; Zwaan, Martin A.

    2015-03-01

    We present spatially resolved (∼50 pc) imaging of molecular gas species in the central kiloparsec of the nearby starburst galaxy NGC 253, based on observations taken with the Atacama Large Millimeter/submillimeter Array. A total of 50 molecular lines are detected over a 13 GHz bandwidth imaged in the 3 mm band. Unambiguous identifications are assigned for 27 lines. Based on the measured high CO/C{sup 17}O isotopic line ratio (≳350), we show that {sup 12}CO(1-0) has moderate optical depths. A comparison of the HCN and HCO{sup +} with their {sup 13}C-substituted isotopologues shows that the HCN(1-0) and HCO{sup +}(1-0) lines have optical depths at least comparable to CO(1-0). H{sup 13}CN/H{sup 13}CO{sup +} (and H{sup 13}CN/HN{sup 13}C) line ratios provide tighter constraints on dense gas properties in this starburst. SiO has elevated abundances across the nucleus. HNCO has the most distinctive morphology of all the bright lines, with its global luminosity dominated by the outer parts of the central region. The dramatic variation seen in the HNCO/SiO line ratio suggests that some of the chemical signatures of shocked gas are being erased in the presence of dominating central radiation fields (traced by C{sub 2}H and CN). High density molecular gas tracers (including HCN, HCO{sup +}, and CN) are detected at the base of the molecular outflow. We also detect hydrogen β recombination lines that, like their α counterparts, show compact, centrally peaked morphologies, distinct from the molecular gas tracers. A number of sulfur based species are mapped (CS, SO, NS, C{sub 2}S, H{sub 2}CS, and CH{sub 3}SH) and have morphologies similar to SiO.

  5. Marine Biotoxins: Laboratory Culture and Molecular Structure

    DTIC Science & Technology

    1991-01-21

    toxins that are associated with the human fish intoxication known as ciguatera , ciguatoxin and maitotoxin. of unknown structure at the outset of this...87-C-7210 Appendix A. Bibliography 1. Ciguatera - what we know and what we would like to know. P.J. Scheuer in "Mycotoxins and Phycotoxins 󈨜". (S...Mycotoxins, and Phycotoxins, Tokyo. Japan, August 1988. 2. Third International Conference on Ciguatera , Puerto Rico. April 1990. C. Personnel Receiving Pay

  6. Marine Toxins Origin, Structure, and Molecular Pharmacology

    DTIC Science & Technology

    1990-01-01

    thin-layer chromatography (TLC) were instrumental in the initial isolation and purification processes. Mass spectrometry (MS), infrared spectroscopy ...Frederick, MD 21701-5011 Methods of detection, metabolism, and pathophysiology of the brevetoxins, PbTx-2 and PbTx-3, are summarized. Infrared spectros...1R), circular dichroism (CD), nuclear magnetic resonance spectroscopy (NMR), and X-ray crystal- lography all played important roles in structure

  7. Molecular Eigensolution Symmetry Analysis and Fine Structure

    PubMed Central

    Harter, William G.; Mitchell, Justin C.

    2013-01-01

    Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

  8. Witnessing the Birth of the Red Sequence: ALMA High-resolution Imaging of [C II] and Dust in Two Interacting Ultra-red Starbursts at z = 4.425

    NASA Astrophysics Data System (ADS)

    Oteo, I.; Ivison, R. J.; Dunne, L.; Smail, I.; Swinbank, A. M.; Zhang, Z.-Y.; Lewis, A.; Maddox, S.; Riechers, D.; Serjeant, S.; Van der Werf, P.; Biggs, A. D.; Bremer, M.; Cigan, P.; Clements, D. L.; Cooray, A.; Dannerbauer, H.; Eales, S.; Ibar, E.; Messias, H.; Michałowski, M. J.; Pérez-Fournon, I.; van Kampen, E.

    2016-08-01

    Exploiting the sensitivity and spatial resolution of the Atacama Large Millimeter/submillimeter Array, we have studied the morphology and the physical scale of the interstellar medium—both gas and dust—in SGP 38326, an unlensed pair of interacting starbursts at z = 4.425. SGP 38326 is the most luminous star bursting system known at z > 4, with a total IR luminosity of L IR ˜ 2.5 × 1013 L ⊙ and a star formation rate of ˜ 4500 M ⊙ yr-1. SGP 38326 also contains a molecular gas reservoir among the most massive yet found in the early universe, and it is the likely progenitor of a massive, red-and-dead elliptical galaxy at z ˜ 3. Probing scales of ˜0.″1 or ˜800 pc we find that the smooth distribution of the continuum emission from cool dust grains contrasts with the more irregular morphology of the gas, as traced by the [C ii] fine structure emission. The gas is also extended over larger physical scales than the dust. The velocity information provided by the resolved [C ii] emission reveals that the dynamics of the two interacting components of SGP 38326 are each compatible with disk-like, ordered rotation, but also reveals an ISM which is turbulent and unstable. Our observations support a scenario where at least a subset of the most distant extreme starbursts are highly dissipative mergers of gas-rich galaxies.

  9. Giant Molecular Cloud Structure and Evolution

    NASA Technical Reports Server (NTRS)

    Hollenbach, David (Technical Monitor); Bodenheimer, P. H.

    2003-01-01

    Bodenheimer and Burkert extended earlier calculations of cloud core models to study collapse and fragmentation. The initial condition for an SPH collapse calculation is the density distribution of a Bonnor-Ebert sphere, with near balance between turbulent plus thermal energy and gravitational energy. The main parameter is the turbulent Mach number. For each Mach number several runs are made, each with a different random realization of the initial turbulent velocity field. The turbulence decays on a dynamical time scale, leading the cloud into collapse. The collapse proceeds isothermally until the density has increased to about 10(exp 13) g cm(exp -3). Then heating is included in the dense regions. The nature of the fragmentation is investigated. About 15 different runs have been performed with Mach numbers ranging from 0.3 to 3.5 (the typical value observed in molecular cloud cores is 0.7). The results show a definite trend of increasing multiplicity with increasing Mach number (M), with the number of fragments approximately proportional to (1 + M). In general, this result agrees with that of Fisher, Klein, and McKee who published three cases with an AMR grid code. However our results show that there is a large spread about this curve. For example, for M=0.3 one case resulted in no fragmentation while a second produced three fragments. Thus it is not only the value of M but also the details of the superposition of the various velocity modes that play a critical role in the formation of binaries. Also, the simulations produce a wide range of separations (10-1000 AU) for the multiple systems, in rough agreement with observations. These results are discussed in two conference proceedings.

  10. Ionization probes of molecular structure and chemistry

    SciTech Connect

    Johnson, P.M.

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  11. The Implications of Extreme Outflows from Extreme Starbursts

    NASA Astrophysics Data System (ADS)

    Heckman, Timothy M.; Borthakur, Sanchayeeta

    2016-05-01

    Interstellar ultraviolet absorption lines provide crucial information about the properties of galactic outflows. In this paper, we augment our previous analysis of the systematic properties of starburst-driven galactic outflows by expanding our sample to include a rare population of starbursts with exceptionally high outflow velocities. In principle, these could be a qualitatively different phenomenon from more typical outflows. However, we find that instead these starbursts lie on, or along the extrapolation of, the trends defined by the more typical systems studied previously by us. We exploit the wide dynamic range provided by this new sample to determine scaling relations of outflow velocity with galaxy stellar mass (M *), circular velocity, star formation rate (SFR), SFR/M *, and SFR/area. We argue that these results can be accommodated within the general interpretational framework we previously advocated, in which a population of ambient interstellar or circumgalactic clouds is accelerated by the combined forces of gravity and the momentum flux from the starburst. We show that this simple physical picture is consistent with both the strong cosmological evolution of galactic outflows in typical star-forming galaxies and the paucity of such galaxies with spectra showing inflows. We also present simple parameterizations of these results that can be implemented in theoretical models and numerical simulations of galaxy evolution.

  12. Starburst galaxies as seen by gamma-ray telescopes

    NASA Astrophysics Data System (ADS)

    Ohm, Stefan

    2016-06-01

    Starburst galaxies have a highly increased star-formation rate compared to regular galaxies and inject huge amounts of kinetic power into the interstellar medium via supersonic stellar winds, and supernova explosions. Supernova remnants, which are considered to be the main source of cosmic rays (CRs), form an additional, significant energy and pressure component and might influence the star-formation process in a major way. Observations of starburst galaxies at γ-ray energies give us the unique opportunity to study non-thermal phenomena associated with hadronic CRs and their relation to the star-formation process. In this work, recent observations of starburst galaxies with space and ground-based γ-ray telescopes are being reviewed, and the current state of theoretical work on the γ-ray emission is discussed. A special emphasis is put on the prospects of the next-generation Cherenkov Telescope Array for the study of starburst galaxies in particular and star-forming galaxies in general. xml:lang="fr"

  13. Revealing the Most Extreme Starbursts in the Early Universe

    NASA Astrophysics Data System (ADS)

    Conley, Alex

    We have developed a systematic method to select high-redshift massive, dusty starbursts using their far-IR red colors in data from the Herschel Space Observatory. Application to science demonstration data from the HerMES project has shown that this population is numerous (~2 per square degree), and follow up of the first few sources spectroscopically has yielded redshifts from 4 to 6.3. The existence of such extreme starbursts (> 1000 solar masses per year) within 1.6 Gyr of the Big Bang is very difficult to reconcile with models of galaxy formation and evolution, which predict only one such source per hundreds to thousands of square degrees. Here we propose to explore the nature of this population by: (a) developing more efficient methods to select these systems in Herschel data, (b) applying them to several hundred degrees of publicly available data from the HerMES and H-ATLAS surveys, and (c) use the resulting catalog to statistically characterize this population - a critical step in understanding what modifications must be made to current models. Our proposal will increase the number of known high-z massive starburst candidates by an order of magnitude. Taking advantage of the exceptional archival data available in these fields from Spitzer, WISE, and HST, we will study physical conditions in these extreme starbursts, placing them in the context of the overall star formation history of these systems.

  14. AN IONIZATION CONE IN THE DWARF STARBURST GALAXY NGC 5253

    SciTech Connect

    Zastrow, Jordan; Oey, M. S.; Veilleux, Sylvain; McDonald, Michael; Martin, Crystal L.

    2011-11-01

    There are few observational constraints on how the escape of ionizing photons from starburst galaxies depends on galactic parameters. Here we report on the first major detection of an ionization cone in NGC 5253, a nearby starburst galaxy. This high-excitation feature is identified by mapping the emission-line ratios in the galaxy using [S III] {lambda}9069, [S II] {lambda}6716, and H{alpha} narrowband images from the Maryland-Magellan Tunable Filter at Las Campanas Observatory. The ionization cone appears optically thin, which suggests the escape of ionizing photons. The cone morphology is narrow with an estimated solid angle covering just 3% of 4{pi} steradians, and the young, massive clusters of the nuclear starburst can easily generate the radiation required to ionize the cone. Although less likely, we cannot rule out the possibility of an obscured active galactic nucleus source. An echelle spectrum along the minor axis shows complex kinematics that are consistent with outflow activity. The narrow morphology of the ionization cone supports the scenario that an orientation bias contributes to the difficulty in detecting Lyman continuum emission from starbursts and Lyman break galaxies.

  15. Syntheses and molecular structures of new cali.

    PubMed

    Attner, J; Radius, U

    2001-01-01

    An unusual disproportionation reaction of the molybdenum(IV) and tungsten(IV) chlorides [MCl4L2] (M=Mo, L=Et2S, Et2O; M=W; L= Et2S) in the presence of p-tBu-calix[4]arene (Cax(OH)4) and triethylamine leads to d0 complexes [(CaxO4)[CaxO2(OH)2]M] (1) and d3 compounds (HNEt3)2[(CaxO4)2M2] (2). Complexes la (M = Mo), 1b (M = W), and the HCl adduct of 2a (M = Mo) have been structurally characterized. Compound 1a represents one of the few examples of a well-characterized molybdenum(VI) hexa-alkoxide complex of the type [Mo(OR)6]. Isolation and structural characterization of the side product [(CaxO4W)[kappa2(O)-kappa1(O)-CaxO3(OH)](CaxO4WCl)] (3) suggests the intermediacy of chloro-containing calix[4]arene complexes in these reaction mixtures. The reaction of 1a with HCI provides [CaxO4MoCl2] (4a), the first well-defined example of a mixed molybdenum(VI) alkoxide halide compound of the general formula [MoClx(OR)6-x].

  16. An Infrared Search for Extinguished Supernovae in Starburst Galaxies

    SciTech Connect

    Grossan, B.; Spillar, E.; Tripp, R.; Pirzkal, N.; Sutin, B.M.; Barnaby, D.

    1999-08-01

    IR and radio-band observations of heavily extinguished regions in starburst galaxies suggest a high supernova (SN) rate associated with such regions. Optically measured SN rates may therefore underestimate the total SN rate by factors of up to 10, as a result of the very high extinction ({ital A}{sub {ital B}}thinsp{approximately}thinsp10{endash}20 mag) to core-collapse SNe in starburst regions. The IR/radio SN rates come from a variety of indirect means, however, which suffer from model dependence and other problems. We describe a direct measurement of the SN rate from a regular patrol of starburst galaxies done with {ital K}{prime}-band imaging to minimize the effects of extinction. A collection of {ital K}{prime}-band measurements of core-collapse SNe near maximum light is presented. Such measurements (excluding 1987A) are not well reported in the literature. Results of a preliminary {ital K}{prime}-band search, using the MIRC camera at the Wyoming Infrared Observatory and an improved search strategy using the new ORCA optics, are described. A monthly patrol of a sample of {ital IRAS} bright (mostly starburst) galaxies within 25 Mpc should yield 1{endash}6 SNe yr{sup {minus}1}, corresponding to the range of estimated SN rates. Our initial MIRC search with low resolution (2&arcsec;2 pixels) failed to find extinguished SNe in the {ital IRAS} galaxies, limiting the SN rate outside the nucleus (at greater than 15{double_prime} radius) to less than 3.8 far-IR SN rate units (SNe per century per 10{sup 10} {ital L}{sub {circle_dot}} measured at 60 and 100 {mu}m, or FIRSRU) at 90{percent} confidence. The MIRC camera had insufficient resolution to search nuclear starburst regions, where starburst and SN activity is concentrated; therefore, we were unable to rigorously test the hypothesis of high SN rates in heavily obscured star-forming regions. We conclude that high-resolution nuclear SN searches in starburst galaxies with small fields are more productive than low

  17. Microwave spectrum and molecular structure of PNO

    NASA Astrophysics Data System (ADS)

    Okabayashi, Toshiaki; Yamazaki, Emi; Tanimoto, Mitsutoshi

    1999-08-01

    The microwave spectra of P14N16O and its isotopomers P15N16O and P14N18O were observed in a dc glow discharge plasma of a mixture of nitric oxide and hydrogen gases over solid red phosphorus placed on the stainless steel electrode. Rotational transitions of the parent P14N16O species were measured in the ground state as well as in the vibrationally excited ν1 (PN str.), ν2 (bend), and 2ν2 states. The l=0 substate of the 2ν2 state interacts with the ν1 state through a Fermi resonance. The rotational constants determined for the ground states of the three isotopomers yield the substitution structure, rs(PN)=151.6516(87) pm and rs(NO)=119.5025(80) pm.

  18. Dusty starburst galaxies in the early Universe as revealed by gravitational lensing.

    PubMed

    Vieira, J D; Marrone, D P; Chapman, S C; De Breuck, C; Hezaveh, Y D; Weiβ, A; Aguirre, J E; Aird, K A; Aravena, M; Ashby, M L N; Bayliss, M; Benson, B A; Biggs, A D; Bleem, L E; Bock, J J; Bothwell, M; Bradford, C M; Brodwin, M; Carlstrom, J E; Chang, C L; Crawford, T M; Crites, A T; de Haan, T; Dobbs, M A; Fomalont, E B; Fassnacht, C D; George, E M; Gladders, M D; Gonzalez, A H; Greve, T R; Gullberg, B; Halverson, N W; High, F W; Holder, G P; Holzapfel, W L; Hoover, S; Hrubes, J D; Hunter, T R; Keisler, R; Lee, A T; Leitch, E M; Lueker, M; Luong-Van, D; Malkan, M; McIntyre, V; McMahon, J J; Mehl, J; Menten, K M; Meyer, S S; Mocanu, L M; Murphy, E J; Natoli, T; Padin, S; Plagge, T; Reichardt, C L; Rest, A; Ruel, J; Ruhl, J E; Sharon, K; Schaffer, K K; Shaw, L; Shirokoff, E; Spilker, J S; Stalder, B; Staniszewski, Z; Stark, A A; Story, K; Vanderlinde, K; Welikala, N; Williamson, R

    2013-03-21

    In the past decade, our understanding of galaxy evolution has been revolutionized by the discovery that luminous, dusty starburst galaxies were 1,000 times more abundant in the early Universe than at present. It has, however, been difficult to measure the complete redshift distribution of these objects, especially at the highest redshifts (z > 4). Here we report a redshift survey at a wavelength of three millimetres, targeting carbon monoxide line emission from the star-forming molecular gas in the direction of extraordinarily bright millimetre-wave-selected sources. High-resolution imaging demonstrates that these sources are strongly gravitationally lensed by foreground galaxies. We detect spectral lines in 23 out of 26 sources and multiple lines in 12 of those 23 sources, from which we obtain robust, unambiguous redshifts. At least 10 of the sources are found to lie at z > 4, indicating that the fraction of dusty starburst galaxies at high redshifts is greater than previously thought. Models of lens geometries in the sample indicate that the background objects are ultra-luminous infrared galaxies, powered by extreme bursts of star formation.

  19. Connecting the density structure of molecular clouds with star formation

    NASA Astrophysics Data System (ADS)

    Kainulainen, Jouni

    In the current paradigm of turbulence-regulated interstellar medium (ISM), star formation rates of entire galaxies are intricately linked to the density structure of the individual molecular clouds. This density structure is essentially encapsulated in the probability distribution function of volume densities (ρ-PDF), which directly affects the star formation rates predicted by analytic models. Contrasting its fundamental role, the ρ-PDF function has remained virtually unconstrained by observations. I describe in this contribution the recent progress in attaining observational constraints for the column density PDFs (N-PDFs) of molecular clouds that function as a proxy of the ρ-PDFs. Specifically, observational works point towards a universal correlation between the shape of the N-PDFs and star formation activity in molecular clouds. The correlation is in place from the scales of a parsec up to the scales of entire galaxies, making it a fundamental, global link between the ISM structure and star formation.

  20. Molecular structure of vapor-deposited amorphous selenium

    NASA Astrophysics Data System (ADS)

    Goldan, A. H.; Li, C.; Pennycook, S. J.; Schneider, J.; Blom, A.; Zhao, W.

    2016-10-01

    The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. We developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

  1. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  2. ISOCAM view of the starburst galaxies M 82, NGC 253 and NGC 1808

    NASA Astrophysics Data System (ADS)

    Förster Schreiber, N. M.; Sauvage, M.; Charmandaris, V.; Laurent, O.; Gallais, P.; Mirabel, I. F.; Vigroux, L.

    2003-03-01

    We present results of mid-infrared lambda = 5.0-16.5 μm spectrophotometric imaging of the starburst galaxies M 82, NGC 253, and NGC 1808 from the ISOCAM instrument on board the Infrared Space Observatory. The mid-infrared spectra of the three galaxies are very similar in terms of features present. The lambda >~ 11 μm continuum attributed to very small dust grains (VSGs) exhibits a large spread in intensity relative to the short-wavelength emission. We find that the 15 mu m dust continuum flux density correlates well with the fine-structure [Ar Ii] 6.99 mu m line flux and thus provides a good quantitative indicator of the level of star formation activity. By contrast, the lambda = 5-11 μm region dominated by emission from polycyclic aromatic hydrocarbons (PAHs) has a nearly invariant shape. Variations in the relative intensities of the PAH features are nevertheless observed, at the 20%-100% level. We illustrate extinction effects on the shape of the mid-infrared spectrum of obscured starbursts, emphasizing the differences depending on the applicable extinction law and the consequences for the interpretation of PAH ratios and extinction estimates. The relative spatial distributions of the PAH, VSG, and [Ar Ii] 6.99 mu m emission between the three galaxies exhibit remarkable differences. The la 1 kpc size of the mid-infrared source is much smaller than the optical extent of our sample galaxies and 70%-100% of the IRAS 12 mu m flux is recovered within the ISOCAM <= 1.5 arcmin2 field of view, indicating that the nuclear starburst dominates the total mid-infrared emission while diffuse light from quiescent disk star formation contributes little. Based on observations with ISO, an ESA project with instruments funded by ESA member states (especially the PI countries: France, Germany, The Netherlands, and the UK), and with participation of ISAS and NASA.

  3. Molecular Evolution, Structure, and Function of Peroxidasins

    PubMed Central

    Soudi, Monika; Zamocky, Marcel; Jakopitsch, Christa; Furtmüller, Paul G; Obinger, Christian

    2012-01-01

    Peroxidasins represent the subfamily 2 of the peroxidase-cyclooxygenase superfamily and are closely related to chordata peroxidases (subfamily 1) and peroxinectins (subfamily 3). They are multidomain proteins containing a heme peroxidase domain with high homology to human lactoperoxidase that mediates one- and two-electron oxidation reactions. Additional domains of the secreted and glycosylated metalloproteins are type C-like immunoglobulin domains, typical leucine-rich repeats, as well as a von Willebrand factor C module. These are typical motifs of extracellular proteins that mediate protein–protein interactions. We have reconstructed the phylogeny of this new family of oxidoreductases and show the presence of four invertebrate clades as well as one vertebrate clade that includes also two different human representatives. The variability of domain assembly in the various clades was analyzed, as was the occurrence of relevant catalytic residues in the peroxidase domain based on the knowledge of catalysis of the mammalian homologues. Finally, the few reports on expression, localization, enzymatic activity, and physiological roles in the model organisms Drosophila melanogaster, Caenorhabditis elegans, and Homo sapiens are critically reviewed. Roles attributed to peroxidasins include antimicrobial defense, extracellular matrix formation, and consolidation at various developmental stages. Many research questions need to be solved in future, including detailed biochemical/physical studies and elucidation of the three dimensional structure of a model peroxidasin as well as the relation and interplay of the domains and the in vivo functions in various organisms including man. PMID:22976969

  4. Importance of Molecular Structure on the Thermophoresis of Binary Mixtures.

    PubMed

    Kumar, Pardeep; Goswami, Debabrata

    2014-12-26

    Using thermal lens spectroscopy, we study the role of molecular structural isomers of butanol on the thermophoresis (or Soret effect) of binary mixtures of methanol in butanol. In this study, we show that the thermal lens signal due to the Soret effect changes its sign for all the different concentrations of binary mixtures of butanol with methanol except for the one containing tertiary-butanol. The magnitude and sign of the Soret coefficients strongly depend on the molecular structure of the isomers of butanol in the binary mixture with methanol. This isomerization dependence is in stark contrast to the expected mass dependence of the Soret effect.

  5. From non-random molecular structure to life and mind

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1989-01-01

    The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

  6. ALMA Reveals Internal Structure of Molecular Clouds in the LMC

    NASA Astrophysics Data System (ADS)

    Sawada, T.; Hasegawa, T.; Koda, J.

    2015-12-01

    We carried out high-resolution (0.7 pc) CO J=1-0 mosaic observations of five giant molecular clouds, which cover a wide range of evolutionary stages based on their associations to recent star formation, in the Large Magellanic Cloud with ALMA. The observations revealed a variety of spatial structures of the gas, from faint and diffuse emission to bright and compact structures. The variation of structures, which is similar to that seen in the Milky Way, is quantified by the brightness distribution function (BDF) and brightness distribution index (BDI) established in our prior studies. The structured molecular gas may indicate the readiness for, rather than the outcome of, star formation.

  7. Origin and structure of polar domains in doped molecular crystals

    PubMed Central

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-01-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals. PMID:27824050

  8. Molecular structure and elastic properties of thermotropic liquid crystals: integrated molecular dynamics--statistical mechanical theory vs molecular field approach.

    PubMed

    Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A

    2013-03-21

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  9. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    NASA Astrophysics Data System (ADS)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  10. Molecular structure of DNA by scanning tunneling microscopy.

    PubMed

    Cricenti, A; Selci, S; Felici, A C; Generosi, R; Gori, E; Djaczenko, W; Chiarotti, G

    1989-09-15

    Uncoated DNA molecules marked with an activated tris(l-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 to 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  11. Molecular Structure of DNA by Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Cricenti, A.; Selci, S.; Felici, A. C.; Generosi, R.; Gori, E.; Djaczenko, W.; Chiarotti, G.

    1989-09-01

    Uncoated DNA molecules marked with an activated tris(1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 and 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  12. THE GREEN BANK TELESCOPE MAPS THE DENSE, STAR-FORMING GAS IN THE NEARBY STARBURST GALAXY M82

    SciTech Connect

    Kepley, Amanda A.; Frayer, David; Leroy, Adam K.; Usero, Antonio; Walter, Fabian

    2014-01-01

    Observations of the Milky Way and nearby galaxies show that dense molecular gas correlates with recent star formation, suggesting that the formation of this gas phase may help regulate star formation. A key test of this idea requires wide-area, high-resolution maps of dense molecular gas in galaxies to explore how local physical conditions drive dense gas formation, but these observations have been limited because of the faintness of dense gas tracers like HCN and HCO{sup +}. Here we demonstrate the power of the Robert C. Byrd Green Bank Telescope (GBT)—the largest single-dish millimeter radio telescope—for mapping dense gas in galaxies by presenting the most sensitive maps yet of HCN and HCO{sup +} in the starburst galaxy M82. The HCN and HCO{sup +} in the disk of this galaxy correlates with both recent star formation and more diffuse molecular gas and shows kinematics consistent with a rotating torus. The HCO{sup +} emission extending to the north and south of the disk is coincident with the outflow previously identified in CO and traces the eastern edge of the hot outflowing gas. The central starburst region has a higher ratio of star formation to dense gas than the outer regions, pointing to the starburst as a key driver of this relationship. These results establish that the GBT can efficiently map the dense molecular gas at 90 GHz in nearby galaxies, a capability that will increase further with the 16 element feed array under construction.

  13. Connecting molecular structure and exciton diffusion length in rubrene derivatives.

    PubMed

    Mullenbach, Tyler K; McGarry, Kathryn A; Luhman, Wade A; Douglas, Christopher J; Holmes, Russell J

    2013-07-19

    Connecting molecular structure and exciton diffusion length in rubrene derivatives demonstrates how the diffusion length of rubrene can be enhanced through targeted functionalization aiming to enhance self-Förster energy transfer. Functionalization adds steric bulk, forcing the molecules farther apart on average, and leading to increased photoluminescence efficiency. A diffusion length enhancement greater than 50% is realized over unsubstituted rubrene.

  14. MUSE Reveals a Recent Merger in the Post-starburst Host Galaxy of the TDE ASASSN-14li

    NASA Astrophysics Data System (ADS)

    Prieto, J. L.; Krühler, T.; Anderson, J. P.; Galbany, L.; Kochanek, C. S.; Aquino, E.; Brown, J. S.; Dong, Subo; Förster, F.; Holoien, T. W.-S.; Kuncarayakti, H.; Maureira, J. C.; Rosales-Ortega, F. F.; Sánchez, S. F.; Shappee, B. J.; Stanek, K. Z.

    2016-10-01

    We present Multi Unit Spectroscopic Explorer (MUSE) integral field spectroscopic observations of the host galaxy (PGC 043234) of one of the closest (z = 0.0206, D ≃ 90 Mpc) and best-studied tidal disruption events (TDEs), ASASSN-14li. The MUSE integral field data reveal asymmetric and filamentary structures that extend up to ≳10 kpc from the post-starburst host galaxy of ASASSN-14li. The structures are traced only through the strong nebular [O iii] λ5007, [N ii] λ6584, and Hα emission lines. The total off-nuclear [O iii] λ5007 luminosity is 4.7 × 1039 erg s-1, and the ionized H mass is ˜ {10}4(500/{n}{{e}}) {M}⊙ . Based on the Baldwin-Phillips-Terlevich diagram, the nebular emission can be driven by either AGN photoionization or shock excitation, with AGN photoionization favored given the narrow intrinsic line widths. The emission line ratios and spatial distribution strongly resemble ionization nebulae around fading AGNs such as IC 2497 (Hanny's Voorwerp) and ionization “cones” around Seyfert 2 nuclei. The morphology of the emission line filaments strongly suggest that PGC 043234 is a recent merger, which likely triggered a strong starburst and AGN activity leading to the post-starburst spectral signatures and the extended nebular emission line features we see today. We briefly discuss the implications of these observations in the context of the strongly enhanced TDE rates observed in post-starburst galaxies and their connection to enhanced theoretical TDE rates produced by supermassive black hole binaries.

  15. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    NASA Astrophysics Data System (ADS)

    Song-Feng, Zhao; Fang, Huang; Guo-Li, Wang; Xiao-Xin, Zhou

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov-Popov-Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  16. Molecular design for growth of supramolecular membranes with hierarchical structure.

    PubMed

    Zha, R Helen; Velichko, Yuri S; Bitton, Ronit; Stupp, Samuel I

    2016-02-07

    Membranes with hierarchical structure exist in biological systems, and bio-inspired building blocks have been used to grow synthetic analogues in the laboratory through self-assembly. The formation of these synthetic membranes is initiated at the interface of two aqueous solutions, one containing cationic peptide amphiphiles (PA) and the other containing the anionic biopolymer hyaluronic acid (HA). The membrane growth process starts within milliseconds of interface formation and continues over much longer timescales to generate robust membranes with supramolecular PA-HA nanofibers oriented orthogonal to the interface. Computer simulation indicates that formation of these hierarchically structured membranes requires strong interactions between molecular components at early time points in order to generate a diffusion barrier between both solutions. Experimental studies using structurally designed PAs confirm simulation results by showing that only PAs with high ζ potential are able to yield hierarchically structured membranes. Furthermore, the chemical structure of such PAs must incorporate residues that form β-sheets, which facilitates self-assembly of long nanofibers. In contrast, PAs that form low aspect ratio nanostructures interact weakly with HA and yield membranes that exhibit non-fibrous fingering protrusions. Furthermore, experimental results show that increasing HA molecular weight decreases the growth rate of orthogonal nanofibers. This result is supported by simulation results suggesting that the thickness of the interfacial contact layer generated immediately after initiation of self-assembly increases with polymer molecular weight.

  17. Molecular, Functional, and Structural Imaging of Major Depressive Disorder.

    PubMed

    Zhang, Kai; Zhu, Yunqi; Zhu, Yuankai; Wu, Shuang; Liu, Hao; Zhang, Wei; Xu, Caiyun; Zhang, Hong; Hayashi, Takuya; Tian, Mei

    2016-06-01

    Major depressive disorder (MDD) is a significant cause of morbidity and mortality worldwide, correlating with genetic susceptibility and environmental risk factors. Molecular, functional, and structural imaging approaches have been increasingly used to detect neurobiological changes, analyze neurochemical correlates, and parse pathophysiological mechanisms underlying MDD. We reviewed recent neuroimaging publications on MDD in terms of molecular, functional, and structural alterations as detected mainly by magnetic resonance imaging (MRI) and positron emission tomography. Altered structure and function of brain regions involved in the cognitive control of affective state have been demonstrated. An abnormal default mode network, as revealed by resting-state functional MRI, is likely associated with aberrant metabolic and serotonergic function revealed by radionuclide imaging. Further multi-modal investigations are essential to clarify the characteristics of the cortical network and serotonergic system associated with behavioral and genetic variations in MDD.

  18. Insights into molecular structure and digestion rate of oat starch.

    PubMed

    Xu, Jinchuan; Kuang, Qirong; Wang, Kai; Zhou, Sumei; Wang, Shuo; Liu, Xingxun; Wang, Shujun

    2017-04-01

    The in vitro digestibility of oat starch and its relationship with starch molecular structure was investigated. The in vitro digestion results showed that the first-order kinetic constant (k) of oat starches (OS-1 and OS-2) was lower than that of rice starch. The size of amylose chains, amylose content and degree of branching (DB) of amylopectin in oat starch were significantly higher than the corresponding parameters in rice starch. The larger molecular size of oat starch may account for its lower digestion rate. The fine structure of amylopectin showed that oat starch had less chains of DP 6-12 and DP>36, which may explain the small difference in digestion rate between oat and rice starch. The biosynthesis model from oat amylopectin fine structure data suggested a lower starch branching enzyme (SBE) activity and/or a higher starch synthase (SS) activity, which may decrease the DB of oat starch and increase its digestion rate.

  19. Photoelectron Angular Distribution and Molecular Structure in Multiply Charged Anions

    SciTech Connect

    Xing, Xiaopeng; Wang, Xue B.; Wang, Lai S.

    2009-02-12

    Photoelectrons emitted from multiply charged anions (MCAs) carry information of the intramolecular Coulomb repulsion (ICR), which is dependent on molecular structures. Using photoelectron imaging, we observed the effects of ICR on photoelectron angular distributions (PAD) of the three isomers of benzene dicarboxylate dianions C6H4(CO2)22– (o-, m- and p-BDC2–). Photoelectrons were observed to peak along the laser polarization due to the ICR, but the anisotropy was the largest for p-BDC2–, followed by the m- and o-isomer. The observed anisotropy is related to the direction of the ICR or the detailed molecular structures, suggesting that photoelectron imaging may allow structural information to be obtained for complex multiply charged anions.

  20. Molecular and electronic structure of electroactive self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Méndez De Leo, Lucila P.; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J.

    2013-03-01

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  1. Molecular and electronic structure of electroactive self-assembled monolayers.

    PubMed

    Méndez De Leo, Lucila P; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J

    2013-03-21

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  2. MOLVIE: an interactive visualization environment for molecular structures.

    PubMed

    Sun, Huandong; Li, Ming; Xu, Ying

    2003-05-01

    A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.

  3. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    PubMed

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  4. Three-dimensional depth profiling of molecular structures.

    PubMed

    Wucher, A; Cheng, J; Zheng, L; Winograd, N

    2009-04-01

    Molecular time of flight secondary ion mass spectrometry (ToF-SIMS) imaging and cluster ion beam erosion are combined to perform a three-dimensional chemical analysis of molecular films. The resulting dataset allows a number of artifacts inherent in sputter depth profiling to be assessed. These artifacts arise from lateral inhomogeneities of either the erosion rate or the sample itself. Using a test structure based on a trehalose film deposited on Si, we demonstrate that the "local" depth resolution may approach values which are close to the physical limit introduced by the information depth of the (static) ToF-SIMS method itself.

  5. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron

    PubMed Central

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons. PMID:27570482

  6. Ultraviolet Imaging of NGC 3310: A Merger-driven Global Starburst

    NASA Astrophysics Data System (ADS)

    Smith, Denise A.; Neff, Susan G.; Bothun, Gregory D.; Fanelli, Michael N.; Offenberg, Joel D.; Waller, William H.; Bohlin, Ralph C.; O'Connell, Robert W.; Roberts, Morton S.; Smith, Andrew M.; Stecher, Theodore P.

    1996-12-01

    We present the first far-ultraviolet (FUV; lambda ~ 1500 A) image of the nearby peculiar SAB(r)bc galaxy NGC 3310. The small 15" (945 pc) diameter circumnuclear starburst ring is the most luminous structure, producing 30% of the total observed FUV luminosity. Diffuse emission from the inner disk (20" < R < 40") contributes another ~20% of the observed FUV flux. A linear feature (the "arrow") appears to be a star-forming tidal feature. A diffuse arc observed at optical wavelengths (the "bow") is not visible in the FUV and is probably a tidally induced shell composed of older stars. Mean star formation rates range from 0.031 Msolar yr-1 kpc-2 in the arrow to 2.1 Msolar yr-1 kpc-2 at the brightest FUV source. The striking similarity between the R1/4 law behavior of the FUV and B-band surface brightness profiles, combined with the very blue colors of NGC 3310, strongly argues that the present morphology is the result of a global starburst triggered by a merger with a dwarf companion.

  7. Gamma-rays from pulsar wind nebulae in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Mannheim, Karl; Elsässer, Dominik; Tibolla, Omar

    2012-07-01

    Recently, gamma-ray emission at TeV energies has been detected from the starburst galaxies NGC253 (Acero et al., 2009) [1] and M82 (Acciari et al., 2009) [2]. It has been claimed that pion production due to cosmic rays accelerated in supernova remnants interacting with the interstellar gas is responsible for the observed gamma rays. Here, we show that the gamma-ray pulsar wind nebulae left behind by the supernovae contribute to the TeV luminosity in a major way. A single pulsar wind nebula produces about ten times the total luminosity of the Sun at energies above 1 TeV during a lifetime of 105 years. A large number of 3 × 104 pulsar wind nebulae expected in a typical starburst galaxy at a distance of 4 Mpc can readily produce the observed TeV gamma rays.

  8. A Perfect Starburst Cluster made in One Go: The NGC 3603 Young Cluster

    NASA Astrophysics Data System (ADS)

    Banerjee, Sambaran; Kroupa, Pavel

    2014-06-01

    Understanding how distinct, near-spherical gas-free clusters of very young, massive stars shape out of vast, complex clouds of molecular hydrogen is one of the biggest challenges in astrophysics. A popular thought dictates that a single gas cloud fragments into many newborn stars which, in turn, energize and rapidly expel the residual gas to form a gas-free cluster. This study demonstrates that the above classical paradigm remarkably reproduces the well-observed central, young cluster (HD 97950) of the Galactic NGC 3603 star-forming region, in particular, its shape, internal motion, and mass distribution of stars naturally and consistently follow from a single model calculation. Remarkably, the same parameters (star formation efficiency, gas expulsion timescale, and delay) reproduce HD 97950, as were found to reproduce the Orion Nebula Cluster, Pleiades, and R136. The present results therefore provide intriguing evidence of formation of star clusters through single-starburst events followed by significant residual gas expulsion.

  9. A perfect starburst cluster made in one go: The NGC 3603 young cluster

    SciTech Connect

    Banerjee, Sambaran; Kroupa, Pavel

    2014-06-01

    Understanding how distinct, near-spherical gas-free clusters of very young, massive stars shape out of vast, complex clouds of molecular hydrogen is one of the biggest challenges in astrophysics. A popular thought dictates that a single gas cloud fragments into many newborn stars which, in turn, energize and rapidly expel the residual gas to form a gas-free cluster. This study demonstrates that the above classical paradigm remarkably reproduces the well-observed central, young cluster (HD 97950) of the Galactic NGC 3603 star-forming region, in particular, its shape, internal motion, and mass distribution of stars naturally and consistently follow from a single model calculation. Remarkably, the same parameters (star formation efficiency, gas expulsion timescale, and delay) reproduce HD 97950, as were found to reproduce the Orion Nebula Cluster, Pleiades, and R136. The present results therefore provide intriguing evidence of formation of star clusters through single-starburst events followed by significant residual gas expulsion.

  10. Numerical models of starburst galaxies: Galactic winds and entrained gas

    NASA Astrophysics Data System (ADS)

    Tanner, Ryan

    My three-dimensional hydro-dynamical simulations of starbursts examine the formation of starburst-driven superbubbles over a range of driving luminosities and mass loadings that determine superbubble growth and wind velocity; floors of both 10 and 10. 4 K are considered. From this I determine the relationshipbetween the velocity of a galactic wind and the characteristics of the starburst. I find a threshold for the formation of a wind, above which the wind speed is not affected by grid resolution or the temperature floor of the radiative cooling employed. Optically bright filaments form at the edge of merging superbubbles, or where a cold dense cloud has been disrupted by the wind. Filaments formed by merging superbubbles will persist and grow to >400 pc in length if anchored to and fed from a star forming complex. For galaxies viewed edge on I use total emission from the superbubble to infer the wind velocity and starburst properties such as thermalization efficiency and mass loading factor. Using synthetic absorption profiles I probe different temperature regimes and measure the velocity of the cold, warm and hot gas phases. I find that the cold and warm gas entrained in the wind move at a much lower velocity than the hot gas, with some of the cold gas in the filaments hardly moving with respect to the galaxy. The absorption profiles show that the velocity of the hot galactic outflow does not depend on the star formation rate (SFR), but the velocity of the warm gas does. The velocity of the warm gas scales as SFR. delta untilthe wind velocity reaches 80 % of the analytic terminal wind speed. The value of delta depends on the atomic ionization with a lower value for low ionization, and a higher value for higher ionization.

  11. HAWK-I infrared supernova search in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Miluzio, M.; Cappellaro, E.; Botticella, M. T.; Cresci, G.; Greggio, L.; Mannucci, F.; Benetti, S.; Bufano, F.; Elias-Rosa, N.; Pastorello, A.; Turatto, M.; Zampieri, L.

    2013-06-01

    Context. The use of SN rates to probe explosion scenarios and to trace the cosmic star formation history received a boost from a number of synoptic surveys. There has been a recent claim of a mismatch by a factor of two between star formation and core collapse SN rates, and different explanations have been proposed for this discrepancy. Aims: We attempted an independent test of the relation between star formation and supernova rates in the extreme environment of starburst galaxies, where both star formation and extinction are extremely high. Methods: To this aim we conducted an infrared supernova search in a sample of local starbursts galaxies. The rationale behind searching in the infrared is to reduce the bias due to extinction, which is one of the putative reasons for the observed discrepancy between star formation and supernova rates. To evaluate the outcome of the search we developed a MonteCarlo simulation tool that is used to predict the number and properties of the expected supernovae based on the search characteristics and the current understanding of starburst galaxies and supernovae. Results: During the search we discovered 6 supernovae (4 with spectroscopic classification), which is in excellent agreement with the prediction of the MonteCarlo simulation tool that is, on average, 5.3 ± 2.3 events. Conclusions: The number of supernovae detected in starburst galaxies is consistent with what is predicted from their high star formation rate when we recognize that a major fraction (~ 60%) of the events remain hidden in the inaccessible, high-density nuclear regions because of a combination of reduced search efficiency and high extinction. ESO proposal: 083.D-0259, 085.D-0335, 085.D-0348, 087.D-0494, 087.D-0922. GTC proposal: GTC50-11B.

  12. A starburst region around l = 347° - 350°

    NASA Astrophysics Data System (ADS)

    Marco, A.; Negueruela, I.; Monguió, M.; González-Fernández, C.; Maíz Apellániz, J.; Dorda, R.; Clark, J. S.

    2017-03-01

    Very recently, a number of obscured massive open clusters have been identified in the Milky Way. A very significant fraction of them lie either close to the base of the Scutum Arm or towards Galactic longitude of 350°. We are studying these clusters and their neighbourhoods, finding very good evidence for a major starburst region close to the near tip of the Galactic Long Bar.

  13. Starburst or AGN dominance in submm-luminous candidate AGN

    NASA Astrophysics Data System (ADS)

    Coppin, Kristen; Alexander, Dave; Aretxaga, Itziar; Blain, Andrew; Chapman, Scott; Clements, Dave; Dunlop, James; Dunne, Loretta; Dye, Simon; Farrah, Duncan; Hughes, David; Ivison, Rob; Kim, Sungeun; Menendez-Delmestre, Karin; Oliver, Sebastian; Page, Mat; Pope, Alexandra; Rowan-Robinson, Michael; Scott, Douglas; Smail, Ian; Swinbank, Mark; Vaccari, Mattia; van Kampen, Eelco

    2008-03-01

    It is widely believed that starbursts/ULIRGs and AGN activity are triggered by galaxy interactions and merging; and sub-mm selected galaxies (SMGs) seem to be simply high redshift ULIRGs, observed near the peak of activity. In this evolutionary picture every SMG would host an AGN, which would eventually grow a black hole strong enough to blow off all of the gas and dust leaving an optically luminous QSO. In order to probe this evolutionary sequence, a crucial sub-sample to focus on would be the 'missing link' sources, which demonstrate both strong starburst and AGN signatures and to determine if the starburst is the main power source even in SMGs when we have evidence that an AGN is present. The best way to determine if a dominant AGN is present is to look in the mid-IR for their signatures, since often even deep X-ray observations miss identifying the presence of AGN in heavily dust-obscured SMGs. We have selected a sample of SMGs which are good candidates for harboring powerful AGN on the basis of their IRAC colours (S8um/S4.5um>2). Once we confirm these SMGs are AGN-dominated, we can then perform an audit of the energy balance between star-formation and AGN within this special sub-population of SMGs where the BH has grown appreciably to begin heating the dust emission. The proposed observations with IRS will probe the physics of how SMGs evolve from a cold-dust starburst-dominated ULIRG to an AGN/QSO by measuring the level of the mid-IR continuum, PAH luminosity, and Si absorption in these intermediate `transitory' AGN/SMGs.

  14. A more direct measure of supernova rates in starburst galaxies

    NASA Technical Reports Server (NTRS)

    Van Buren, Dave; Greenhouse, Matthew A.

    1994-01-01

    We determine ages for young supernova remnants in the starburst galaxies M82 and NGC 253 by applying Chevalier's model for radio emission from supernova blast waves expanding into the ejecta of their precursor stars. Absolute ages are determined by calibrating the model with radio observations of Cas A. We derive supernova rates of 0.10 and 0.08/yr for M82 and NGC 253, respectively. Assuming L (sub FIR) to be proportional to the supernova rate, we find r(sub SN) approximately equal 2 x 10(exp -12) x L(sub FIR), solar yr(exp -1) for these archetypal starburst galaxies. This approach is unique in that the supernova rate is derived from direct observation of supernova remnants rather than from star formation rates and an assumed initial mass function (IMF). We suggest that the approach presented here can be used to derive star-formation rates that are more directly related to observable quantities than those derived by other methods. We find that the supernova rate, far infrared (FIR) luminosity, and dynamical mass of the M82 starburst place few constraints on the initial mass function (IMF) slope and mass limits.

  15. Searching for Tidal Disruption Events in Post-Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Guevel, David; Arcavi, Iair

    2016-06-01

    Tidal Disruption Events (TDEs) are a class of transient phenomena that occur when a star passes sufficiently close to a supermassive black hole (SMBH) to be destroyed by tidal forces. Increasing the number of known TDEs will facilitate the study of SMBHs and black hole accretion physics. Recently it has been shown that TDEs occur most often in quiescent post-starburst galaxies (identified by strong Balmer absorption), some of which are know as "E+A" galaxies. These galaxies may have undergone a merger possibly contributing to the likelihood of TDEs. Using Las Cumbres Observatory Global Telescope (LCOGT) we are conducting a transient survey, called SEATiDE (Searching E+A Galaxies for Tidal Disruption Events), of 100 E+A galaxies. We experiment with different image subtraction techniques to improve our ability of detecting TDE flares in the centers of these galaxies. A future survey will cover an order of magnitude more post-starburst galaxies to measure their TDE rates in more detail with the aim of understanding why TDEs so strongly prefer post-starburst environments.

  16. Solution structures and molecular interactions of selective melanocortin receptor antagonists.

    PubMed

    Lee, Chul-Jin; Yun, Ji-Hye; Lim, Sung-Kil; Lee, Weontae

    2010-12-01

    The solution structures and inter-molecular interaction of the cyclic melanocortin antagonists SHU9119, JKC363, HS014, and HS024 with receptor molecules have been determined by NMR spectroscopy and molecular modeling. While SHU9119 is known as a nonselective antagonist, JKC363, HS014, and HS024 are selective for the melanocortin subtype-4 receptor (MC4R) involved in modulation of food intake. Data from NMR and molecular dynamics suggest that the conformation of the Trp9 sidechain in the three MC4R-selective antagonists is quite different from that of SHU9119. This result strongly supports the concept that the spatial orientation of the hydrophobic aromatic residue is more important for determining selectivity than the presence of a basic, "arginine-like" moiety responsible for biological activity. We propose that the conformation of hydrophobic residues of MCR antagonists is critical for receptor-specific selectivity.

  17. Study of the structuring of pure molecular liquids

    NASA Astrophysics Data System (ADS)

    Letamendia, L.; Duplessix, R.; Nouchi, G.; Vaucamps, C.

    Recent experiments have shown that changes in the slope of specific heat variation as a function of temperature in liquids are not always regular. In this study, the authors consider the possibility that fluid structure can change with temperature, by shifting from one form to another. They study such molecular liquids as benzene, hexafluorobenzene, and quinoleine using Rayleigh-Brillouin and depolarized Rayleigh diffusion, and total intensity diffusion. The authors clearly found anomalies for all collective properties of the medium in the liquids studied, though purely molecular properties were undisturbed. The accidents observed occurred at the same temperatures, whatever the collective or intermolecular property under study. But it took some time (several hours) for them to manifest themselves, which suggests that molecular liquids are characterized by a long thermodynamic equilibrium. Results also show a disturbance in hydrodynamic state at accident temperatures, which are similar to those generated by long spatial correlation processes.

  18. Molecular structures in the charmonium spectrum: the XYZ puzzle

    NASA Astrophysics Data System (ADS)

    Ortega, P. G.; Entem, D. R.; Fernández, F.

    2013-06-01

    We study in the framework of a constituent quark model the possible contributions of molecular structures to the XYZ charmonium-like states. We analyze simultaneously the c\\bar{c} structures and the possible molecular components in the coupled channel formalism. In the 1++ sector two states appear which could be identified with X(3872) and X(3940). The recently confirmed X(3915) state appears as a mixture of c\\bar{c} and D\\bar{D} components as a JPC = 0++ state in agreement with the new measurements. A second broad resonance which may correspond with the so-called Y(3940) state is found with these quantum numbers. In the JPC = 1-- sector we also found significant contributions of the molecular structures which may affect the phenomenology. In particular the study allows us to understand the G(3900) state recently observed in Belle and BaBar. All these resonances together with the prediction of the model of a c\\bar{c} structure for Z(3930) provide a reasonable scenario for the so-called XYZ states with masses near 3.9 GeV.

  19. Starburst galaxies in the COSMOS field: clumpy star-formation at redshift 0 < z < 0.5

    NASA Astrophysics Data System (ADS)

    Hinojosa-Goñi, R.; Muñoz-Tuñón, C.; Méndez-Abreu, J.

    2016-08-01

    -forming knots in our sample follows the same L(Hα) vs. size scaling relation as local giant HII regions. However, they slightly differ from the one provided using samples at high redshift. This result highlights the importance of spatially resolving the star-forming regions for this kind of study. Star-forming clumps in the central regions of Mknots galaxies are more massive, and present higher star formation rates, than those in the outskirts. This trend is less clear when we consider either the mass surface density or surface star formation rate. Sknot galaxies do show properties similar to both dwarf elliptical and irregulars in the surface brightness (μ) versus Mhost diagram in the B-band, and to spheroidals and ellipticals in the μ versus Mhost diagram in the V-band. Conclusions: The properties of our star-forming knots in Sknot+diffuse and Mknots/clumpy galaxies support the predictions of recent numerical simulations claiming that they have been produced by violent disk instabilities. We suggest that the evolution of these knots means that large and massive clumps at the galaxy centers represent the end product of the coalescence of surviving smaller clumps from the outskirts. Our results support this mechanism and make it unlikely that mergers are the reason behind the observed starburst knots. Sknot galaxies might be transitional phases of the Blue Compact Dwarfs (BCD) class, with their properties consistent with spheroidal-like, but blue structures. Tables 3 and 4 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/592/A122

  20. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  1. Ultrafast Photoresponsive Starburst and Dendritic Fullerenyl Nanostructures for Broadband Nonlinear Photonic Material Applications

    DTIC Science & Technology

    2014-08-20

    AFRL-OSR-VA-TR-2014-0197 ULTRAFAST PHOTORESPONSIVE STARBURST AND DENDRITIC FULLERENYL NOSTRUCTURES FOR BROADBAND NONLINEAR PHOTONIC MATERIAL...Report 3. DATES COVERED (From - To) 03-01-2009 – 05-31-2014 4. TITLE AND SUBTITLE Ultrafast Photoresponsive Starburst and Dendritic Fullerenyl...photophysical properties of ultrafast photoresponsive starburst and dendritic C60/C70-light harvesting antenna-based organic nanostructures for broadband

  2. Molecular solutes in ionic liquids: a structural perspective.

    PubMed

    Pádua, Agílio A H; Costa Gomes, Margarida F; Canongia Lopes, José N A

    2007-11-01

    Understanding physicochemical properties of ionic liquids is important for their rational use in extractions, reactions, and other applications. Ionic liquids are not simple fluids: their ions are generally asymetric, flexible, with delocalized electrostatic charges, and available in a wide variety. It is difficult to capture their subtle properties with models that are too simplistic. Molecular simulation using atomistic force fields, which describe structures and interactions in detail, is an excellent tool to gain insights into their liquid-state organization, how they solvate different compounds, and what molecular factors determine their properties. The identification of certain ionic liquids as self-organized phases, with aggregated nonpolar and charged domains, provides a new way to interpret the solvation and structure of their mixtures. Many advances are the result of a successful interplay between experiment and modeling, possible in this field where none of the two methodologies had a previous advance.

  3. Molecular modelling of miraculin: Structural analyses and functional hypotheses.

    PubMed

    Paladino, Antonella; Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2008-02-29

    Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies. Since structural data of miraculin are not available, we have predicted its three-dimensional structure and simulated both its dimer and tetramer forms by comparative modelling and molecular docking techniques. Finally, molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies.

  4. Nanoparticle Probes for Structural and Functional Photoacoustic Molecular Tomography

    PubMed Central

    Chen, Haobin; Yuan, Zhen; Wu, Changfeng

    2015-01-01

    Nowadays, nanoparticle probes have received extensive attention largely due to its potential biomedical applications in structural, functional, and molecular imaging. In addition, photoacoustic tomography (PAT), a method based on the photoacoustic effect, is widely recognized as a robust modality to evaluate the structure and function of biological tissues with high optical contrast and high acoustic resolution. The combination of PAT with nanoparticle probes holds promises for detecting and imaging diseased tissues or monitoring their treatments with high sensitivity. This review will introduce the recent advances in the emerging field of nanoparticle probes and their preclinical applications in PAT, as well as relevant perspectives on future development. PMID:26609534

  5. FilFinder: Filamentary structure in molecular clouds

    NASA Astrophysics Data System (ADS)

    Koch, Eric W.; Rosolowsky, Erik W.

    2016-08-01

    FilFinder extracts and analyzes filamentary structure in molecular clouds. In particular, it is capable of uniformly extracting structure over a large dynamical range in intensity. It returns the main filament properties: local amplitude and background, width, length, orientation and curvature. FilFinder offers additional tools to, for example, create a filament-only image based on the properties of the radial fits. The resulting mask and skeletons may be saved in FITS format, and property tables may be saved as a CSV, FITS or LaTeX table.

  6. Distribution of Molecules in the Circumnuclear Disk and Surrounding Starburst Ring in the Seyfert Galaxy NGC 1068 Observed with ALMA

    NASA Astrophysics Data System (ADS)

    Takano, S.; Nakajima, T.; Kohno, K.; Harada, N.; Herbst, E.; Tamura, Y.; Izumi, T.; Taniguchi, A.; Tosaki, T.

    2015-12-01

    We report distributions of several molecular transitions including shock and dust related species (13CO and C18O J = 1-0, 13CN N = 1-0, CS J = 2-1, SO JN = 32-21, HNCO JKa,Kc = 50,5-40,4, HC3N J = 11-10, 12-11, CH3OH JK = 2K-1K, and CH3CN JK = 6K-5K) in the nearby Seyfert 2 galaxy NGC 1068 observed with ALMA. The central ˜1' (˜4.3 kpc) of this galaxy was observed in the 100 GHz region with an angular resolution of ˜4" x 2" (290 pc x 140 pc) to study the effects of an active galactic nucleus and its surrounding starburst ring on molecular abundances. We report a classification of molecular distributions into three main categories. Organic molecules such as CH3CN are found to be concentrated in the circumnuclear disk. In the starburst ring, the intensity of methanol at each clumpy region is not consistent with that of 13CO.

  7. Sculpting Molecular Potentials to Design Optimized Materials: The Inverse Design of New Molecular Structures

    DTIC Science & Technology

    2010-05-10

    Miloradovic, A. Persoons, T . Verbiest, M. J . Therien, and K. Clays, "Molecular Symmetry and Solution Phase Structure Interrogated by Hyper-Raleigh...34 Nano Lett., 8, 2814-2818 (2008).  T . V. Duncan, K. Song, S.- T . Hung, I. Miloradovic, A. Persoons, T . Verbiest, M. J . Therien, and K. Clays...Beratan, Weitao Yang, Michael J . Therien, Koen Clays Duke University Office of Research Support Duke University Durham, NC 27705 - REPORT

  8. Molecular structures of amyloid and prion fibrils: consensus versus controversy.

    PubMed

    Tycko, Robert; Wickner, Reed B

    2013-07-16

    Many peptides and proteins self-assemble into amyloid fibrils. Examples include mammalian and fungal prion proteins, polypeptides associated with human amyloid diseases, and proteins that may have biologically functional amyloid states. To understand the propensity for polypeptides to form amyloid fibrils and to facilitate rational design of amyloid inhibitors and imaging agents, it is necessary to elucidate the molecular structures of these fibrils. Although fibril structures were largely mysterious 15 years ago, a considerable body of reliable structural information about amyloid fibril structures now exists, with essential contributions from solid state nuclear magnetic resonance (NMR) measurements. This Account reviews results from our laboratories and discusses several structural issues that have been controversial. In many cases, the amino acid sequences of amyloid fibrils do not uniquely determine their molecular structures. Self-propagating, molecular-level polymorphism complicates the structure determination problem and can lead to apparent disagreements between results from different laboratories, particularly when different laboratories study different polymorphs. For 40-residue β-amyloid (Aβ₁₋₄₀) fibrils associated with Alzheimer's disease, we have developed detailed structural models from solid state NMR and electron microscopy data for two polymorphs. These polymorphs have similar peptide conformations, identical in-register parallel β-sheet organizations, but different overall symmetry. Other polymorphs have also been partially characterized by solid state NMR and appear to have similar structures. In contrast, cryo-electron microscopy studies that use significantly different fibril growth conditions have identified structures that appear (at low resolution) to be different from those examined by solid state NMR. Based on solid state NMR and electron paramagnetic resonance (EPR) measurements, the in-register parallel β-sheet organization

  9. Distributions of molecules in the circumnuclear disk and surrounding starburst ring in the Seyfert galaxy NGC 1068 observed with ALMA

    NASA Astrophysics Data System (ADS)

    Takano, Shuro; Nakajima, Taku; Kohno, Kotaro; Harada, Nanase; Herbst, Eric; Tamura, Yoichi; Izumi, Takuma; Taniguchi, Akio; Tosaki, Tomoka

    2014-07-01

    Sensitive observations with the Atacama Large Millimeter/submillimeter Array (ALMA) allow astronomers to observe the detailed distributions of molecules with relatively weak intensity in nearby galaxies. In particular, we report distributions of several molecular transitions including shock and dust related species (13CO J = 1-0, C18O J = 1-0, 13CN N = 1-0, CS J = 2-1, SO JN = 32-21, HNCO JKa,Kc = 50,5-40,4, HC3N J = 11-10, 12-11, CH3OH JK = 2K-1K, and CH3CN JK = 6K-5K) in the nearby Seyfert 2 galaxy NGC 1068 observed with the ALMA early science program. The central ˜ 1'(˜ 4.3 kpc) of this galaxy was observed in the 100-GHz region covering ˜ 96-100 GHz and ˜ 108-111 GHz with an angular resolution of ˜ 4'' × 2'' (290 pc × 140 pc) to study the effects of an active galactic nucleus and its surrounding starburst ring on molecular abundances. Here, we present images and report a classification of molecular distributions into three main categories: (1) molecules concentrated in the circumnuclear disk (CND) (SO JN = 32-21, HC3N J = 11-10, 12-11, and CH3CN JK = 6K-5K), (2) molecules distributed both in the CND and the starburst ring (CS J = 2-1 and CH3OH JK = 2K-1K), and (3) molecules distributed mainly in the starburst ring (13CO J = 1-0 and C18O J = 1-0). Since most of the molecules such as HC3N observed in the CND are easily dissociated by UV photons and X-rays, our results indicate that these molecules must be effectively shielded. In the starburst ring, the relative intensity of methanol at each clumpy region is not consistent with those of 13CO, C18O, or CS. This difference is probably caused by the unique formation and destruction mechanisms of CH3OH.

  10. The essential signature of a massive starburst in a distant quasar.

    PubMed

    Solomon, P; Vanden Bout, P; Carilli, C; Guelin, M

    2003-12-11

    Observations of carbon monoxide emission in high-redshift (zeta > 2) galaxies indicate the presence of large amounts of molecular gas. Many of these galaxies contain an active galactic nucleus powered by accretion of gas onto a supermassive black hole, and a key question is whether their extremely high infrared luminosities result from the active galactic nucleus, from bursts of massive star formation (associated with the molecular gas), or both. In the Milky Way, high-mass stars form in the dense cores of interstellar molecular clouds, where gas densities are n(H2) > 10(5) cm(-3) (refs 1, 2). Recent surveys show that virtually all galactic sites of high-mass star formation have similarly high densities. The bulk of the cloud material traced by CO observations, however, is at a much lower density. For galaxies in the local Universe, the HCN molecule is an effective tracer of high-density molecular gas. Here we report observations of HCN emission from the infrared-luminous 'Cloverleaf' quasar (at a redshift zeta = 2.5579). The HCN line luminosity indicates the presence of 10 billion solar masses of very dense gas, an essential feature of an immense starburst, which contributes, together with the active galactic nucleus it harbours, to its high infrared luminosity.

  11. A MULTIWAVELENGTH STUDY ON THE FATE OF IONIZING RADIATION IN LOCAL STARBURSTS

    SciTech Connect

    Hanish, D. J.; Oey, M. S.; Rigby, J. R.; Lee, J. C.; De Mello, D. F.

    2010-12-20

    The fate of ionizing radiation is vital for understanding cosmic ionization, energy budgets in the interstellar and intergalactic medium, and star formation rate indicators. The low observed escape fractions of ionizing radiation have not been adequately explained, and there is evidence that some starbursts have high escape fractions. We examine the spectral energy distributions (SEDs) of a sample of local star-forming galaxies, containing 13 local starburst galaxies and 10 of their ordinary star-forming counterparts, to determine if there exist significant differences in the fate of ionizing radiation in these galaxies. We find that the galaxy-to-galaxy variations in the SEDs are much larger than any systematic differences between starbursts and non-starbursts. For example, we find no significant differences in the total absorption of ionizing radiation by dust, traced by the 24 {mu}m, 70 {mu}m, and 160 {mu}m MIPS bands of the Spitzer Space Telescope, although the dust in starburst galaxies appears to be hotter than that of non-starburst galaxies. We also observe no excess ultraviolet flux in the Galaxy Evolution Explorer bands that could indicate a high escape fraction of ionizing photons in starburst galaxies. The small H{alpha} fractions of the diffuse, warm ionized medium (WIM) in starburst galaxies are apparently due to temporarily boosted H{alpha} luminosity within the star-forming regions themselves, with an independent, constant WIM luminosity. This independence of the WIM and starburst luminosities contrasts with WIM behavior in non-starburst galaxies and underscores our poor understanding of radiation transfer in both ordinary and starburst galaxies.

  12. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  13. Structural characterization of polymorphs and molecular complexes of finasteride

    NASA Astrophysics Data System (ADS)

    Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

    1999-01-01

    The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

  14. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  15. Biological spectra analysis: Linking biological activity profiles to molecular structure

    PubMed Central

    Fliri, Anton F.; Loging, William T.; Thadeio, Peter F.; Volkmann, Robert A.

    2005-01-01

    Establishing quantitative relationships between molecular structure and broad biological effects has been a longstanding challenge in science. Currently, no method exists for forecasting broad biological activity profiles of medicinal agents even within narrow boundaries of structurally similar molecules. Starting from the premise that biological activity results from the capacity of small organic molecules to modulate the activity of the proteome, we set out to investigate whether descriptor sets could be developed for measuring and quantifying this molecular property. Using a 1,567-compound database, we show that percent inhibition values, determined at single high drug concentration in a battery of in vitro assays representing a cross section of the proteome, provide precise molecular property descriptors that identify the structure of molecules. When broad biological activity of molecules is represented in spectra form, organic molecules can be sorted by quantifying differences between biological spectra. Unlike traditional structure–activity relationship methods, sorting of molecules by using biospectra comparisons does not require knowledge of a molecule's putative drug targets. To illustrate this finding, we selected as starting point the biological activity spectra of clotrimazole and tioconazole because their putative target, lanosterol demethylase (CYP51), was not included in the bioassay array. Spectra similarity obtained through profile similarity measurements and hierarchical clustering provided an unbiased means for establishing quantitative relationships between chemical structures and biological activity spectra. This methodology, which we have termed biological spectra analysis, provides the capability not only of sorting molecules on the basis of biospectra similarity but also of predicting simultaneous interactions of new molecules with multiple proteins. PMID:15625110

  16. Discovering structural alerts for mutagenicity using stable emerging molecular patterns.

    PubMed

    Métivier, Jean-Philippe; Lepailleur, Alban; Buzmakov, Aleksey; Poezevara, Guillaume; Crémilleux, Bruno; Kuznetsov, Sergei O; Le Goff, Jérémie; Napoli, Amedeo; Bureau, Ronan; Cuissart, Bertrand

    2015-05-26

    This study is dedicated to the introduction of a novel method that automatically extracts potential structural alerts from a data set of molecules. These triggering structures can be further used for knowledge discovery and classification purposes. Computation of the structural alerts results from an implementation of a sophisticated workflow that integrates a graph mining tool guided by growth rate and stability. The growth rate is a well-established measurement of contrast between classes. Moreover, the extracted patterns correspond to formal concepts; the most robust patterns, named the stable emerging patterns (SEPs), can then be identified thanks to their stability, a new notion originating from the domain of formal concept analysis. All of these elements are explained in the paper from the point of view of computation. The method was applied to a molecular data set on mutagenicity. The experimental results demonstrate its efficiency: it automatically outputs a manageable number of structural patterns that are strongly related to mutagenicity. Moreover, a part of the resulting structures corresponds to already known structural alerts. Finally, an in-depth chemical analysis relying on these structures demonstrates how the method can initiate promising processes of chemical knowledge discovery.

  17. The mid-infrared appearance of the galactic mini-starburst W49A

    SciTech Connect

    Stock, D. J.; Peeters, E.; Choi, W. D.-Y.; Shannon, M. J.

    2014-08-20

    The massive star-forming region W49A represents one of the largest complexes of massive star formation present in the Milky Way and contains at least 50 young massive stars still enshrouded in their natal molecular cloud. We employ Spitzer/Infrared Spectrometer spectral mapping observations of the northern part of W49A to investigate the mid-infrared (MIR) spatial appearance of the polycyclic aromatic hydrocarbon (PAH) bands, PAH plateau features, atomic lines, and continuum emission. We examine the spatial variations of the MIR emission components in slices through two of the ultra-compact-H II (UC-H II) regions. We find that the PAH bands reproduce known trends, with the caveat that the 6.2 μm PAH band seems to decouple from the other ionized PAH bands in some of the UC-H II regions—an effect previously observed only in one other object: the giant star forming region N66 in the Large Magellanic Cloud. Furthermore, we compare the nature of the emission surrounding W49A to that of 'diffuse' sightlines. It is found that the surrounding emission can be explained by line of sight emission and does not represent true 'diffuse' material. Additionally, we examine the MIR appearance of star formation on various scales from UC-H II regions to starburst galaxies, including a discussion of the fraction of PAH emission in the 8 μm IRAC filter. We find that the MIR appearance of W49A is that of a starburst on large scales, yet its individual components are consistent with other galactic H II regions.

  18. Anatomy of Starbursts in Extragalactic Giant HII Regions: M51 Case Study

    NASA Astrophysics Data System (ADS)

    Evans, Jessica Marie; Chu, You-Hua

    2013-03-01

    Extragalactic giant HII regions (EGHRs) are sites of active, concentrated star formation, and thus provide excellent labs to analyze the starburst phenomenon. Although they have been known for a long time, ground-based observations cannot resolve the physical structures and stellar content of EGHRs. The high resolution and sensitivity of Hubble Space Telescope (HST) are ideal for detailed studies of EGHRs. We have searched the Hubble Legacy Archives (HLA) and found 17 nearby galaxies, within ˜15 Mpc, with Hα and continuum images; to determine the best methods for analyzing these data, we perform an in-depth analysis of the EGHRs in M51. M51 is a face-on spiral galaxy ˜8.4 Mpc away, with well-resolved multi-wavelength observations in the HLA. We sample the 25 most luminous HII regions in M51, many of which are bonafide EGHRs with an H-alpha luminosity > 1039 ergs s-1. We use the Hα image to study the distribution and physical structure of the gas in each HII region and determine its Hα luminosity and required ionizing flux. We use the continuum images to determine whether super stellar clusters (SSCs) are found in these HII regions, and use photometric measurements to determine the mass and age spread of the resolved stellar population. These are then compared with the interstellar structures. The results help us provide the groundwork for studying EGHRs in multiple galaxies and elucidate the starburst phenomenon by investigating questions such as: What role does environment play in the formation of EGHRs? How do EGHRs evolve? How does star formation proceed in an EGHR?

  19. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    NASA Astrophysics Data System (ADS)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P < 0.05) in the CH 2 asymmetric to CH 3 asymmetric stretching band peak intensity ratios for the flaxseed. There were linear and quadratic effects ( P < 0.05) of the treatment time from 0, 20, 40 and 60 min on the ratios of the CH 2 asymmetric to CH 3 asymmetric stretching vibration intensity. Autoclaving had no significant effect ( P > 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study

  20. State of water, molecular structure, and cytotoxicity of silk hydrogels.

    PubMed

    Numata, Keiji; Katashima, Takuya; Sakai, Takamasa

    2011-06-13

    A novel technique was developed to regulate the bulk water content of silk hydrogels by adjusting the concentrations of silk proteins, which is helpful to investigate the effects of the state of water in polymeric hydrogel on its biological functions, such as cytotoxicity. Gelation of the silk hydrogel was induced with ethanol and its gelation behavior was analyzed by rheometry. The silk hydrogels prepared at various silk concentrations were characterized with respect to their water content, molecular and network structures, state of water, mechanical properties, and cytotoxicity to human mesenchymal stem cells. The network structure of silk hydrogel was heterogeneous with β-sheet and fibrillar structures. The influence of the state of water in the silk hydrogel on the cytotoxicity was recognized by means of differential scanning calorimetry and cell proliferation assay, which revealed that the bound water will support cell-adhesion proteins in the cellular matrix to interact with the surface of the silk hydrogels.

  1. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    NASA Astrophysics Data System (ADS)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  2. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  3. State of the gas in intense lensed starbursts

    NASA Astrophysics Data System (ADS)

    George, Richard David

    2015-11-01

    The most intensely star-forming galaxies lie at z ˜ 2 and are thought to be the progenitors of the most massive galaxies today, yet study of this important population has been hampered by vast quantities of dust, making them almost invisible in the optical and ultraviolet (UV) regimes, and by the low sensitivity and angular resolution of many infrared (IR) facilities. Chapter 2 describes the use of the flux and angular extent boost provided by strong gravitational lensing in the detailed study of individual high-redshift dusty star-forming galaxies (DSFGs). The low number density of such systems has been overcome by recent wide area far-infrared (FIR)-mm surveys, and a sample of candidate systems which are bright enough to study with single-dish FIR telescopes are assembled from these surveys. The chapter further describes spectra of these galaxies obtained using the the Spectral and Photometric Imaging REceiver (SPIRE; Griffin et al. 2010) Fourier transform spectrometer (FTS) on board the Herschel Space Observatory (Pilbratt et al. 2010), exploiting the increased flux densities to search for FIR atomic and ionic spectral lines: important coolants of warm gas surrounding star-formation regions. Chapter 3 describes the first "blind" redshift obtained using Herschel, via the detection of [C II] 158 μm in one of our spectra. Confirmation of this redshift was provided by detection of CO lines with the Combined Array for Research in Millimeter-wave Astronomy (CARMA) and the Plateau de Bure Interferometer (PdBI), and along with multi-wavelength photometric follow-up, allowed a characterisation of the galaxy, indicating both a merger-driven starburst and an active galactic nucleus (AGN) within the system. Chapter 4 describes the first detection of a massive outflow of molecular gas at high-redshift. Stacking five repeat spectra of the Cosmic Eyelash, one of the best-studied strongly lensed DSFGs, one of the massive star-forming clumps is shown to drive this outflow

  4. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

    NASA Astrophysics Data System (ADS)

    Myasnikov, Alexander G.; Afonina, Zhanna A.; Ménétret, Jean-François; Shirokov, Vladimir A.; Spirin, Alexander S.; Klaholz, Bruno P.

    2014-11-01

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

  5. Three decades of structure- and property-based molecular design.

    PubMed

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been involved in this transformation process, to have been able to collaborate with, direct, guide, or simply encourage outstanding experts in various disciplines to build and further develop what has become a major pillar of modern small-molecule drug discovery. This article is an account of major events that took place since the early decision of Roche to implement computer-assisted molecular modeling 32 years ago and is devoted to the key players involved. It highlights the internal build-up of structural biology, with protein X-ray structure determination at its core, and the early setup of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries. These developments were accompanied by the rise of miniaturized parallel compound property analytics which resulted in a major paradigm shift in medicinal chemistry from linear to multi-dimensional lead optimization. The rapid growth of huge collections of property data stimulated the development of various novel data mining concepts with 'matched molecular pair' analysis and novel variants thereof playing crucial roles. As compound properties got more prominent in molecular design, exploration of specific structural motifs for property modulation became a research activity complementary to target-oriented medicinal chemistry. The exploration of oxetane is given as an example. For the sake of brevity, this account cannot detail all further developments that have taken place in each individual area of

  6. Structure of a molecular liquid GeI4

    NASA Astrophysics Data System (ADS)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-11-01

    A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ˜1 Å-1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed.

  7. THE RADIO–GAMMA CORRELATION IN STARBURST GALAXIES

    SciTech Connect

    Eichmann, B.; Tjus, J. Becker

    2016-04-20

    We present a systematic study of non-thermal electron–proton plasma and its emission processes in starburst galaxies in order to explain the correlation between the luminosity in the radio band and the recently observed gamma luminosity. In doing so, a steady state description of the cosmic-ray (CR) electrons and protons within the spatially homogeneous starburst is considered where continuous momentum losses are included as well as catastrophic losses due to diffusion and advection. The primary source of the relativistic CRs, e.g., supernova remnants, provides a quasi-neutral plasma with a power-law spectrum in momentum where we account for rigidity-dependent differences between the electron and proton spectrum. We examine the resulting leptonic and hadronic radiation processes by synchrotron radiation, inverse Compton scattering, Bremsstrahlung, and hadronic pion production. Finally, the observations of NGC 253, M82, NGC 4945, and NGC 1068 in the radio and gamma-ray bands as well as the observed supernova rate are used to constrain a best-fit model. In the case of NGC 253, M82, and NGC 4945 our model is able to accurately describe the data, showing that: (i) supernovae are the dominant particle accelerators for NGC 253, M82, and NGC 4945, but not for NGC 1068; (ii) all considered starburst galaxies are poor proton calorimeters in which for NGC 253 the escape is predominantly driven by the galactic wind, whereas the diffusive escape dominates in NGC 4945 and M82 (at energies >1 TeV); and (iii) secondary electrons from hadronic pion production are important to model the radio flux, but the associated neutrino flux is below the current observation limit.

  8. Starburst-driven Galactic Superbubbles Radiating to 10 K

    NASA Astrophysics Data System (ADS)

    Tanner, Ryan; Cecil, Gerald; Heitsch, Fabian

    2016-04-01

    Our three-dimensional hydrodynamical simulations of starbursts examine the formation of superbubbles over a range of driving luminosities and mass loadings that determine superbubble growth and wind velocity. From this we determine the relationship between the velocity of a galactic wind (GW) and the power of the starburst. We find a threshold for the formation of a wind, above which the speed of the wind is not affected by grid resolution or the temperature floor of our radiative cooling. We investigate the effect that two different temperature floors in our radiative cooling prescription have on wind kinematics and content. We find that cooling to 10 K instead of to 104 K increases the mass fraction of cold neutral and hot X-ray gas in the GW, while halving that in warm Hα. Our simulations show that the mass of cold gas transported into the lower halo does not depend on the starburst strength. Optically bright filaments form at the edge of merging superbubbles, or where a cold dense cloud has been disrupted by the wind. Filaments formed by merging superbubbles will persist and grow to \\gt 400 pc in length if anchored to a star forming complex. Filaments embedded in the hot GW contain warm and cold gas that moves 300-1200 km s-1 slower than the surrounding wind, with the coldest gas hardly moving with respect to the Galaxy. Warm and cold matter in the GW show asymmetric absorption profiles consistent with observations, with a thin tail up to the wind velocity.

  9. A Multiwavelength Study of the Starburst Galaxy NGC 7771

    NASA Technical Reports Server (NTRS)

    Davies, Richard I.; Alonso-Herrero, Almudena; Ward, Martin J.

    1997-01-01

    We present a multiwavelength study of the interacting starburst galaxy NGC 7771, including new optical and ultra-violet spectra and a previously unpublished soft X-ray ROSAT image and spectrum. The far-infrared, radio, and X-ray fluxes suggest that a massive burst of star-formation is currently in progress but the small equivalent width of the Balmer emission lines (equivalent width H(alpha approximately equals 100 A), the weak UV flux, the low abundance of ionised oxygen, and the shape of the optical spectrum lead us to conclude that there are few 0 stars. This might normally suggest that star-formation has ceased but the galaxy's barred gravitational potential and large gas reserves imply that this should not be so, and we therefore consider other explanations. We argue that the observations cannot be due to effects of geometry, density bounded nebulae, or dust within the nebulae, and conclude that a truncated IMF is required. The dwarf galaxy NGC 7770 appears to be in the initial stages of a merger with NGC 7771, and the resulting tidal perturbations may have induced the apparent two-armed spiral pattern, and driven a substantial fraction of the disk gas inwards. The presence of a bulge in NGC 7771 may be moderating the starburst so that, while still occuring on a large scale with a supernova rate of 0.8-1/yr, it is less violent and the IMF has a relatively low upper mass limit. We find that there is a cluster of stars obscuring part of the starburst region, and we offer an explanation of its origin.

  10. Structure-based molecular modeling approaches to GPCR oligomerization.

    PubMed

    Kaczor, Agnieszka A; Selent, Jana; Poso, Antti

    2013-01-01

    Classical structure-based drug design techniques using G-protein-coupled receptors (GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a single receptor. Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have, however, crucial relevance for drug design. Targeting these complexes selectively or designing small molecules that affect receptor-receptor interactions might provide new opportunities for novel drug discovery. In order to study the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to understand the dynamic process of receptor-receptor association and to identify regions that are suitable for selective drug binding, which may be determined with experimental methods such as Förster resonance energy transfer (FRET) or Bioluminescence resonance energy transfer (BRET) and computational sequence- and structure-based approaches. The aim of this chapter is to provide a comprehensive description of the structure-based molecular modeling methods for studying GPCR dimerization, that is, protein-protein docking, molecular dynamics, normal mode analysis, and electrostatics studies.

  11. Optical investigation of molecular structure of sophisticated materials for photonics

    NASA Astrophysics Data System (ADS)

    Gnyba, Marcin; Keraenen, Mikko

    2003-10-01

    Permanent development of photonics stimulates a searching for new materials, which have better optical, mechanical and electrical properties. One of the new classes of materials with large application and development potential are hybrid polymers, synthesized in sol-gel technology. Thanks to incorporation of organic components into an in organic network, a combination of advantages of both class of materials became available. Properties of hybrids may be formed in wide range. These materials can be used in photonics to produce planar waveguides, lenses, Bragg gratings and components for integrated optics. Moreover, dielectric layers, coatings and packaging are made from hybrids. Additionally, research to apply them in optical fiber sensors (including bio-sensors) and solid state lasers is underway. However, to obtain a high quality product, a strict control of its molecular structure must be ensured. This is a very difficult task, because of a sophisticated structure of hybrid polymers. To address these problems, optical, non-destructive measurement techniques such as Raman and infrared spectroscopy were used. They are compementary methods, so their simultaneous application, as it was shown in this paper, can significantly increase the amoung of information about molecular structure of materials and process of their synthesis.

  12. The multifrequency spectrum of the starburst galaxy NGC 2782

    NASA Technical Reports Server (NTRS)

    Kinney, A. L.; Bregman, J. N.; Huggins, P. J.; Glassgold, A. E.; Cohen, R. D.

    1984-01-01

    The nuclear region of NGC 2782 has been observed at radio, millimeter, infrared, optical, ultraviolet, and X-ray frequencies to understand the ionization source that gives rise to the narrow emission lines. The continuum is probably caused by a normal galactic population plus considerable numbers of young stars and warm dust. In the ultraviolet and optical spectra, which are powerful diagnostics, no strong lines are detected in the 1200 A-3200 A region aside from L-alpha, and the optical emission lines cover only a narrow ionization range. The line and continuum properties suggest that NGC 2782 is a starburst galaxy, in which young stars photoionize the surrounding gas.

  13. Search for Supernovae in Starburst Galaxies with HAWK-I

    NASA Astrophysics Data System (ADS)

    Miluzio, M.

    2014-03-01

    With the aim of testing the relation between supernova (SN) rate and star formation rate, we conducted a SN search in a sample of local starburst galaxies (SBs) where both star formation rates and extinction are extremely high. The search was performed in the near-infrared, where the bias due to extinction is reduced using HAWK-I on the VLT. We discovered six SNe, in excellent agreement with expectations, when considering that, even in our search, about 60% of events remain hidden in the nuclear regions due to a combination of reduced search efficiency and very high extinction.

  14. Kinetic Effects of Aromatic Molecular Structures on Diffusion Flame Extinction

    SciTech Connect

    Won, Sang Hee; Dooley, S.; Dryer, F. L.; Ju, Yiguang

    2011-01-01

    Kinetic effects of aromatic molecular structures for jet fuel surrogates on the extinction of diffusion flames have been investigated experimentally and numerically in the counterflow configuration for toluene, n-propylbenzene, 1,2,4-trimethylbenzene, and 1,3,5-trimethylbenzene. Quantitative measurement of OH concentration for aromatic fuels was conducted by directly measuring the quenching rate from the emission lifetimes of OH planar laser induced fluorescence (LIF). The kinetic models for toluene and 1,2,4-trimethylbenzene were validated against the measurements of extinction strain rates and LIF measurements. A semi-detailed n-propylbenzene kinetic model was developed and tested. The experimental results showed that the extinction limits are ranked from highest to lowest as n-propylbenzene, toluene, 1,2,4-trimethylbenzene, and 1,3,5-trimethylbenzene. The present models for toluene and n-propylbenzene agree reasonably well with the measurements, whereas the model for 1,2,4-trimethylbenzene under-estimates extinction limits. Kinetic pathways of OH production and consumption were analyzed to investigate the impact of fuel fragmentation on OH formation. It was found that, for fuels with different molecular structures, the fuel decomposition pathways and their propagation into the formation of radical pool play an important role to determine the extinction limits of diffusion flames. Furthermore, OH concentrations were found to be representative of the entire radical pool concentration, the balance between chain branching and propagation/termination reactions and the balance between heat production from the reaction zone and heat losses to the fuel and oxidizer sides. Finally, a proposed “OH index,” was defined to demonstrate a linear correlation between extinction strain rate and OH index and fuel mole fraction, suggesting that the diffusion flame extinctions for the tested aromatic fuels can be determined by the capability of a fuel to establish a radical pool

  15. Bohm's Quantum Potential and the Visualization of Molecular Structure

    NASA Technical Reports Server (NTRS)

    Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

  16. Structurally Defined Molecular Hypervalent Iodine Catalysts for Intermolecular Enantioselective Reactions

    PubMed Central

    Haubenreisser, Stefan; Wöste, Thorsten H.; Martínez, Claudio; Ishihara, Kazuaki

    2015-01-01

    Abstract Molecular structures of the most prominent chiral non‐racemic hypervalent iodine(III) reagents to date have been elucidated for the first time. The formation of a chirally induced supramolecular scaffold based on a selective hydrogen‐bonding arrangement provides an explanation for the consistently high asymmetric induction with these reagents. As an exploratory example, their scope as chiral catalysts was extended to the enantioselective dioxygenation of alkenes. A series of terminal styrenes are converted into the corresponding vicinal diacetoxylation products under mild conditions and provide the proof of principle for a truly intermolecular asymmetric alkene oxidation under iodine(I/III) catalysis. PMID:26596513

  17. Relationship between antimold activity and molecular structure of cinnamaldehyde analogues.

    PubMed

    Zhang, Yuanyuan; Li, Shujun; Kong, Xianchao

    2013-03-01

    A quantitative structure-activity relationship (QSAR) modeling of the antimold activity of cinnamaldehyde analogues against of Aspergillus niger and Paecilomyces variotii was presented. The molecular descriptors of cinnamaldehyde analogues were calculated by the CODESSA program, and these descriptors were selected by best multi-linear regression method (BMLR). Satisfactory multilinear regression models of Aspergillus niger and Paecilomyces variotii were obtained with R(2)=0.9099 and 0.9444, respectively. The models were also satisfactorily validated using internal validation and leave one out validation. The QSAR models provide the guidance for further synthetic work.

  18. Structural Organization of {pi} Conjugated Highly Luminescent Molecular Material

    SciTech Connect

    Toudic, B.; Limelette, P.; Le Gac, F.; Moreac, A.; Rabiller, P.; Froyer, G.

    2005-11-18

    We report on striking evidence for a room temperature structural phase instability in p-hexaphenyl, inducing a nonplanar conformation of the molecules. Solid state proton NMR and single crystal x-ray diffraction allow the analysis of the organization, the individual dynamics and the involved symmetry breaking. The analysis of Raman spectra above and below room temperature reveals a singular behavior suggesting a modification of the overlap between the electronic wave function induced by the nonplanarity. These results provide a new basis to answer fundamental issues related to molecular and electronic materials and, in particular, luminescent organic devices.

  19. Molecular and electronic structures of cerium and cerium suboxide clusters

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Topolski, Josey E.; Jarrold, Caroline Chick

    2016-10-01

    The anion photoelectron (PE) spectra of Ce2Oy- (y = 1, 2), Ce3Oy- (y = 0-4), Ce4Oy- (y = 0-2), and Ce5Oy- (y = 1, 2) are reported and analyzed with supporting results from density functional theory calculations. The PE spectra all exhibit an intense electronic transition to the neutral ground state, all falling in the range of 0.7 to 1.1 eV electron binding energy, with polarization dependence consistent with detachment from diffuse Ce 6s-based molecular orbitals. There is no monotonic increase in electron affinity with increasing oxidation. A qualitative picture of how electronic structure evolves with an oxidation state emerges from comparison between the spectra and the computational results. The electronic structure of the smallest metallic cluster observed in this study, Ce3, is similar to the bulk structure in terms of atomic orbital occupancy (4f 5d2 6s). Initial cerium cluster oxidation involves largely ionic bond formation via Ce 5d and O 2p orbital overlap (i.e., larger O 2p contribution), with Ce—O—Ce bridge bonding favored over Ce=O terminal bond formation. With subsequent oxidation, the Ce 5d-based molecular orbitals are depleted of electrons, with the highest occupied orbitals described as diffuse Ce 6s based molecular orbitals. In the y ≤ (x + 1) range of oxidation states, each Ce center has a singly occupied non-bonding 4f orbital. The PE spectrum of Ce3O4- is unique in that it exhibits a single nearly vertical transition. The highly symmetric structure predicted computationally is the same structure determined from Ce3O4+ IR predissociation spectra [A. M. Burow et al., Phys. Chem. Chem. Phys. 13, 19393 (2011)], indicating that this structure is stable in -1, 0, and +1 charge states. Spectra of clusters with x ≥ 3 exhibit considerable continuum signal above the ground state transition; the intensity of the continuum signal decreases with increasing oxidation. This feature is likely the result of numerous quasi-bound anion states or two

  20. THE NATURE OF STARBURSTS. III. THE SPATIAL DISTRIBUTION OF STAR FORMATION

    SciTech Connect

    McQuinn, Kristen B. W.; Skillman, Evan D.; Dalcanton, Julianne J.; Weisz, Daniel R.; Williams, Benjamin F.; Cannon, John M.; Dolphin, Andrew E.; Holtzman, Jon

    2012-11-01

    We map the spatial distribution of recent star formation over a few Multiplication-Sign 100 Myr timescales in 15 starburst dwarf galaxies using the location of young blue helium burning stars identified from optically resolved stellar populations in archival Hubble Space Telescope observations. By comparing the star formation histories from both the high surface brightness central regions and the diffuse outer regions, we measure the degree to which the star formation has been centrally concentrated during the galaxies' starbursts, using three different metrics for the spatial concentration. We find that the galaxies span a full range in spatial concentration, from highly centralized to broadly distributed star formation. Since most starbursts have historically been identified by relatively short timescale star formation tracers (e.g., H{alpha} emission), there could be a strong bias toward classifying only those galaxies with recent, centralized star formation as starbursts, while missing starbursts that are spatially distributed.

  1. Large-Field CO(J = 1→0) Observations of the Starburst Galaxy M 82

    NASA Astrophysics Data System (ADS)

    Salak, Dragan; Nakai, Naomasa; Miyamoto, Yusuke; Yamauchi, Aya; Tsuru, Takeshi G.

    2013-06-01

    We present large-field (15.7 × 16.9 arcmin2) CO(J = 1→0) observations of the starburst galaxy M 82, at an angular resolution of 22" with the NRO 45-m telescope. The CO emission was detected in the galactic disk, outflow (driven by the galactic wind) up to ˜2 kpc above the galactic plane in the halo, and in tidal streams. The kinematics of the outflow (including CO line splitting) suggests that it has the shape of a cylinder that is diverging outwards. The mass and kinetic energy of the molecular gas outflow are estimated to be (0.26-1.0) × 109 M⊙ and (1-4) × 1056 erg. A clump of CO gas was discovered 3.5 kpc above the galactic plane; it coincides with a dark lane previously found in X-ray observations, and a peak in H I emission. A comparison with H I, hot molecular hydrogen and dust suggests that the molecular gas shows signatures of warm and cool components in the outflow and tidal streams, respectively.

  2. Gas distribution and starbursts in shell galaxies

    NASA Technical Reports Server (NTRS)

    Weil, Melinda L.; Hernquist, Lars

    1993-01-01

    Detailed maps of most elliptical galaxies reveal that, whereas the greatest part of their luminous mass originates from a smooth distribution with a surface brightness approximated by a de Vaucouleurs law, a small percentage of their light is contributed by low surface brightness distortions termed 'fine structures'. The sharp-edged features called 'shells' are successfully reproduced by merger and infall models involving accretion from less massive companions. In this context, dwarf spheroidal and compact disk galaxies are likely progenitors of these stellar phenomena. However, it is probable that the sources of shell-forming material also contain significant amounts of gas. This component may play an important role in constraining the formation and evolution of shell galaxies. To investigate the effects of the gaseous component, numerical simulations were performed to study the tidal disruption of dwarf galaxies containing both gas and stars by more massive primaries, and the evolution of the ensuing debris. The calculations were performed with a hybrid N-body/hydrodynamics code. Collisionless matter is evolved using a conventional N-body technique and gas is treated using smoothed particle hydrodynamics in which self-gravitating fluid elements are represented as particles evolving according to Lagrangian hydrodynamic equations. An isothermal equation of state is employed so the gas remains at a temperature 104 K. Owing to the large mass ratio between the primary and companion, the primary is modeled as a rigid potential and the self-gravity of both galaxies is neglected.

  3. Molecular structure of uranium carbides: isomers of UC3.

    PubMed

    Zalazar, M Fernanda; Rayón, Víctor M; Largo, Antonio

    2013-03-21

    In this article, the most relevant isomers of uranium tricarbide are studied through quantum chemical methods. It is found that the most stable isomer has a fan geometry in which the uranium atom is bonded to a quasilinear C3 unit. Both, a rhombic and a ring CU(C2) structures are found about 104-125 kJ/mol higher in energy. Other possible isomers including linear geometries are located even higher. For each structure, we provide predictions for those molecular properties (vibrational frequencies, IR intensities, dipole moments) that could eventually help in their experimental detection. We also discuss the possible routes for the formation of the different UC3 isomers as well as the bonding situation by means of a topological analysis of the electron density.

  4. Crystal and molecular structures of new enantiopure quinuclidines.

    PubMed

    Kania, Iwona; Stadnicka, Katarzyna; Oleksyn, Barbara J

    2004-03-01

    X-ray crystal structure analysis was performed on single crystals of two diastereomeric enantiopure quinuclidines, (3R,8R)-3-vinyl-8-hydroxymethyl-quinuclidine (quincoridine, QCD) and (3R,8S)-3-vinyl-8-hydroxymethyl-quinuclidine (quincorine, QCI) as their salts with tartaric and p-toluenesulphonate anions, respectively. The molecules of these quinuclidine derivatives are considered here as fragments of the Cinchona alkaloids, quinidine and quinine. A comparison of the conformational features of QCD, QCI, and Cinchona alkaloids in the crystalline state shows that the molecular geometry of the title compounds is similar to that of threo-alkaloids (e.g., R,R isomer of epicinchonine) rather than to quinidine and quinine. The packing of the molecules in both structures is dominated by intermolecular hydrogen bonds.

  5. Noninvasive structural, functional, and molecular imaging in drug development.

    PubMed

    Rudin, Markus

    2009-06-01

    Modern drug research is mechanism-based and the development of disease modifying therapies involves the identification of molecular key players in the pathological cascade. Today, noninvasive imaging tools enable the visualization and quantitative assessment of the expression of molecular targets, of their interaction with potential ligands, as well as of the functional consequence of this interaction at a molecular (e.g. activation of signaling cascades), cellular, metabolic, physiological, and morphological level in a temporo-spatially resolved manner. The ability to gather such information from the intact organism with all regulatory processes in place renders imaging highly attractive for the biomedical researcher and for the drug developer in particular. Molecular imaging is potentially capable of providing this information. Today, proof-of-principle has been established that imaging is in fact adding value to the drug discovery and development processes. Numerous studies have used structural and functional imaging readouts to document therapy efficacy, mainly during lead optimization. Similarly, major efforts have been devoted to the development and evaluation of imaging biomarkers that might serve as early readouts for therapy response with the potential of being used in the clinical drug evaluation thereby facilitating translational research. In this contribution, we illustrate the role and potential of imaging in modern drug discovery and development with selected examples. Yet, despite its huge potential the impact of imaging on drug discovery has been modest in the past; potential reasons will be discussed. Nevertheless, noninvasive imaging methods are rapidly evolving and it is beyond doubt that their importance for biomedical research will increase.

  6. Phenol-formaldehyde resins: A quantitative NMR study of molecular structure and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ottenbourgs, Benjamin Tony

    Phenol-formaldehyde (PF) resins have been the subject of this work. 13C liquid-state and solid-state NMR has been used to investigate the molecular structure of mainly novolak and partially of resole resins. 1H wideline in combination with 13C solid-state NMR relaxometry has been applied to study the curing and the molecular dynamics of phenolic resins. It was the intention to provide an insight in the relationship between resin composition, resin structure and subsequent resin properties (by means of the molecular dynamics). An improved 13C liquid-state NMR quantification technique of novolaks in THF-CDCl3 solutions is demonstrated. Full quantitative 13C liquid-state spectra of phenol-formaldehyde resins with high signal- to-noise ratio were obtained by using chromium acetylacetonate under optimized spectral conditions within a few hours spectrometer time. Attached proton test (APT) spectra enabled proper peak assignments in the region with significant overlap. For several novolaks, prepared under different catalytic conditions, the degree of polymerization, degree of branching, number average molecular weight, isomeric distribution, and the number of unreacted ortho and para phenol ring positions was determined with a reduced margin of error, by analyzing and integrating the 13C spectra. The power of 13C solid-state NMR in the analysis of cured PF resins is shown. Particular importance was ascribed to the question of the quantifiability of the experiments when it was desired to measure the degree of conversion by means of a 13C CP/MAS contact time study. The network structure present, and thus also the mechanical properties, is critically dependent upon the final degree of conversion obtained after curing. The degree of conversion, which depended on the cure conditions (cure temperature, cure pressure and cure time), was limited by vitrification as was demonstrated by DSC experiments. Changes in the spin-lattice relaxation time T 1H were observed, providing

  7. The molecular structure of waxy maize starch nanocrystals.

    PubMed

    Angellier-Coussy, Hélène; Putaux, Jean-Luc; Molina-Boisseau, Sonia; Dufresne, Alain; Bertoft, Eric; Perez, Serge

    2009-08-17

    The insoluble residues obtained by submitting amylopectin-rich native starch granules from waxy maize to a mild acid hydrolysis consist of polydisperse platelet nanocrystals that have retained the allomorphic type of the parent granules. The present investigation is a detailed characterization of their molecular composition. Two major groups of dextrins were found in the nanocrystals and were isolated. Each group was then structurally characterized using beta-amylase and debranching enzymes (isoamylase and pullulanase) in combination with anion-exchange chromatography. The chain lengths of the dextrins in both groups corresponded with the thickness of the crystalline lamellae in the starch granules. Only approximately 62 mol% of the group of smaller dextrins with an average degree of polymerization (DP) 12.2 was linear, whereas the rest consisted of branched dextrins. The group of larger dextrins (DP 31.7) apparently only consisted of branched dextrins, several of which were multiply branched molecules. It was shown that many of the branch linkages were resistant to the action of the debranching enzymes. The distribution of branched molecules in the two populations of dextrins suggested that the nanocrystals possessed a regular and principally homogeneous molecular structure.

  8. Anti-cancer chalcones: Structural and molecular target perspectives.

    PubMed

    Mahapatra, Debarshi Kar; Bharti, Sanjay Kumar; Asati, Vivek

    2015-06-15

    Chalcone or (E)-1,3-diphenyl-2-propene-1-one scaffold remained a fascination among researchers in the 21st century due to its simple chemistry, ease of synthesis and a wide variety of promising biological activities. Several natural and (semi) synthetic chalcones have shown anti-cancer activity due to their inhibitory potential against various targets namely ABCG2/P-gp/BCRP, 5α-reductase, aromatase, 17-β-hydroxysteroid dehydrogenase, HDAC/Situin-1, proteasome, VEGF, VEGFR-2 kinase, MMP-2/9, JAK/STAT signaling pathways, CDC25B, tubulin, cathepsin-K, topoisomerase-II, Wnt, NF-κB, B-Raf and mTOR etc. In this review, a comprehensive study on molecular targets/pathways involved in carcinogenesis, mechanism of actions (MOAs), structure activity relationships (SARs) and patents granted have been highlighted. With the knowledge of molecular targets, structural insights and SARs, this review may be helpful for (medicinal) chemists to design more potent, safe, selective and cost effective anti-cancer chalcones.

  9. Structure, molecular evolution, and hydrolytic specificities of largemouth bass pepsins.

    PubMed

    Miura, Yoko; Suzuki-Matsubara, Mieko; Kageyama, Takashi; Moriyama, Akihiko

    2016-02-01

    The nucleotide sequences of largemouth bass pepsinogens (PG1, 2 and 3) were determined after molecular cloning of the respective cDNAs. Encoded PG1, 2 and 3 were classified as fish pepsinogens A1, A2 and C, respectively. Molecular evolutionary analyses show that vertebrate pepsinogens are classified into seven monophyletic groups, i.e. pepsinogens A, F, Y (prochymosins), C, B, and fish pepsinogens A and C. Regarding the primary structures, extensive deletion was obvious in S'1 loop residues in fish pepsin A as well as tetrapod pepsin Y. This deletion resulted in a decrease in hydrophobic residues in the S'1 site. Hydrolytic specificities of bass pepsins A1 and A2 were investigated with a pepsin substrate and its variants. Bass pepsins preferred both hydrophobic/aromatic residues and charged residues at the P'1 sites of substrates, showing the dual character of S'1 sites. Thermodynamic analyses of bass pepsin A2 showed that its activation Gibbs energy change (∆G(‡)) was lower than that of porcine pepsin A. Several sites of bass pepsin A2 moiety were found to be under positive selection, and most of them are located on the surface of the molecule, where they are involved in conformational flexibility. The broad S'1 specificity and flexible structure of bass pepsin A2 are thought to cause its high proteolytic activity.

  10. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  11. THE DRIVING MECHANISM OF STARBURSTS IN GALAXY MERGERS

    SciTech Connect

    Teyssier, Romain; Chapon, Damien; Bournaud, Frederic

    2010-09-10

    We present hydrodynamic simulations of a major merger of disk galaxies, and study the interstellar medium (ISM) dynamics and star formation (SF) properties. High spatial and mass resolutions of 12 pc and 4 x 10{sup 4} M {sub sun} allow us to resolve cold and turbulent gas clouds embedded in a warmer diffuse phase. We compare lower-resolution models, where the multiphase ISM is not resolved and is modeled as a relatively homogeneous and stable medium. While merger-driven bursts of SF are generally attributed to large-scale gas inflows toward the nuclear regions, we show that once a realistic ISM is resolved, the dominant process is actually gas fragmentation into massive and dense clouds and rapid SF therein. As a consequence, SF is more efficient by a factor of up to {approx}10 and is also somewhat more extended, while the gas density probability distribution function rapidly evolves toward very high densities. We thus propose that the actual mechanism of starburst triggering in galaxy collisions can only be captured at high spatial resolution and when the cooling of gas is modeled down to less than 10{sup 3} K. Not only does our model reproduce the properties of the Antennae system, but it also explains the 'starburst mode' recently revealed in high-redshift mergers compared to quiescent disks.

  12. MID-INFRARED SPECTRAL PROPERTIES OF POST-STARBURST QUASARS

    SciTech Connect

    Wei Peng; Shang Zhaohui; Brotherton, Michael S.; Dale, Daniel A.; Cales, Sabrina L.; Hines, Dean C.; Ganguly, Rajib; Canalizo, Gabriela

    2013-07-20

    We present Spitzer InfraRed Spectrograph low-resolution spectra of 16 spectroscopically selected post-starburst quasars (PSQs) at z {approx} 0.3. The optical spectra of these broad-lined active galactic nuclei (AGNs) simultaneously show spectral signatures of massive intermediate-aged stellar populations making them good candidates for studying the connections between AGNs and their hosts. The resulting spectra show relatively strong polycyclic aromatic hydrocarbon (PAH) emission features at 6.2 and 11.3 {mu}m and a very weak silicate feature, indicative of ongoing star formation and low dust obscuration levels for the AGNs. We find that the mid-infrared composite spectrum of PSQs has spectral properties between ULIRGs and QSOs, suggesting that PSQs are hybrid AGN and starburst systems as also seen in their optical spectra. We also find that PSQs in early-type host galaxies tend to have relatively strong AGN activities, while those in spiral hosts have stronger PAH emission, indicating more star formation.

  13. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    ERIC Educational Resources Information Center

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  14. Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.

    PubMed

    Tao, Peng; Wu, Xiongwu; Brooks, Bernard R

    2012-10-07

    An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency.

  15. Electronic and Magnetic Structure of Octahedral Molecular Sieves

    NASA Astrophysics Data System (ADS)

    Morey-Oppenheim, Aimee M.

    The major part of this research consists of magnetic and electronic studies of metal doped cryptomelane-type manganese oxide octahedral molecular sieves (KOMS-2). The second part of this study involves the magnetic characterization of cobalt doped MCM-41 before and after use in the synthesis of single walled carbon nanotubes. Manganese oxides have been used widely as bulk materials in catalysis, chemical sensors, and batteries due to the wide range of possible stable oxidation states. The catalytic function of manganese oxides is further tuned by doping the material with numerous transition metals. It is of particular interest the oxidation states of Mn present after doping. New titrations to determine the oxidation state of Mn were investigated. To further examine the structure of KOMS-2, the magnetic contribution of dopant metals was also examined. The KOMS-2 structure having both diamagnetic and paramagnetic metal ions substitutions was studied. MCM-41 with the incorporation of cobalt into the structure was analyzed for its magnetic properties. The material undergoes significant structural change during the synthesis of single walled carbon nanotubes. It was the focus of this portion of the research to do a complete magnetic profile of both the before and after reaction material.

  16. Molecular Clouds in the North American and Pelican Nebulae: Structures

    NASA Astrophysics Data System (ADS)

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

    We present observations of a 4.25 deg2 area toward the North American and Pelican Nebulae in the J = 1-0 transitions of 12CO, 13CO, and C18O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M ⊙ pc-2 and a mean H2 column density of 5.8, 3.4, and 11.9 × 1021 cm-2 for 12CO, 13CO, and C18O, respectively. We obtain a total mass of 5.4 × 104 M ⊙ (12CO), 2.0 × 104 M ⊙ (13CO), and 6.1 × 103 M ⊙ (C18O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (~10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of 13CO emission range within 2-10 pc2 with mass of (1-5) × 103 M ⊙ and line width of a few km s-1. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the 13CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  17. Mathematical analysis of compressive/tensile molecular and nuclear structures

    NASA Astrophysics Data System (ADS)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  18. The Secrets of the Nearest Starburst Cluster. I. Very Large Telescope/ISAAC Photometry of NGC 3603

    NASA Astrophysics Data System (ADS)

    Stolte, Andrea; Brandner, Wolfgang; Brandl, Bernhard; Zinnecker, Hans; Grebel, Eva K.

    2004-08-01

    VLT/ISAAC JHKL photometry with subarcsecond resolution of the dense, massive starburst cluster NGC 3603 YC forming the core of the NGC 3603 giant molecular cloud is analyzed to reveal characteristics of the stellar population in unprecedented detail. The color-magnitude plane features a strong pre-main-sequence/main-sequence (PMS/MS) transition region, including the PMS/MS transition point, and reveals a secondary sequence for the first time in a nearby young starburst cluster. Arguments for a possible binary nature of this sequence are given. The resolved PMS/MS transition region allows isochrone fitting below the hydrogen-burning turn-on in NGC 3603 YC, yielding an independent estimate of global cluster parameters. A distance modulus of 13.9 mag, equivalent to d=6.0+/-0.3 kpc, is derived, as well as a line-of-sight extinction of AV=4.5+/-0.6 toward PMS stars in the cluster center. The interpretation of a binary candidate sequence suggests a single age of 1 Myr for NGC 3603 YC, providing evidence for a single burst of star formation without the need to employ an age spread in the PMS population, as argued for in earlier studies. Disk fractions are derived from L-band excesses, indicating a radial increase in the disk frequency from 20% to 40% from the core to the cluster outskirts. The low disk fraction in the cluster core, as compared to the 42% L-band excess fraction found for massive stars in the Trapezium cluster of a comparably young age, indicates strong photoevaporation in the cluster center. The estimated binary fraction of 30%, as well as the low disk fraction, suggest strong impacts on low-mass star formation due to stellar interactions in the dense starburst. The significant differences between NGC 3603 YC and less dense and massive young star clusters in the Milky Way reveal the importance of using local starbursts as templates for massive extragalactic star formation. Based on observations obtained at the ESO VLT on Paranal, Chile, under programs 63.I

  19. ON THE HYDRODYNAMIC INTERPLAY BETWEEN A YOUNG NUCLEAR STARBURST AND A CENTRAL SUPERMASSIVE BLACK HOLE

    SciTech Connect

    Hueyotl-Zahuantitla, Filiberto; Tenorio-Tagle, Guillermo; Silich, Sergiy; Wuensch, Richard; Palous, Jan

    2010-06-10

    We present one-dimensional numerical simulations, which consider the effects of radiative cooling and gravity on the hydrodynamics of the matter reinserted by stellar winds and supernovae within young nuclear starbursts (NSBs) with a central supermassive black hole (SMBH). The simulations confirm our previous semi-analytic results for low-energetic starbursts, evolving in a quasi-adiabatic regime, and extend them to more powerful starbursts evolving in the catastrophic cooling regime. The simulations show a bimodal hydrodynamic solution in all cases. They present a quasi-stationary accretion flow onto the black hole, defined by the matter reinserted by massive stars within the stagnation volume and a stationary starburst wind, driven by the high thermal pressure acquired in the region between the stagnation and the starburst radii. In the catastrophic cooling regime, the stagnation radius rapidly approaches the surface of the starburst region, as one considers more massive starbursts. This leads to larger accretion rates onto the SMBH and concurrently to powerful winds able to inhibit interstellar matter from approaching the NSB. Our self-consistent model thus establishes a direct physical link between the SMBH accretion rate and the nuclear star formation activity of the host galaxy and provides a good upper limit to the accretion rate onto the central black hole.

  20. Structured illumination microscopy for vibrational molecular imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Watanabe, Kozue; Palonpon, Almar F.; Smith, Nicholas I.; Chiu, Liang-da; Kasai, Atsushi; Hashimoto, Hitoshi; Kawata, Satoshi; Fujita, Katsumasa

    2016-09-01

    Raman microscopy is a powerful tool for analytical imaging. The wavelength shift of Raman scattering corresponds to molecular vibrational energy. Therefore, we can access rich chemical information, such as distribution, concentration, and chemical environment of sample molecules. Despite these strengths of Raman microscopy, the spatial resolution has been a limiting factor for many practical applications. In this study, we developed a large-area, high-resolution Raman microscope by utilizing structured illumination microscopy (SIM) to overcome the spatial resolution limit. A structured line-illumination (SLI) Raman microscope was constructed. The structured illumination is introduced along the line direction by the interference of two line-shaped beams. In SIM, the spatial frequency mixing between structured illumination and Raman scattering from the sample allows access to the high spatial frequency information beyond the conventional cut-off. As a result, the FWHM of 40-nm fluorescence particle images showed a clear resolution enhancement in the line direction: 366 nm in LI and 199 nm in SLI microscope. Using the developed microscope, we successfully demonstrated high-resolution Raman imaging of various kinds of specimens, such as few-layer graphene, graphite, mouse brain tissue, and polymer nanoparticles. The high resolution Raman images showed the capability to extract original spectral features from the mixed Raman spectra of a multi-component sample because of the enhanced spatial resolution, which is advantageous in observing complex spectral features. The Raman microscopy technique reported here enables us to see the detailed chemical structures of chemical, biological, and medical samples with a spatial resolution smaller than 200 nm.

  1. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    SciTech Connect

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  2. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    SciTech Connect

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  3. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-07

    The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  4. Hydration structure of salt solutions from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-01

    The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  5. Hydration structure of salt solutions from ab initio molecular dynamics.

    PubMed

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L

    2013-01-07

    The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  6. Molecular and structural insight into plasmodium falciparum RIO2 kinase.

    PubMed

    Chouhan, Devendra K; Sharon, Ashoke; Bal, Chandralata

    2013-02-01

    Among approximately 65 kinases of the malarial genome, RIO2 (right open reading frame) kinase belonging to the atypical class of kinase is unique because along with a kinase domain, it has a highly conserved N-terminal winged helix (wHTH) domain. The wHTH domain resembles the wing like domain found in DNA binding proteins and is situated near to the kinase domain. Ligand binding to this domain may reposition the kinase domain leading to inhibition of enzyme function and could be utilized as a novel allosteric site to design inhibitor. In the present study, we have generated a model of RIO2 kinase from Plasmodium falciparum utilizing multiple modeling, simulation approach. A novel putative DNA-binding site is identified for the first time in PfRIO2 kinase to understand the DNA binding events involving wHTH domain and flexible loop. Induced fit DNA docking followed by minimization, molecular dynamics simulation, energetic scoring and binding mode studies are used to reveal the structural basis of PfRIO2-ATP-DNA complex. Ser105 as a potential site of phosphorylation is revealed through the structural studies of ATP binding in PfRIO2. Overall the present study discloses the structural facets of unknown PfRIO2 complex and opens an avenue toward exploration of novel drug target.

  7. Transmission electron microscopy in molecular structural biology: A historical survey.

    PubMed

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.

  8. Structural and molecular interrogation of intact biological systems

    PubMed Central

    Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

    2014-01-01

    Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

  9. Solving structures of protein complexes by molecular replacement with Phaser

    SciTech Connect

    McCoy, Airlie J.

    2007-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

  10. Guiding Molecular Motors with Nano-Imprinted Structures

    NASA Astrophysics Data System (ADS)

    Bunk, Richard; Carlberg, Patrick; Månsson, Alf; Nicholls, Ian A.; Omling, Pär; Sundberg, Mark; Tågerud, Sven; Montelius, Lars

    2005-05-01

    This work, for the first time, demonstrates that nano-imprinted samples, with 100 nm wide polymer lines, can act as guides for molecular motors consisting of motor proteins actin and myosin. The motor protein function was characterized using fluorescence microscopy and compared to actomyosin motility on non-structured nitrocellulose surfaces. Our results open for further use of the nano-imprint technique in the production of disposable chips for bio-nanotechnological applications and miniaturized biological test systems. We discuss how the nano-imprinted motor protein assay system may be optimized and also how it compares to previously tested assay systems involving low-resolution UV-lithography and low throughput but high-resolution electron beam lithography.

  11. The molecular structure of naphthalene by electron diffraction

    NASA Astrophysics Data System (ADS)

    Ketkar, S. N.; Fink, M.

    1981-11-01

    The molecular structure of gaseous naphthalene has been studied by electron diffraction at a nozzle tip temperature of about 25°C. The molecule has D 2h symmetry to within experimental error. The results for the distances ( ra), bond angle and r.m.s. amplitude ( l) are r(CH) = 1.092(6) Å, r(C 9C 1) = 1.422(2) Å, r(C 1C 2) = 1.381(2) Å, r(C 2C 3) = 1.417(4) Å, r(C 10C 9) = 1.412(8) Å, ∠C 10C 9C 1 = 119.5(3)°, ∠CCH = 119.9(7)°, l(CH) = 0.076(6) Å, l(CC) = 0.047(2) Å.

  12. Diffusion and structure in silica liquid: a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Hung, P. K.; Hong, N. V.; Vinh, L. T.

    2007-11-01

    Diffusion and structure in liquid silica under pressure have been investigated by a molecular dynamics model of 999 atoms with the inter-atomic potentials of van Beest, Kramer and van Santen. The simulation reveals that silica liquid is composed of the species SiO4, SiO5 and SiO6 with a fraction dependent on pressure. The density as well as volume of voids can be expressed as a linear function of the fraction of those species. Low-density liquid is mainly constructed of SiO4 and has a large number of O- and Si-voids and a large void tube. This tube contains most O-voids and is spread over the whole system. The anomalous diffusion behavior is observed and discussed.

  13. Crystal and molecular structure of three biologically active nitroindazoles

    NASA Astrophysics Data System (ADS)

    Cabildo, Pilar; Claramunt, Rosa M.; López, Concepción; García, M. Ángeles; Pérez-Torralba, Marta; Pinilla, Elena; Torres, M. Rosario; Alkorta, Ibon; Elguero, José

    2011-01-01

    3-Bromo-1-methyl-7-nitro-1 H-indazole ( 1), 3-bromo-2-methyl-7-nitro-2 H-indazole ( 2) and 3,7-dinitro-1(2) H-indazole ( 3) have been synthesized and characterized by X-ray diffraction, 13C and 15N NMR spectroscopy in solution and in solid-state. The dihedral angles obtained in the crystal structures are in good agreement with the molecular parameters calculated using DFT B3LYP calculations employing the 6-311++G(d,p) basis set. Compounds 1 and 2 present intermolecular halogen bonds between the bromine and the oxygen atoms of the nitro group and in compound 3 inter- and intramolecular hydrogen bonding exists.

  14. Molecular structure and exciton dynamics in organic conjugated polymers

    NASA Astrophysics Data System (ADS)

    Thomas, Alan K.

    , quenchable, isolated singlet excitations. The structure of J aggregates which leads to isolated excitations, and the role which inter-chain contact sites play in triplet formation from these singlet excitations is revealed. New structure-function relationships were uncovered in poly (3-alkyl-thienylenevinylene) (P3ATV) derivatives using resonance Raman and photocurrent spectroscopies. Time-dependent spectroscopic theory was used to interpret experimental Raman and absorption spectra that revealed the presence of structural polymorphs. These polymorphs provide an explanation of the spectroscopic evidence without presumption of a deactivating dark state in this unusually non-fluorescence material. Photovoltaic devices constructed from blends of poly (2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) and PCBM blends were examined using Raman and photocurrent imaging techniques. These techniques were used to identify different packing states in blended thin films and correlate photocurrent production with local order. Intensity modulated spectroscopic techniques (IMPS) were then used to locate regions of non-geminate charge recombination at interfaces between amorphous and crystalline regions in working devices. Next, P3HT/PCBM OPV devices were exposed to ionizing radiation in a vacuum chamber. These devices were characterized before and after exposure, using standardized solar cell tests, Raman imaging, wide-field IMPS, and IMVS spectroscopies. An analysis of the spectroscopic data determined that the donor polymer is highly resistant to radiation damage, and that the degradation of device performance is due to an effect (cross-linking or degradation) within aggregates of the acceptor. This dissertation concludes with an interpretation of the significance of the findings contained herein to organic electronics, followed by a brief outlook for future work in these fields. Potential theories to describe and predict molecular interactions for organic polymers in

  15. Molecular structure of cyclic deoxydiadenylic acid at atomic resolution.

    PubMed

    Frederick, C A; Coll, M; van der Marel, G A; van Boom, J H; Wang, A H

    1988-11-01

    The molecular structure of a small cyclic nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-A resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) A, b = 24.785 (3) A, c = 13.743 (3) A, and beta = 94.02 (2) degrees. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles alpha/zeta in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associates with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

  16. Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

    NASA Astrophysics Data System (ADS)

    Ivanova, Bojidarka B.; Spiteller, Michael

    2012-09-01

    A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with α2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

  17. Radio identifications of UGC galaxies - starbursts and monsters

    SciTech Connect

    Condon, J.J.; Broderick, J.J.

    1988-07-01

    New and previously published observational data on galaxies with declination less than +82 deg from the Uppsala General Catalog (Nilson, 1973) are compiled in extensive tables and characterized in detail. Optical positions are confirmed by measurement of Palomar Sky Survey O prints, and radio identifications for 176 galaxies are made on the basis of 1.4-GHz Green Bank sky maps or 1.49-GHz observations obtained with the C configuration of the VLA in November-December 1986; contour maps based on the latter observations are provided. Radio-selected and IR-selected galaxy populations are found to be similar (and distinct from optically selected populations), and three radio/IR criteria are developed to distinguish galaxies powered by starbursts from those with supermassive black holes or other monster energy sources. 197 references.

  18. Westerlund 1: monolithic formation of a starburst cluster

    NASA Astrophysics Data System (ADS)

    Negueruela, Ignacio; Clark, J. Simon; Ritchie, Ben W.; Goodwin, Simon P.

    2017-03-01

    Westerlund 1 is in all likelihood the most massive young cluster in the Milky Way, with a mass on the order of 105 M ⊙. To determine its bulk properties we have made multi-epoch radial velocity measurements for a substantial fraction of its OB stars and evolved supergiants and obtained multi-object spectroscopy of candidate cluster members in its locale. The results of these two studies show that Westerlund 1 is apparently subvirial and appears completely isolated, with hardly any massive star in its vicinity that could be associated with it in terms of distance modulus or radial velocity. The cluster halo does not extend much further than five parsec away from the centre. All these properties are very unusual among starburst clusters in the Local Universe, which tend to form in the context of large star-forming regions.

  19. The ULX Population in the Starburst Galaxy NGC 253

    NASA Technical Reports Server (NTRS)

    Weaver, K. A.; Heckman, T. M.; Strickland, D. K.

    2004-01-01

    Optimism is mounting for the existence of intermediate mass black holes (IMBH), which occupy the mass spectrum somewhere between the stellar-mass and supermassive varieties. IMBH are naturally predicted by theoretical stellar and black hole evolution models, but the strong attention to them began only recently with the discovery of ultraluminous x-ray sources (ULX). If isotropic and accreting normally, ULX have luminosities tens to thousands of times greater than the Eddington luminosity of a neutron star or stellar-mass black hole. A standard interpretation of their x-ray flux implies that they are powered by IMBH. On the other hand, they may be stellar-mass black holes that are beamed or emit anisotropically. Therefore, the exact nature of ULX is highly controversial. ULX are common in starburst galaxies. At a distance of only 3 Mpc, NGC 253 is bright, nearby, and one of the best-studied starburst galaxies. Approximately 50 distinct x-ray point sources are detected in or near the plane of the galaxy. At least six of these are ULX, with luminosities greater than 10 times that expected for a stellar-mass, accreting compact object. We present new Chandra data from an 80 ksec observation of NGC 253 obtained in 2003 that provides high quality spectra of these sources. Comparing the 1999 and 2003 Chandra observations, the sources have varied significantly over the course of four years, with one of the ULX disappearing completely. The ULX spectra are similar to black-hole XRBs and at least one appears to possess an iron K line. We will discuss what insight these data provide for the nature of ULX in NGC 253 .

  20. MODELING MID-INFRARED DIAGNOSTICS OF OBSCURED QUASARS AND STARBURSTS

    SciTech Connect

    Snyder, Gregory F.; Jonsson, Patrik; Hernquist, Lars; Hayward, Christopher C.; Sajina, Anna; Cox, Thomas J.; Hopkins, Philip F.; Yan Lin

    2013-05-10

    We analyze the link between active galactic nuclei (AGNs) and mid-infrared flux using dust radiative transfer calculations of starbursts realized in hydrodynamical simulations. Focusing on the effects of galaxy dust, we evaluate diagnostics commonly used to disentangle AGN and star formation in ultraluminous infrared galaxies (ULIRGs). We examine these quantities as a function of time, viewing angle, dust model, AGN spectrum, and AGN strength in merger simulations representing two possible extremes of the ULIRG population: one is a typical gas-rich merger at z {approx} 0, and the other is characteristic of extremely obscured starbursts at z {approx} 2-4. This highly obscured burst begins star-formation-dominated with significant polycyclic aromatic hydrocarbon (PAH) emission, and ends with a {approx}10{sup 9} yr period of red near-IR colors. At coalescence, when the AGN is most luminous, dust obscures the near-infrared AGN signature, reduces the relative emission from PAHs, and enhances the 9.7 {mu}m absorption by silicate grains. Although generally consistent with previous interpretations, our results imply none of these indicators can unambiguously estimate the AGN luminosity fraction in all cases. Motivated by the simulations, we show that a combination of the extinction feature at 9.7 {mu}m, the PAH strength, and a near-infrared slope can simultaneously constrain the AGN fraction and dust grain distribution for a wide range of obscuration. We find that this indicator, accessible to the James Webb Space Telescope, may estimate the AGN power as tightly as the hard X-ray flux alone, thereby providing a valuable future cross-check and constraint for large samples of distant ULIRGs.

  1. Galactic Starburst NGC 3603 from X-Rays to Radio

    NASA Technical Reports Server (NTRS)

    Moffat, A. F. J.; Corcoran, M. F.; Stevens, I. R.; Skalkowski, G.; Marchenko, S. V.; Muecke, A.; Ptak, A.; Koribalski, B. S.; Brenneman, L.; Mushotzky, R.; White, Nicholas E. (Technical Monitor)

    2002-01-01

    NGC 3603 is the most massive and luminous visible starburst region in the Galaxy. We present the first Chandra/ACIS-I X-ray image and spectra of this dense, exotic object, accompanied by deep cm-wavelength ATCA radio image at similar or less than 1 inch spatial resolution, and HST/ground-based optical data. At the S/N greater than 3 level, Chandra detects several hundred X-ray point sources (compared to the 3 distinct sources seen by ROSAT). At least 40 of these sources are definitely associated with optically identified cluster O and WR type members, but most are not. A diffuse X-ray component is also seen out to approximately 2 feet (4 pc) form the center, probably arising mainly from the large number of merging/colliding hot stellar winds and/or numerous faint cluster sources. The point-source X-ray fluxes generally increase with increasing bolometric brightnesses of the member O/WR stars, but with very large scatter. Some exceptionally bright stellar X-ray sources may be colliding wind binaries. The radio image shows (1) two resolved sources, one definitely non-thermal, in the cluster core near where the X-ray/optically brightest stars with the strongest stellar winds are located, (2) emission from all three known proplyd-like objects (with thermal and non-thermal components, and (3) many thermal sources in the peripheral regions of triggered star-formation. Overall, NGC 3603 appears to be a somewhat younger and hotter, scaled-down version of typical starbursts found in other galaxies.

  2. HUBBLE SPACE TELESCOPE IMAGING OF POST-STARBURST QUASARS

    SciTech Connect

    Cales, S. L.; Brotherton, M. S.; Shang Zhaohui; Bennert, Vardha Nicola; Canalizo, G.; Stoll, R.; Ganguly, R.; Vanden Berk, D.; Paul, C.; Diamond-Stanic, A. E-mail: mbrother@uwyo.edu E-mail: bennert@physics.ucsb.edu E-mail: stoll@astronomy.ohio-state.edu E-mail: daniel.vandenberk@email.stvincent.edu E-mail: aleks@ucsd.edu

    2011-11-10

    We present images of 29 post-starburst quasars (PSQs) from a Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) Wide Field Channel Snapshot program. These broadlined active galactic nuclei (AGNs) possess the spectral signatures of massive (M{sub burst} {approx} 10{sup 10} M{sub sun}), moderate-aged stellar populations (hundreds of Myr). Thus, their composite nature provides insight into the AGN-starburst connection. We measure quasar-to-host galaxy light contributions via semi-automated two-dimensional light profile fits of point-spread-function-subtracted images. We examine the host morphologies and model the separate bulge and disk components. The HST/ACS-F606W images reveal an equal number of spiral (13/29) and early-type (13/29) hosts, with the remaining three hosts having indeterminate classifications. AGNs hosted by early-type galaxies have on average greater luminosity than those hosted by spiral galaxies. Disturbances such as tidal tails, shells, star-forming knots, and asymmetries are seen as signposts of interaction/merger activity. Disturbances like these were found in 17 of the 29 objects and are evenly distributed among early-type and spiral galaxies. Two of these systems are clearly merging with their companions. Compared to other AGNs of similar luminosity and redshift, these PSQs have a higher fraction of early-type hosts and disturbances. Our most luminous objects with disturbed early-type host galaxies appear to be consistent with merger products. Thus, these luminous galaxies may represent a phase in an evolutionary scenario for merger-driven activity. Our less luminous objects appear to be consistent with Seyfert galaxies not requiring triggering by major mergers. Many of these Seyferts are barred spiral galaxies.

  3. Modeling Mid-infrared Diagnostics of Obscured Quasars and Starbursts

    NASA Astrophysics Data System (ADS)

    Snyder, Gregory F.; Hayward, Christopher C.; Sajina, Anna; Jonsson, Patrik; Cox, Thomas J.; Hernquist, Lars; Hopkins, Philip F.; Yan, Lin

    2013-05-01

    We analyze the link between active galactic nuclei (AGNs) and mid-infrared flux using dust radiative transfer calculations of starbursts realized in hydrodynamical simulations. Focusing on the effects of galaxy dust, we evaluate diagnostics commonly used to disentangle AGN and star formation in ultraluminous infrared galaxies (ULIRGs). We examine these quantities as a function of time, viewing angle, dust model, AGN spectrum, and AGN strength in merger simulations representing two possible extremes of the ULIRG population: one is a typical gas-rich merger at z ~ 0, and the other is characteristic of extremely obscured starbursts at z ~ 2-4. This highly obscured burst begins star-formation-dominated with significant polycyclic aromatic hydrocarbon (PAH) emission, and ends with a ~109 yr period of red near-IR colors. At coalescence, when the AGN is most luminous, dust obscures the near-infrared AGN signature, reduces the relative emission from PAHs, and enhances the 9.7 μm absorption by silicate grains. Although generally consistent with previous interpretations, our results imply none of these indicators can unambiguously estimate the AGN luminosity fraction in all cases. Motivated by the simulations, we show that a combination of the extinction feature at 9.7 μm, the PAH strength, and a near-infrared slope can simultaneously constrain the AGN fraction and dust grain distribution for a wide range of obscuration. We find that this indicator, accessible to the James Webb Space Telescope, may estimate the AGN power as tightly as the hard X-ray flux alone, thereby providing a valuable future cross-check and constraint for large samples of distant ULIRGs.

  4. Structural and molecular basis of starch viscosity in hexaploid wheat.

    PubMed

    Ral, J-P; Cavanagh, C R; Larroque, O; Regina, A; Morell, M K

    2008-06-11

    Wheat starch is considered to have a low paste viscosity relative to other starches. Consequently, wheat starch is not preferred for many applications as compared to other high paste viscosity starches. Increasing the viscosity of wheat starch is expected to increase the functionality of a range of wheat flour-based products in which the texture is an important aspect of consumer acceptance (e.g., pasta, and instant and yellow alkaline noodles). To understand the molecular basis of starch viscosity, we have undertaken a comprehensive structural and rheological analysis of starches from a genetically diverse set of wheat genotypes, which revealed significant variation in starch traits including starch granule protein content, starch-associated lipid content and composition, phosphate content, and the structures of the amylose and amylopectin fractions. Statistical analysis highlighted the association between amylopectin chains of 18-25 glucose residues and starch pasting properties. Principal component analysis also identified an association between monoesterified phosphate and starch pasting properties in wheat despite the low starch-phosphate level in wheat as compared to tuber starches. We also found a strong negative correlation between the phosphate ester content and the starch content in flour. Previously observed associations between internal starch granule fatty acids and the swelling peak time and pasting temperature have been confirmed. This study has highlighted a range of parameters associated with increased starch viscosity that could be used in prebreeding/breeding programs to modify wheat starch pasting properties.

  5. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    NASA Astrophysics Data System (ADS)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

  6. Molecular Structures and Interactions in the Yeast Kinetochore

    PubMed Central

    Cho, U.-S.; Corbett, K.D.; Al-Bassam, J.; Bellizzi, J.J.; De Wulf, P.; Espelin, C.W.; Miranda, J.J.; Simons, K.; Wei, R.R.; Sorger, P.K.; Harrison, S.C.

    2011-01-01

    Kinetochores are the elaborate protein assemblies that attach chromosomes to spindle microtubules in mitosis and meiosis. The kinetochores of point-centromere yeast appear to represent an elementary module, which repeats a number of times in kinetochores assembled on regional centromeres. Structural analyses of the discrete protein subcomplexes that make up the budding-yeast kinetochore have begun to reveal principles of kinetochore architecture and to uncover molecular mechanisms underlying functions such as transmission of tension and establishment and maintenance of bipolar attachment. The centromeric DNA is probably wrapped into a compact organization, not only by a conserved, centromeric nucleosome, but also by interactions among various other DNA-bound kinetochore components. The rod-like, heterotetrameric Ndc80 complex, roughly 600 Å long, appears to extend from the DNA-proximal assembly to the plus end of a microtubule, to which one end of the complex is known to bind. Ongoing structural studies will clarify the roles of a number of other well-defined complexes. PMID:21467141

  7. Bonding and structure in dense multi-component molecular mixtures

    SciTech Connect

    Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D.; Collins, Lee A.

    2015-10-30

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  8. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    PubMed

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  9. Chitosan Molecular Structure as a Function of N-Acetylation

    SciTech Connect

    Franca, Eduardo F.; Freitas, Luiz C.; Lins, Roberto D.

    2011-07-01

    Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with f and w values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N-acetyl groups are unevenly distributed. Systems with 60% or higher N-acetylation levels are insoluble and present similar degrees of swelling regardless the distribution of their N-acetyl groups. Overall particle solvation is highly affected by electrostatic forces resulting from the degree of acetylation. The water mobility and orientation around the polysaccharide chains affects the stability of the intramolecular O3- HO3(n) ... O5(n+ 1) hydrogen bond, which in turn controls particle aggregation.

  10. Bonding and structure in dense multi-component molecular mixtures

    DOE PAGES

    Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; ...

    2015-10-30

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systemsmore » engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.« less

  11. Molecular structure of tetramethylgermane from gas electron diffraction

    NASA Astrophysics Data System (ADS)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István

    1991-05-01

    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  12. Magnetic Field Structure in Molecular Clouds by Polarization Measurements

    NASA Astrophysics Data System (ADS)

    Chen, W. P.; Su, B. H.; Eswaraiah, C.; Pandey, A. K.; Wang, C. W.; Lai, S. P.; Tamura, M.; Sato, S.

    2015-03-01

    We report on a program to delineate magnetic field structure inside molecular clouds by optical and infrared polarization observations. An ordered magnetic field inside a dense cloud may efficiently align the spinning dust grains to cause a detectable level of optical and near-infrared polarization of otherwise unpolarized background starlight due to dichroic extinction. The near-infrared polarization data were taken by SIRPOL mounted on IRSF in SAAO. Here we present the SIRPOL results in RCW 57, for which the magnetic field is oriented along the cloud filaments, and in Carina Nebula, for which no intrinsic polarization is detected in the turbulent environment. We further describe TRIPOL, a compact and efficient polarimer to acquire polarized images simultaneously at g', r', and i' bands, which is recently developed at Nagoya University for adaption to small-aperture telescopes. We show how optical observations probe the translucent outer parts of a cloud, and when combining with infrared observations probing the dense parts, and with millimeter and submillimeter observations to sutdy the central embedded protostar, if there is one, would yield the magnetic field structure on different length scales in the star-formation process.

  13. Molecular clouds in the North American and Pelican Nebulae: structures

    SciTech Connect

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

    We present observations of a 4.25 deg{sup 2} area toward the North American and Pelican Nebulae in the J = 1-0 transitions of {sup 12}CO, {sup 13}CO, and C{sup 18}O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M {sub ☉} pc{sup –2} and a mean H{sub 2} column density of 5.8, 3.4, and 11.9 × 10{sup 21} cm{sup –2} for {sup 12}CO, {sup 13}CO, and C{sup 18}O, respectively. We obtain a total mass of 5.4 × 10{sup 4} M {sub ☉} ({sup 12}CO), 2.0 × 10{sup 4} M {sub ☉} ({sup 13}CO), and 6.1 × 10{sup 3} M {sub ☉} (C{sup 18}O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (∼10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of {sup 13}CO emission range within 2-10 pc{sup 2} with mass of (1-5) × 10{sup 3} M {sub ☉} and line width of a few km s{sup –1}. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the {sup 13}CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  14. Infrared fine-structure line diagnostics of shrouded active galactic nuclei

    NASA Technical Reports Server (NTRS)

    Voit, G. M.

    1992-01-01

    The ultraluminous far-IR galaxies revealed by IRAS, quasar-like in luminosity but smothered in molecular gas, probably conceal either immense starbursts or luminous active nuclei. In both scenarios, these objects ought to produce copious infrared fine-structure emission with several lines comparable to H-beta in luminosity. We show how these lines, if detected, can be used to determine the electron densities and far-IR obscurations of shrouded photoionized regions and to constrain the shape and ionization parameter of the ionizing spectra. The presence of Ne v emission in particular will distinguish shrouded AGNs from shrouded starbursts. Since all active galaxies photoionize at least some surrounding material, these diagnostics can also be applied to active galaxies in general and will aid in studying how an active nucleus interacts with the interstellar medium of its host galaxy.

  15. Ab initio study of structural and mechanical property of solid molecular hydrogens

    NASA Astrophysics Data System (ADS)

    Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

    2015-06-01

    Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

  16. Synchrotron-based and globar-sourced molecular (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery.

    PubMed

    Yang, Ling; Yu, Peiqiang

    2017-01-02

    This paper aimed to review synchrotron-based and globar-sourced molecular infrared (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery in ruminants. It reviewed recent progress in barley varieties, its utilization for animal and human, inherent structure features and chemical make-up, evaluation and research methodology, breeding progress, rumen degradation, and intestinal digestion. The emphasis of this review was focused on the effect of alteration of carbohydrate traits of newly developed hulless barley on molecular structure changes and nutrient delivery and quantification of the relationship between molecular structure features and changes and truly absorbed nutrient supply to ruminants. This review provides an insight into how inherent structure changes on a molecular basis affect nutrient utilization and availability in ruminants.

  17. Prediction of molecular properties including symmetry from quantum-based molecular structural formulas, VIF.

    PubMed

    Alia, Joseph D; Vlaisavljevich, Bess; Abbot, Matthew; Warneke, Hallie; Mastin, Tyson

    2008-10-09

    Structurally covariant valency interaction formulas, VIF, gain chemical significance by comparison with resonance structures and natural bond orbital, NBO, bonding schemes and at the same time allow for additional prediction such as symmetry of ring systems and destabilization of electron pairs with respect to reference energy of -1/2 Eh. Comparisons are based on three chemical interpretations of Sinanoğlu's theory of structural covariance: (1) sets of structurally covariant quantum structural formulas, VIF, are interpreted as the same quantum operator represented in linearly related basis frames; (2) structurally covariant VIF pictures are interpreted as sets of molecular species with similar energy; and (3) the same VIF picture can be interpreted as different quantum operators, one-electron density or Hamiltonian; for example. According to these three interpretations, bond pair, lone pair, and free radical electrons understood in terms of a localized orbital representation are recognized as having energies above, below, or equal to a predetermined reference, frequently-1/2 Eh. The probable position of electron pairs and radical electrons is predicted. The selectivity of concerted ring closures in allyl anion and cation is described. Symmetries of conjugated ring systems are predicted according to their numbers of pi-electrons and spin-multiplicity. The pi-distortivity of benzene is predicted.The 3c/2e- H-bridging bonds in diborane are derived in a natural way according to the notion that the bridging bonds will have delocalizing interactions between them consistent with results of the NBO method. Key chemical bonding motifs are described using VIF. These include 2c/1e-, 2c/2e-, 2c/3e-, 3c/2e-, 3c/3e-,3c/4e-, 4n antiaromatic, and 4n+2 aromatic bonding systems. Some common organic functional groups are represented as VIF pictures and because these pictures can be interpreted simultaneously as one-electron density and Hamiltonian operators, the valence shell

  18. Molecular tendrils feeding star formation in the Eye of the Medusa. The Medusa merger in high resolution 12CO 2-1 maps

    NASA Astrophysics Data System (ADS)

    König, S.; Aalto, S.; Lindroos, L.; Muller, S.; Gallagher, J. S.; Beswick, R. J.; Petitpas, G.; Jütte, E.

    2014-09-01

    Studying molecular gas properties in merging galaxies gives us important clues to the onset and evolution of interaction-triggered starbursts. NGC 4194 (the Medusa merger) is particularly interesting to study, since its FIR-to-CO luminosity ratio rivals that of ultraluminous galaxies (ULIRGs), despite its lower luminosity compared to ULIRGs, which indicates a high star formation efficiency (SFE) that is relative to even most spirals and ULIRGs. We study the molecular medium at an angular resolution of 0.65'' × 0.52'' (~120 × 98 pc) through our observations of 12CO 2-1 emission using the Submillimeter Array (SMA). We compare our 12CO 2-1 maps with the optical Hubble Space Telescope and high angular resolution radio continuum images to study the relationship between molecular gas and the other components of the starburst region. The molecular gas is tracing the complicated dust lane structure of NGC 4194 with the brightest emission being located in an off-nuclear ring-like structure with ~320 pc radius, the Eye of the Medusa. The bulk CO emission of the ring is found south of the kinematical center of NGC 4194. The northern tip of the ring is associated with the galaxy nucleus, where the radio continuum has its peak. Large velocity widths associated with the radio nucleus support the notion of NGC 4194 hosting an active galactic nucleus. A prominent, secondary emission maximum in the radio continuum is located inside the molecular ring. This suggests that the morphology of the ring is partially influenced by massive supernova explosions. From the combined evidence, we propose that the Eye of the Medusa contains a shell of swept up material where we identify a number of giant molecular associations. We propose that the Eye may be the site of an efficient starburst of 5-7 M⊙ yr-1, but it would still constitute only a fraction of the 30-50 M⊙ yr-1 star formation rate of the Medusa. Furthermore, we find that ~50% of the molecular mass of NGC 4194 is found in

  19. The Impact of Massive Starbursts on the Chemical Evolution of Galaxies

    NASA Astrophysics Data System (ADS)

    Kobulnicky, Henry A.

    Young, compact star clusters containing hundreds to thousands of the most massive OB and Wolf-Rayet type stars are common features of actively star-forming galaxies. Radio-wave H scI and millimeter-wave CO aperture synthesis observations of the interstellar gas in several such systems reveal strong evidence for recent collisions or mergers with other galaxies which probably triggered the present burst. Most of the oxygen in the universe, and to a lesser extent carbon and nitrogen, is synthesized within massive stars and returned to the interstellar gas by stellar winds and supernova explosions as these stars evolve. Yet, spatially-resolved spectroscopic investigations of the ionized gas in several starburst galaxies fail to find any sign of recent nucleosynthesis products in the vicinity of evolved starclusters. The chemical abundances of O, N, He, and probably C, appear very homogeneous on scales of ~1 kpc or less, despite the fact that models of the chemical enrichment expected from a single 106/ Msolar burst show that large localized chemical enhancements should occur. That there is no evidence of localized chemical enrichment within the H scII regions of most metal-poor galaxies suggests the recently-released heavy elements are 'hiding' either in a hot, 106 phase or in a cool neutral atomic or molecular phase. In either case, the timescale for visible enrichment in galaxies appears to exceed the lifetimes of the H scII regions and the spatial scales must exceed 1 kpc. These data are inconsistent with the H scII region 'self-enrichment' or 'pollution' hypothesis. For now, heavy elements produced in starbursts can be considered 'missing', but upcoming X-ray observatories may be able to establish their physical phase and location. Hubble Space Telescope spectroscopic measurements show evidence for a correlation between C and N abundances among galaxies with similar metallicity (O/H). The existence of such a correlation implies that C and N production mechanisms

  20. Quantitative structure-property relationships for predicting Henry's law constant from molecular structure.

    PubMed

    Dearden, John C; Schüürmann, Gerrit

    2003-08-01

    Various models are available for the prediction of Henry's law constant (H) or the air-water partition coefficient (Kaw), its dimensionless counterpart. Incremental methods are based on structural features such as atom types, bond types, and local structural environments; other regression models employ physicochemical properties, structural descriptors such as connectivity indices, and descriptors reflecting the electronic structure. There are also methods to calculate H from the ratio of vapor pressure (p(v)) and water solubility (S(w)) that in turn can be estimated from molecular structure, and quantum chemical continuum-solvation models to predict H via the solvation-free energy (deltaG(s)). This review is confined to methods that calculate H from molecular structure without experimental information and covers more than 40 methods published in the last 26 years. For a subset of eight incremental methods and four continuum-solvation models, a comparative analysis of their prediction performance is made using a test set of 700 compounds that includes a significant number of more complex and drug-like chemical structures. The results reveal substantial differences in the application range as well as in the prediction capability, a general decrease in prediction performance with decreasing H, and surprisingly large individual prediction errors, which are particularly striking for some quantum chemical schemes. The overall best-performing method appears to be the bond contribution method as implemented in the HENRYWIN software package, yielding a predictive squared correlation coefficient (q2) of 0.87 and a standard error of 1.03 log units for the test set.

  1. Crystal and molecular structure of the antimalarial agent enpiroline.

    PubMed Central

    Karle, J M; Karle, I L

    1989-01-01

    To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu

  2. Lyman Break Analogs: Constraints on the Formation of Extreme Starbursts at Low and High Redshift

    NASA Technical Reports Server (NTRS)

    Goncalves, Thiago S.; Overzier, Roderik; Basu-Zych, Antara; Martin, D. Christopher

    2011-01-01

    Lyman Break Analogs (LBAs), characterized by high far-UV luminosities and surface brightnesses as detected by GALEX, are intensely star-forming galaxies in the low-redshift universe (z approximately equal to 0.2), with star formation rates reaching up to 50 times that of the Milky Way. These objects present metallicities, morphologies and other physical properties similar to higher redshift Lyman Break Galaxies (LBGs), motivating the detailed study of LBAs as local laboratories of this high-redshift galaxy population. We present results from our recent integral-field spectroscopy survey of LBAs with Keck/OSIRIS, which shows that these galaxies have the same nebular gas kinematic properties as high-redshift LBGs. We argue that such kinematic studies alone are not an appropriate diagnostic to rule out merger events as the trigger for the observed starburst. Comparison between the kinematic analysis and morphological indices from HST imaging illustrates the difficulties of properly identifying (minor or major) merger events, with no clear correlation between the results using either of the two methods. Artificial redshifting of our data indicates that this problem becomes even worse at high redshift due to surface brightness dimming and resolution loss. Whether mergers could generate the observed kinematic properties is strongly dependent on gas fractions in these galaxies. We present preliminary results of a CARMA survey for LBAs and discuss the implications of the inferred molecular gas masses for formation models.

  3. Loss of CPEB3 Upregulates MEGF10 to Impair Mosaic Development of ON Starburst Amacrine Cells

    PubMed Central

    Chen, Yin-Peng; Bai, Geng-Shuo; Wu, Meng-Fang; Chiao, Chuan-Chin; Huang, Yi-Shuian

    2016-01-01

    Cytoplasmic polyadenylation element binding protein 3 (CPEB3) regulates target RNA translation in neurons. Here, we examined CPEB3 distribution and function in the mouse retina. CPEB3 is expressed in retinal neurons, including those located in the inner nuclear layer (INL) and ganglion cell layer (GCL) but not in cone and rod photoreceptors in the outer nuclear layer (ONL). A previous study found CPEB3 expressed in cholinergic starburst amacrine cells (SACs). We first examined these cells and observed aberrant SAC mosaicism in CPEB3-knockout (KO) retinas. Retinal neurons showed orderly spatial arrangements. Many individual subtypes are organized non-randomly in patterns called mosaics. Despite CPEB3 being expressed in both populations of SACs, OFF SACs in the INL and ON SACs in the GCL, aberrant mosaic regularity was observed in only ON SACs of CPEB3-KO retinas. Molecular characterization revealed that translation of multiple epidermal growth factor 10 (Megf10) RNA is suppressed by CPEB3 during the first week of postnatal development, when MEGF10 is primarily expressed in SACs and mediates homotypic repulsive interactions to define intercellular spacing of SACs. Thus, elevated MEGF10 expression in the absence of the translational repressor CPEB3 may account for the defective spatial organization of ON SACs. Our findings uncover for the first time that translational control plays a role in shaping retinal mosaic arrangement. PMID:27822178

  4. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

    2009-01-01

    The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect

  5. Pervasive small-scale structure in molecular clouds

    NASA Technical Reports Server (NTRS)

    Martin, B.; Lada, E.

    1986-01-01

    An unbiased CO survey of molecular cloud cores was completed, and the profiles were analyzed within the context of a model for emission from clumpy clouds. It was found that all sources observed contain a significant amount of structure that is not resolved with our 2.3-arcmin beam, and that the parameters which describe the degree of clumping span a remarkably narrow range of the possible values. We studied two separate samples of cloud cores: a large sample of warm cores from the Massachusetts-Stony Brook 12CO survey of the first galactic quadrant, and a sample of cool cores in the Taurus dark clouds chosen primarily on the basis of H2CO emission. We observed all sources in the 1-0 transition of 12CO and 13CO with the 5-m telescope of the Millimeter Wave Observatory. The 12CO/13CO ratios can be explained if there is unresolved structure giving rise to significant variations of opacity across the beam. Our model cloud consists of a large number of identical clumps distributed randomly in the beam. These clumps have velocity widths v small compared to the width of the observed profile, which is determined by the relative motion of the clumps. The entire cloud is isothermal and in local thermodynamic equilibrium. With these assumptions the intensity and linewidth ratios depend on three parameters: the abundance ratio; the peak 13CO opacity through a single clump, tau(0); and the average number of clumps on a line of sight N. Small tau(0) and large N correspond to the microturbulent limit, which is indistinguishable from a uniform gas distribution. In the other extreme, large tau(0) and snall N, at a given velocity at most one clump contributes to the profile on each line of sight. A figure is presented which shows the model parameters which reproduce the measured intensity and linewidth ratios for the sample of warm cores, assuming an abundance ratio of 75.

  6. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    PubMed Central

    de Steenhuijsen Piters, Wouter A. A.

    2016-01-01

    ABSTRACT The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

  7. CONNECTIONS BETWEEN GALAXY MERGERS AND STARBURST: EVIDENCE FROM THE LOCAL UNIVERSE

    SciTech Connect

    Luo, Wentao; Yang, Xiaohu; Zhang, Youcai E-mail: xyang@sjtu.edu.cn

    2014-07-01

    Major mergers and interactions between gas-rich galaxies with comparable masses are thought to be the main triggers of starburst. In this work, we study, for a large stellar mass range, the interaction rate of the starburst galaxies in the local universe. We focus independently on central and satellite star forming galaxies extracted from the Sloan Digital Sky Survey. Here the starburst galaxies are selected in the star formation rate (SFR) stellar mass plane with SFRs five times larger than the median value found for ''star forming'' galaxies of the same stellar mass. Through visual inspection of their images together with close companions determined using spectroscopic redshifts, we find that ∼50% of the ''starburst'' populations show evident merger features, i.e., tidal tails, bridges between galaxies, double cores, and close companions. In contrast, in the control sample we selected from the normal star forming galaxies, only ∼19% of galaxies are associated with evident mergers. The interaction rates may increase by ∼5% for the starburst sample and 2% for the control sample if close companions determined using photometric redshifts are considered. The contrast of the merger rate between the two samples strengthens the hypothesis that mergers and interactions are indeed the main causes of starburst.

  8. Automatic molecular structure perception for the universal force field.

    PubMed

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks.

  9. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

    NASA Technical Reports Server (NTRS)

    Lee, Seungwon; vonAllmen, Paul

    2007-01-01

    A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

  10. Death Associated Protein Kinases: Molecular Structure and Brain Injury

    PubMed Central

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-01-01

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1. PMID:23880846

  11. Death associated protein kinases: molecular structure and brain injury.

    PubMed

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-07-04

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  12. Molecular structures of fructans from Agave tequilana Weber var. azul.

    PubMed

    Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

    2003-12-31

    Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

  13. Structural basis for the antifolding activity of a molecular chaperone

    PubMed Central

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

    2016-01-01

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase (PhoA) and maltose binding protein (MBP) captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of the non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone. PMID:27501151

  14. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  15. The Influence of Molecular Cooling in Pregalactic Structure Formation

    NASA Astrophysics Data System (ADS)

    Stancil, P. C.; Abel, T.; Lepp, S.; Dalgarno, A.

    1999-12-01

    The detailed chemistry and cooling in collapsing primordial clouds will be presented for total baryonic densities up to 106 cm-3. The model consists of 160 reactions of 23 species including H2, HD, HeH+, and LiH, and accounts for 8 different cooling and heating mechanisms. The hydrodynamic evolution of the gas is modeled under the assumptions of free-fall, isothermal, and isobaric collapse as well as for the central regions of 105 M⊙ objects in hierarchical scenarios. The latter being drawn from three-dimensional cosmological hydrodynamical simulations. The dominant processes in the reaction network are identified and a minimal model that accurately predicts the full chemistry will be presented. It is found that radiative cooling due to collisional excitation of HD can lower the temperature in a primordial cloud below that reachable through H2 cooling alone. Further, the temperature evolution is influenced by the choice of the adopted H2 radiative cooling function. Implications for globular cluster and primordial star formation, as well as structure formation on small scales and the importance of molecular cooling in general will be discussed. The work of P.C.S. was supported by the DoE ORNL LDRD Seed Money Fund. T.A. acknowledges support from NSF Grant ASC--9318185. The work of S.L. and A.D. was supported by NSF Cooperative Agreement OSR-9353227 and Astronomical Sciences Grant AST-93-01099, respectively.

  16. Structural basis for the antifolding activity of a molecular chaperone

    NASA Astrophysics Data System (ADS)

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

    2016-09-01

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase and maltose-binding protein captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone.

  17. Investigating molecular structures: Rapidly examining molecular fingerprints through fast passage broadband fourier transform microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    Grubbs, Garry Smith Smitty, II

    Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation off, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 mus) than the molecular relaxation (≈100 mus). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and

  18. A 2 Millimeter Spectral Line Survey of the Starburst Galaxy NGC 253

    NASA Astrophysics Data System (ADS)

    Martín, S.; Mauersberger, R.; Martín-Pintado, J.; Henkel, C.; García-Burillo, S.

    2006-06-01

    We present the first unbiased molecular line survey toward an extragalactic source, namely the nuclear region of the starburst galaxy NGC 253. The scan covers the frequency band from 129.1 to 175.2 GHz, i.e., most of the 2 mm atmospheric window. We identify 111 spectral features as transitions from 25 different molecular species. Eight of which (three tentatively) are detected for the first time in the extragalactic interstellar medium. Among these newly detected species, we detected the rare isotopomers 34SO and HC18O+. Tentative detections of two deuterated species, DNC and N2D+, are reported for the first time from a target beyond the Magellanic Clouds. In addition, three hydrogen recombination lines are identified, while no organic molecules larger than methanol are detected. Column densities and rotation temperatures are calculated for all the species, including an upper limit to the ethanol abundance. A comparison of the chemical composition of the nuclear environment of NGC 253 with those of selected nearby galaxies demonstrates the chemical resemblance of IC 342 and NGC 4945 to that of NGC 253. On the other hand, the chemistries characterizing NGC 253 and M82 are clearly different. We also present a comparison of the chemical composition of NGC 253 with those observed in Galactic prototypical sources. The chemistry of NGC 253 shows a striking similarity with the chemistry observed toward the Galactic center molecular clouds, which are thought to be dominated by low-velocity shocks. This resemblance strongly suggests that the heating in the nuclear environment of NGC 253 is dominated by the same mechanism as that in the central region of the Milky Way.

  19. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  20. How Molecular Structure Affects Mechanical Properties of an Advanced Polymer

    NASA Technical Reports Server (NTRS)

    Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.; Hinkley, Jeffrey A.

    2000-01-01

    density was performed over a range of temperatures below the glass transition temperature. The physical characterization, elastic properties and notched tensile strength all as a function of molecular weight and test temperature were determined. For the uncrosslinked SI material, it was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature. For the crosslinked PETI-SI material, it was shown that the effect of crosslinking significantly enhances the mechanical performance of the low molecular weight material; comparable to that exhibited by the high molecular weight material.

  1. Star Dust Formation Activities in AzTEC-3: A Starburst Galaxy at z=5.3

    NASA Technical Reports Server (NTRS)

    Dwek, Eliahu

    2011-01-01

    Analyses of of high-redshift ultraluminous infrared OR) galaxies traditionally use the observed optical to submillimeter spectral energy distribution (SED) and estimates of the dynamical mass as observational constraints to derive the star formation rate (SFR), the stellar mass, and age of these objects. In this lecture we add this constraint to the analysis of AzTEC-3, a starburst galaxy at z=5.3. We construct different stellar and chemical evolutionary scenarios, constrained to produce the inferred dust mass and observed luminosity before the associated stellar mass exceeds the observational limit. A robust result of our models is that all scenarios require most of the radiating dust mass to have been accreted in molecular clouds. Our new procedure highlights the importance of a multi wavelength approach, and of the use of dust evolution models in constraining the age and the star formation activity and history in galaxies.

  2. Star and Dust Formation Activities in AzTEC-3: A Starburst Galaxy at z equals 5.3

    NASA Technical Reports Server (NTRS)

    Dwek, Eliahu

    2011-01-01

    Analyses of of high-redshift ultraluminous infrared (IR) galaxies traditionally use the observed optical to submillimeter spectral energy distribution (SED) and estimates of the dynamical mass as observational constraints to derive the star formation rate (SFR), the stellar mass, and age of these objects. In this lecture we add this constraint to the analysis of AzTEC-3, a starburst galaxy at z=5.3. We construct different stellar and chemical evolutionary scenarios, constrained to produce the inferred dust mass and observed luminosity before the associated stellar mass exceeds the observational limit. A robust result of our models is that all scenarios require most of the radiating dust mass to have been accreted in molecular clouds. Our new procedure highlights the importance of a multi wavelength approach, and of the use of dust evolution models in constraining the age and the star formation activity and history in galaxies.

  3. Star and Dust Formation Activities in AzTEC-3: A Starburst Galaxy at z=5.3

    NASA Technical Reports Server (NTRS)

    Dwek, Eliahu

    2011-01-01

    Analyses of of high-redshift ultraluminous infrared (IR) galaxies traditionally use the observed optical to submillimeter spectral energy distribution (SED) and estimates of the dynamical mass as observational constraints to derive the star formation rate (SFR), the stellar mass, and age of these objects. In this lecture we add this constraint to the analysis of AzTEC-3, a starburst galaxy at z=5.3. We construct different stellar and chemical evolutionary scenarios, constrained to produce the inferred dust mass and observed luminosity before the associated stellar mass exceeds the observational limit. A robust result of our models is that all scenarios require most of the radiating dust mass to have been accreted in molecular clouds. Our new procedure highlights the importance of a multiwavelength approach, and of the use of dust evolution models in constraining the age and the star formation activity and history in galaxies.

  4. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    SciTech Connect

    Nagaoka, Masataka

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  5. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    NASA Astrophysics Data System (ADS)

    Nagaoka, Masataka

    2015-12-01

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical `atomistic' molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  6. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  7. Resolving the properties of massive, high-redshift starbursts

    NASA Astrophysics Data System (ADS)

    Simpson, James Matthew

    2015-06-01

    Sub-millimeter galaxies (SMGs) are a population of dusty, obscured sources that represent some of the most extreme sites of star-formation in the Universe. These galaxies have total far-infrared (FIR) luminosities of 10E12-10E13Lsol and colossal star formation rates (SFRs) of ∼100-1000 Msol/yr, with the FIR-emission arising due to the reprocessing of ultraviolet radiation from massive, young stars by dust. Despite their discovery nearly 20 years ago, our understanding of the SMG population has been hampered by the coarse resolution (FWHM = 15-30") of single-dish sub-millimeter surveys. In this thesis I present observations of FIR-bright (S870≳1mJy) galaxies that have precise identifications from high-resolution imaging taken with sub-mm/mm interferometers. I present a multi-wavelength study of 96 SMGs that have unambiguous identifications from observations with Atacama Large Millimeter sub-millimeter Array (ALMA) and determine that the photometric redshift distribution for the SMG population has a median of zphot=2.5±0.2. I show that if the star formation activity in SMGs has a timescale of ∼100Myr then their descendants at z∼0 would have a space density and absolute H -band magnitude distribution that are in good agreement with a volume limited sample of local ellipticals. The low resolution of single-dish surveys has led to concerns about the blending of multiple individual galaxies into a single sub-millimeter source. I present ALMA observations of a sample of 30 bright, single-dish-identified sub-mm sources and show that 61(+19 -15)% are comprised of a blend of multiple SMGs brighter than ≳1mJy. Furthermore, I show that source blending boosts the apparent single-dish number counts by 20% at S870>7.5 mJy. A morphological analysis of the far-infrared emission from a subset of 23 of the brightest sources detected in the ALMA maps shows that the intense starburst in SMGs occurs in a compact region with a median physical half-light diameter of 2.4±0.2kpc

  8. Local starburst galaxies and their descendants. Statistics from the Sloan Digital Sky Survey

    NASA Technical Reports Server (NTRS)

    Bergvall, Nils; Marquart, Thomas; Way, Michael J.; Blomqvist, Anna; Holst, Emma; Ostlin, Goran; Zackrisson, Erik

    2016-01-01

    Despite strong interest in the starburst phenomenon in extragalactic astronomy, the concept remains ill-defined. Here we use a strict definition of starburst to examine the statistical properties of starburst galaxies in the local universe. We also seek to establish links between starburst galaxies, post-starburst (hereafter postburst) galaxies, and active galaxies. Data were selected from the Sloan Digital Sky Survey DR7. We applied a novel method of treating dust attenuation and derive star formation rates, ages, and stellar masses assuming a two-component stellar population model. Dynamical masses are calculated from the width of the H-alpha line. These masses agree excellently with the photometric masses. The mass (gas+stars) range is approximately 10( exp 9) - 10(exp 11.5) solar mass. As a selection criterion for starburst galaxies, we use, the birthrate parameter, b = SFR/SFR, requiring that b is greater than 3. For postburst galaxies, we use, the equivalent width of Hdelta in absorption with the criterion EW (sub Hdelta_abs) is greater than 6 A. Results. We find that only 1% of star-forming galaxies are starburst galaxies. They contribute 3-6% to the stellar production and are therefore unimportant for the local star formation activity. The median starburst age is 70 Myr roughly independent of mass, indicating that star formation is mainly regulated by local feedback processes. The b-parameter strongly depends on burst age. Values close to b = 60 are found at ages approximately 10 Myr, while almost no starbursts are found at ages greater than 1 Gyr. The median baryonic burst mass fraction of sub-L galaxies is 5% and decreases slowly towards high masses. The median mass fraction of the recent burst in the postburst sample is 5-10%. A smaller fraction of the postburst galaxies, however, originates in non-bursting galaxies. The age-mass distribution of the postburst progenitors (with mass fractions is greater than 3%) is bimodal with a break at logM(solar mass

  9. Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development.

    PubMed

    Chen, Zhen; Wilmanns, Matthias; Zeng, An-Ping

    2010-10-01

    The future of industrial biotechnology requires efficient development of highly productive and robust strains of microorganisms. Present praxis of strain development cannot adequately fulfill this requirement, primarily owing to the inability to control reactions precisely at a molecular level, or to predict reliably the behavior of cells upon perturbation. Recent developments in two areas of biology are changing the situation rapidly: structural biology has revealed details about enzymes and associated bioreactions at an atomic level; and synthetic biology has provided tools to design and assemble precisely controllable modules for re-programming cellular metabolic circuitry. However, because of different emphases, to date, these two areas have developed separately. A linkage between them is desirable to harness their concerted potential. We therefore propose structural synthetic biotechnology as a new field in biotechnology, specifically for application to the development of industrial microbial strains.

  10. Radio identifications of UGC galaxies - Starbursts and monsters

    NASA Astrophysics Data System (ADS)

    Condon, J. J.; Broderick, J. J.

    1988-07-01

    Radio identifications of galaxies in the Uppsala General Catalogue of Galaxies with δ < +82° were made from the Green Bank 1400 MHz sky maps. Every source having peak flux density SP ≥ 150 mJy in the ≈12 arcmin FWHM map point-source response and position <5 arcmin in both coordinates from the optical position of any UGC galaxy was considered a candidate identification to ensure that very extended (up to 1 Mpc) and asymmetric sources would not be missed. Maps in the literature or new 1.49 GHz VLA C array maps made with 18 arcsec resolution were used to confirm or reject candidate identifications. The resulting list of 176 confirmed identifications should be complete, reliable, and suitable for statistical investigations of radio emission from nearby (D < 300 Mpc for H0 = 50 km s-1Mpc-1) galaxies of all morphological types. Three criteria for distinguishing starbursts from monsters on the basis of radio and far-infrared continuum only are given and used to classify the dominant energy sources in the N = 176 confirmed galaxy identifications.

  11. STAR-FORMING OR STARBURSTING? THE ULTRAVIOLET CONUNDRUM

    SciTech Connect

    Boquien, M.; Calzetti, D.; Hong, S.; Kennicutt, R.; Dale, D.; Engelbracht, C.; Portouw, J.; Gordon, K. D.; Lee, J. C.

    2009-11-20

    Compared to starburst galaxies, normal star-forming galaxies have been shown to display a much larger dispersion of the dust attenuation at fixed reddening through studies of the IRX-beta diagram (the IR/UV ratio 'IRX' versus the UV color 'beta'). To investigate the causes of this larger dispersion and attempt to isolate second parameters, we have used GALEX UV, ground-based optical, and Spitzer infrared imaging of eight nearby galaxies, and examined the properties of individual UV and 24 mum selected star-forming regions. We concentrated on star-forming regions, in order to isolate simpler star formation histories than those that characterize whole galaxies. We find that (1) the dispersion is not correlated with the mean age of the stellar populations; (2) a range of dust geometries and dust extinction curves are the most likely causes for the observed dispersion in the IRX-beta diagram, (3) together with some potential dilution of the most recent star-forming population by older unrelated bursts, at least in the case of star-forming regions within galaxies; and (4) we also recover some general characteristics of the regions, including a tight positive correlation between the amount of dust attenuation and the metal content. Although generalizing our results to whole galaxies may not be immediate, the possibility of a range of dust extinction laws and geometries should be accounted for in the latter systems as well.

  12. Starburst or AGN Dominance in Submillimetre-Luminous Candidate AGN?

    NASA Astrophysics Data System (ADS)

    Coppin, Kristen; Pope, Alexandra; Menéndez-Delmestre, Karín; Alexander, David M.; Dunlop, James

    2010-06-01

    It is widely believed that ultraluminous infrared (IR) galaxies and active galactic nuclei (AGN) activity are triggered by galaxy interactions and merging, with the peak of activity occurring at z~2, where submillimetre galaxies are thousands of times more numerous than local ULIRGs. In this evolutionary picture, submillimetre galaxies (SMGs) would host an AGN, which would eventually grow a black hole (BH) strong enough to blow off all of the gas and dust leaving an optically luminous QSO. To probe this evolutionary sequence we have focussed on the `missing link' sources, which demonstrate both strong starburst (SB) and AGN signatures, in order to determine if the SB is the main power source even in SMGs when we have evidence that an AGN is present from their IRAC colours. The best way to determine if a dominant AGN is present is to look for their signatures in the mid-infrared with the Spitzer IRS, since often even deep X-ray observations miss identifying the presence of AGN in heavily dust-obscured SMGs. We present the results of our audit of the energy balance between star-formation and AGN within this special sub-population of SMGs-where the BH has grown appreciably to begin heating the dust emission.

  13. STAR CLUSTER DISRUPTION IN THE STARBURST GALAXY MESSIER 82

    SciTech Connect

    Li, Shuo; Li, Chengyuan; De Grijs, Richard; Anders, Peter

    2015-01-01

    Using high-resolution, multiple-passband Hubble Space Telescope images spanning the entire optical/near-infrared wavelength range, we obtained a statistically complete U-band-selected sample of 846 extended star clusters across the disk of the nearby starburst galaxy M82. Based on a careful analysis of the clusters' spectral energy distributions, we determined their galaxy-wide age and mass distributions. The M82 clusters exhibit three clear peaks in their age distribution, thus defining relatively young, log (t yr{sup –1}) ≤ 7.5, intermediate-age, log (t yr{sup –1}) in [7.5, 8.5], and old samples, log (t yr{sup –1}) ≥ 8.5. Comparison of the completeness-corrected mass distributions offers a firm handle on the galaxy's star cluster disruption history. The most massive star clusters in the young and old samples are (almost) all concentrated in the most densely populated central region, while the intermediate-age sample's most massive clusters are more spatially dispersed, which may reflect the distribution of the highest-density gas throughout the galaxy's evolutionary history, combined with the solid-body nature of the galaxy's central region.

  14. Gas Dynamics and Outflow in the Barred Starburst Galaxy NGC 1808 Revealed with ALMA

    NASA Astrophysics Data System (ADS)

    Salak, Dragan; Nakai, Naomasa; Hatakeyama, Takuya; Miyamoto, Yusuke

    2016-05-01

    NGC 1808 is a nearby barred starburst galaxy with an outflow from the nuclear region. To study the inflow and outflow processes related to star formation and dynamical evolution of the galaxy, we have carried out 12CO (J=1-0) mapping observations of the central r ˜ 4 kpc of NGC 1808 using the Atacama Large Millimeter/submillimeter Array. Four distinct components of molecular gas are revealed at high spatial resolution of 2″ (˜100 pc): (1) a compact (r < 200 pc) circumnuclear disk (CND), (2) r ˜ 500 pc ring, (3) gas-rich galactic bar, and (4) spiral arms. Basic geometric and kinematic parameters are derived for the central 1 kpc region using tilted-ring modeling. The derived rotation curve reveals multiple mass components that include (1) a stellar bulge, (2) a nuclear bar and molecular CND, and (3) an unresolved massive (˜107 M ⊙) core. Two systemic velocities, 998 km s-1 for the CND and 964 km s-1 for the 500 pc ring, are revealed, indicating a kinematic offset. The pattern speed of the primary bar, derived by using a cloud-orbit model, is 56 ± 11 km s-1 kpc-1. Noncircular motions are detected associated with a nuclear spiral pattern and outflow in the central 1 kpc region. The ratio of the mass outflow rate to the star formation rate is {\\dot{M}}{out}/{SFR}˜ 0.2 in the case of optically thin CO (1-0) emission in the outflow, suggesting low efficiency of star formation quenching.

  15. The Evolution of Post-starburst Galaxies from z ~ 1 to the Present

    NASA Astrophysics Data System (ADS)

    Pattarakijwanich, Petchara; Strauss, Michael A.; Ho, Shirley; Ross, Nicholas P.

    2016-12-01

    Post-starburst galaxies are in the transitional stage between blue, star-forming galaxies and red, quiescent galaxies and therefore hold important clues for our understanding of galaxy evolution. In this paper, we systematically searched for and identified a large sample of post-starburst galaxies from the spectroscopic data set of the Sloan Digital Sky Survey (SDSS) Data Release 9. In total, we found more than 6000 objects with redshifts between z ˜ 0.05 and z ˜ 1.3, making this the largest sample of post-starburst galaxies in the literature. We calculated the luminosity function of the post-starburst galaxies using two uniformly selected subsamples: the SDSS main galaxy sample and the Baryon Oscillation Spectroscopic Survey CMASS sample. The luminosity functions are reasonably fit by half-Gaussian functions. The peak magnitudes shift as a function of redshift from M ˜ -23.5 at z ˜ 0.8 to M ˜ -20.3 at z ˜ 0.1. This is consistent with the downsizing trend, whereby more massive galaxies form earlier than low-mass galaxies. We compared the mass of the post-starburst stellar population found in our sample to the decline of the global star formation rate and found that only a small amount (˜1%) of all star formation quenching in the redshift range z = 0.2-0.7 results in post-starburst galaxies in the luminosity range our sample is sensitive to. Therefore, luminous post-starburst galaxies are not the place where most of the decline in the star formation rate of the universe is happening.

  16. Chemical biology at the crossroads of molecular structure and mechanism.

    PubMed

    Doudna, Jennifer A

    2005-11-01

    Chemical insight into biological function is the holy grail of structural biology. Small molecules are central players as building blocks, effectors and probes of macromolecular structure and function.

  17. Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Reilly, Anthony M.; Habershon, Scott; Morrison, Carole A.; Rankin, David W. H.

    2010-03-01

    Path-integral molecular dynamics (PIMD) simulations with an empirical interaction potential have been used to determine the experimental equilibrium structure of solid nitromethane at 4.2 and 15 K. By comparing the time-averaged molecular structure determined in a PIMD simulation to the calculated minimum-energy (zero-temperature) molecular structure, we have derived structural corrections that describe the effects of thermal motion. These corrections were subsequently used to determine the equilibrium structure of nitromethane from the experimental time-averaged structure. We find that the corrections to the intramolecular and intermolecular bond distances, as well as to the torsion angles, are quite significant, particularly for those atoms participating in the anharmonic motion of the methyl group. Our results demonstrate that simple harmonic models of thermal motion may not be sufficiently accurate, even at low temperatures, while molecular simulations employing more realistic potential-energy surfaces can provide important insight into the role and magnitude of anharmonic atomic motions.

  18. Effect of valence of lanthanide ion and molecular symmetry in polyoxotungstoborate on the molecular structure and spectrochemical properties

    NASA Astrophysics Data System (ADS)

    Iijima, Jun; Naruke, Haruo

    2017-01-01

    The compound K9(NH4)H[CeIV(α-BW11O39)(W5O18)]·16H2O (1) was successfully isolated and structurally characterized. The structural investigation revealed that 1 displayed a less molecular distortion, whereas Ln3+-analogs exhibited a large molecular distortion. IR spectroscopy demonstrated that the spectral patterns of 1 and Ce3+-analog were depending on each valence of Ce (IV/III). 11B-NMR spectroscopy showed that a decrease in site symmetry of B atom in the polyoxotungstoborate was related with an increase in a half width of NMR peak. There is a difference in molecular distortion between 1 and Ce3+-analog, but they have similar large half widths because of the same site symmetry of B atom. The 4f electron in Ce atom exhibited less effect on the chemical shift.

  19. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    SciTech Connect

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  20. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

    PubMed

    Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-01

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  1. 3D spectroscopy of merger Seyfert galaxy Mrk 334: nuclear starburst, superwind and the circumnuclear cavern

    NASA Astrophysics Data System (ADS)

    Smirnova, Aleksandrina; Moiseev, Alexei

    2010-01-01

    We are presenting new results on kinematics and structure of the Mrk 334 Seyfert galaxy. Panoramic (3D) spectroscopy is performed at the 6-m telescope of the Special Astrophysical Observatory of the Russian Academy of Sciences using the integral-field Multi-Pupil Fiber Spectrograph (MPFS) and scanning Fabry-Pérot interferometer. The deep images have revealed that Mrk 334 is observed during the final stage of its merging with a massive companion. A possible mass ratio ranges from 1/5 to 1/3. The merger has triggered mass redistribution in the disc resulting in an intensification of nuclear activity and in a burst of star formation in the inner region of the galaxy. The circumnuclear starburst is so intense that its contribution to the gas ionization exceeds that contribution of the active galactic nuclei (AGN). We interpret the nuclear gas outflow with velocities of ~200kms-1 as a galactic superwind that accompanies the violent star formation. This suggestion is consistent with the asymmetric X-ray brightness distribution in Mrk 334. The trajectory of the fragments of the disrupted satellite in the vicinity of the main galaxy nucleus can be traced. In the galaxy disc, a cavern is found that is filled with a low-density ionized gas. We consider this region to be the place where the remnants of the companion have recently penetrated through the gaseous disc of the main galaxy.

  2. The Star Formation History of Local Starbursts as Benchmark for High Redshifts

    NASA Astrophysics Data System (ADS)

    Schmitt, Henrique R.; Calzetti, Daniela; Armus, Lee

    2001-08-01

    We propose to use the WIYN telescope and MIMO to obtain broad band B and R, and narrow band H(alpha) and H(beta) images for a sample of 13 local starburst galaxies detected by ISO at 170-200(micron) and for which we are obtaining ultraviolet (1600Å) images with an approved HST/STIS program. With these observations we will complete the ground based portion of this project. This sample spans a wide range in the luminosity, star formation rate, metallicity and morphology parameters, and will be used as a low-redshift benchmark to explore the relationship between the Lyman-break and the SCUBA galaxies at z~3. The broad- band ground-based and HST images will be used to characterize the stellar populations and determine the ages of the star forming regions of these galaxies, while the H(alpha)/H(beta) ratio will be used to determine the reddening and gas morphology of these regions. We will study the conditions for the escape of UV light from a dusty galaxy, as a function of the sample parameters. The H(alpha) and UV HST images will be combined to derive a relative empirical calibration between these two star formation indicators. We will measure the fraction of nuclear and disk emission, the fraction of star formation in massive clusters and the properties of those star clusters, the structural properties of star forming bars, rings, and tidally-driven star formation in IR-bright galaxies.

  3. The Star Formation History of Local Starbursts as Benchmark for High Redshifts

    NASA Astrophysics Data System (ADS)

    Schmitt, Henrique R.; Calzetti, Daniela; Armus, Lee

    2001-02-01

    We propose to use the WIYN telescope and MIMO to obtain broad band B and R, and narrow band H(alpha) and H(beta) images for a sample of 22 local starburst galaxies detected by ISO at 170-200(micron) and for which we are obtaining ultraviolet (1600Å) images with an approved HST/STIS program. This sample spans a wide range in the luminosity, star formation rate, metallicity and morphology parameters, and will be used as a low-redshift benchmark to explore the relationship between the Lyman-break and the SCUBA galaxies at z~3. The broad-band ground- based and HST images will be used to characterize the stellar populations and determine the ages of the star forming regions of these galaxies, while the H(alpha)/H(beta) ratio will be used to determine the reddening and gas morphology of these regions. We will study the conditions for the escape of UV light from a dusty galaxy, as a function of the sample parameters. The H(alpha) and UV HST images will be combined to derive a relative empirical calibration between these two star formation indicators. We will measure the fraction of nuclear and disk emission, the fraction of star formation in massive clusters and the properties of those star clusters, the structural properties of star forming bars, rings, and tidally-driven star formation in IR-bright galaxies.

  4. The effect of galaxy mass ratio on merger-driven starbursts

    NASA Astrophysics Data System (ADS)

    Cox, T. J.; Jonsson, Patrik; Somerville, Rachel S.; Primack, Joel R.; Dekel, Avishai

    2008-02-01

    We employ numerical simulations of galaxy mergers to explore the effect of galaxy mass ratio on merger-driven starbursts. Our numerical simulations include radiative cooling of gas, star formation, and stellar feedback to follow the interaction and merger of four disc galaxies. The galaxy models span a factor of 23 in total mass and are designed to be representative of typical galaxies in the local universe. We find that the merger-driven star formation is a strong function of merger mass ratio, with very little, if any, induced star formation for large mass ratio mergers. We define a burst efficiency that is useful to characterize the merger-driven star formation and test that it is insensitive to uncertainties in the feedback parametrization. In accord with previous work we find that the burst efficiency depends on the structure of the primary galaxy. In particular, the presence of a massive stellar bulge stabilizes the disc and suppresses merger-driven star formation for large mass ratio mergers. Direct, coplanar merging orbits produce the largest tidal disturbance and yield the most intense burst of star formation. Contrary to naive expectations, a more compact distribution of gas or an increased gas fraction both decrease the burst efficiency. Owing to the efficient feedback model and the newer version of smoothed particle hydrodynamics employed here, the burst efficiencies of the mergers presented here are smaller than in previous studies.

  5. Lots of Small Stars Born in Starburst Region

    NASA Astrophysics Data System (ADS)

    1999-10-01

    Decisive Study of NGC 3603 with the VLT and ISAAC An international group of astronomers [1] has used the ESO Very Large Telescope (VLT) at Paranal (Chile) to perform unique observations of an interstellar nebula in which stars are currently being born. Thanks to the excellent imaging properties of the first of the four 8.2-m VLT Unit Telescopes, ANTU, they were able to demonstrate, for the first time, the presence of large numbers of small and relatively light, new-born stars in NGC 3603, a well-known "starburst" region in the Milky Way Galaxy . Until now, it has only been possible to observe brighter and much heavier stars in such nebulae. The new observations show that stars of all masses are being born together in the same starburst event, a fundamental result for our understanding of the very complex process of star formation. Background of the project The present research programme was granted observing time with VLT ANTU in April 1999. Its general aim is to investigate collective, massive star formation, in particular the coalescence of high- and low-mass stars in the violent environments of starburst regions . These are areas in which the processes that lead to the birth of new stars are particularly active just now. Several fundamental questions arise in this context. A very basic one is whether low-mass stars form at all in such environments. And if so, do they form together with the most massive stars in a starburst event or do they form at different times, before or after or perhaps on different timescales? Are low-mass stars born with any "preferred" mass that may possibly give further clues to the ongoing processes? All of this is most important in order to understand the detailed mechanisms of star formation. Most current theoretical scenarios explain how single stars form in an isolated, contracting gas cloud, but most stars in the Universe did not form in that simple way. Once some massive stars have formed in some place and start to shine, they

  6. Designing π-stacked molecular structures to control heat transport through molecular junctions

    SciTech Connect

    Kiršanskas, Gediminas; Li, Qian; Solomon, Gemma C.; Flensberg, Karsten; Leijnse, Martin

    2014-12-08

    We propose and analyze a way of using π stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.

  7. Mid-infrared spectroscopy of starbursts : from Spitzer-IRS to JWST-MIRI

    NASA Astrophysics Data System (ADS)

    Martínez-Galarza, Juan Rafael

    2012-06-01

    The Spectral Energy Distributions (SEDs) of star-forming regions and starburst galaxies are unique tracers of the star formation processes in these environments, since they contain information on the escaping and processed photons emitted by newly formed massive stars. Understanding these internal processes is crucial in our physical interpretation of observations of unresolved star formation in the Universe. In the first part of this thesis, we study the physical conditions in resolved starburst regions using Bayesian fitting of their spatially integrated infrared SEDs, including both the thermal continuum and the atomic emission lines. We then apply the method to unresolved starburst to learn about their star formation physics. Our approach leads to robust constraints on physical parameters such as age, compactness, and amount of currently ongoing star formation in starburst, which are otherwise biased by model degeneracies, and allows us to link the resolved properties of giant H II regions to the star formation process at larger scales. In the second part of this thesis, we discuss the wavelength calibration of the next instrument to study the midinfrared spectral properties of starbursts, with improved resolution and sensitivity: the mid-infrared instrument (MIRI), which will fly onboard the James Webb Space Telescope in 2018.

  8. Zooming in on major mergers: dense, starbursting gas in cosmological simulations

    NASA Astrophysics Data System (ADS)

    Sparre, Martin; Springel, Volker

    2016-11-01

    We introduce the `Illustris zoom simulation project', which allows the study of selected galaxies forming in the Λcold dark matter (ΛCDM) cosmology with a 40 times better mass resolution than in the parent large-scale hydrodynamical Illustris simulation. We here focus on the starburst properties of the gas in four cosmological simulations of major mergers. The galaxies in our high-resolution zoom runs exhibit a bursty mode of star formation with gas consumption time-scales 10 times shorter than for the normal star formation mode. The strong bursts are only present in the simulations with the highest resolution, hinting that a too low resolution is the reason why the original Illustris simulation showed a dearth of starburst galaxies. Very pronounced bursts of star formation occur in two out of four major mergers we study. The high star formation rates, the short gas consumption time-scales and the morphology of these systems strongly resemble observed nuclear starbursts. This is the first time that a sample of major mergers is studied through self-consistent cosmological hydrodynamical simulations instead of using isolated galaxy models setup on a collision course. We also study the orbits of the colliding galaxies and find that the starbursting gas preferentially appears in head-on mergers with very high collision velocities. Encounters with large impact parameters do typically not lead to the formation of starbursting gas.

  9. The role of magnetic fields in starburst galaxies as revealed by OH megamasers

    SciTech Connect

    McBride, James; Quataert, Eliot; Heiles, Carl; Bauermeister, Amber E-mail: eliot@astro.berkeley.edu

    2014-01-10

    We present estimates of magnetic field strengths in the interstellar media of starburst galaxies derived from measurements of Zeeman splitting associated with OH megamasers. The results for eight galaxies with Zeeman detections suggest that the magnetic energy density in the interstellar medium of starburst galaxies is comparable to their hydrostatic gas pressure, as in the Milky Way. We discuss the significant uncertainties in this conclusion, and possible measurements that could reduce these uncertainties. We also compare the Zeeman splitting derived magnetic field estimates to magnetic field strengths estimated using synchrotron fluxes and assuming that the magnetic field and cosmic rays have comparable energy densities, known as the 'minimum energy' argument. We find that the minimum energy argument systematically underestimates magnetic fields in starburst galaxies, and that the conditions that would be required to produce agreement between the minimum energy estimate and the Zeeman derived estimate of interstellar medium magnetic fields are implausible. The conclusion that magnetic fields in starburst galaxies exceed the minimum energy magnetic fields is consistent with starburst galaxies adhering to the linearity of the far-infrared-radio correlation.

  10. Molecular structure of amino alcohols on aluminum surface

    NASA Astrophysics Data System (ADS)

    Masoud, M. S.; Awad, M. K.; Ali, Alaa E.; El-Tahawy, M. M. T.

    2014-04-01

    Quantum chemical calculations were applied on monoethanolamine (MEA), diethanolamine (DEA) and triethanolamine (TEA) as corrosion inhibitors for aluminum exterior using ab initio Møller-Plesset (MP2) and Density Function Theory (DFT-B3LYP) at 6-311++G(d,p) ground set. Quantum chemical parameters such as the maximum employed molecular orbital energy (EHOMO), the minimum unemployed molecular orbital energy (ELUMO), energy disparity (ΔE), dipole moment (μ), sum of the total negative charge (TNC), molecular volume (MV), electronegativity (χ), chemical potential (Pi), global hardness (η), softness (σ) and the fraction of electrons transferred (ΔN), were calculated. Further calculations were done to explore the effects of inhibitors and solvent. Furthermore, the inhibitors’ interactions with the metal exterior were studied by applying COMPASS method. R2 values showed good correlations between the corrosion inhibitors’ effectiveness and several quantum parameters.

  11. Molecular analysis of neocortical layer structure in the ferret

    PubMed Central

    Rowell, Joanna J.; Mallik, Atul K.; Dugas-Ford, Jennifer; Ragsdale, Clifton W.

    2010-01-01

    Molecular markers that distinguish specific layers of rodent neocortex are increasingly employed to study cortical development and the physiology of cortical circuits. The extent to which these markers represent general features of neocortical cell type identity across mammals is, however, unknown. To assess the conservation of layer markers more broadly, we isolated orthologs for fifteen layer-enriched genes in the ferret, a carnivore with a large, gyrencephalic brain, and analyzed their patterns of neocortical gene expression. Our major findings are: (1) Many but not all layer markers tested show similar patterns of layer-specific gene expression between mouse and ferret cortex, supporting the view that layer-specific cell type identity is conserved at a molecular level across mammalian superorders; (2) Our panel of deep layer markers (ER81/ETV1, SULF2, PCP4, FEZF2/ZNF312, CACNA1H, KCNN2/SK2, SYT6, FOXP2, CTGF) provides molecular evidence that the specific stratifications of layer 5 and 6 into 5a, 5b, 6a and 6b are also conserved between rodents and carnivores. (3) Variations in layer-specific gene expression are more pronounced across areas of ferret cortex than between homologous areas of mouse and ferret cortex; (4) This variation of area gene expression was clearest with the superficial layer markers studied (SERPINE2, MDGA1, CUX1, UNC5D, RORB/NR1F2, EAG2/KCNH5). Most dramatically, the layer 4 markers RORB and EAG2 disclosed a molecular sublamination to ferret visual cortex and demonstrated a molecular dissociation among the so-called agranular areas of the neocortex. Our findings establish molecular markers as a powerful complement to cytoarchitecture for neocortical layer and cell-type comparisons across mammals. PMID:20575059

  12. An optical-near-IR study of a triplet of super star clusters in the starburst core of M82

    SciTech Connect

    Westmoquette, M. S.; Bastian, N.; Smith, L. J.; Seth, A. C.; Gallagher III, J. S.; Ryon, J. E.; O'Connell, R. W.; Silich, S.; Mayya, Y. D.; González, D. Rosa; Muñoz-Tuñón, C.

    2014-07-10

    We present HST/STIS optical and Gemini/NIFS near-IR IFU spectroscopy and archival Hubble Space Telescope (HST) imaging of the triplet of super star clusters (A1, A2, and A3) in the core of the M82 starburst. Using model fits to the Space Telescope Imaging Spectrograph (STIS) spectra and the weakness of red supergiant CO absorption features (appearing at ∼6 Myr) in the NIFS H-band spectra, the ages of A2 and A3 are 4.5 ± 1.0 Myr. A1 has strong CO bands, consistent with our previously determined age of 6.4 ± 0.5 Myr. The photometric masses of the three clusters are 4-7 × 10{sup 5} M{sub ☉}, and their sizes are R{sub eff} = 159, 104, 59 mas (∼2.8, 1.8, 1.0 pc) for A1, A2, and A3. The STIS spectra yielded radial velocities of 320 ± 2, 330 ± 6, and 336 ± 5 km s{sup –1} for A1, A2, and A3, placing them at the eastern end of the x{sub 2} orbits of M82's bar. Clusters A2 and A3 are in high-density (800-1000 cm{sup –3}) environments, and like A1, are surrounded by compact H II regions. We suggest the winds from A2 and A3 have stalled, as in A1, due to the high ISM ambient pressure. We propose that the three clusters were formed in situ on the outer x{sub 2} orbits in regions of dense molecular gas subsequently ionized by the rapidly evolving starburst. The similar radial velocities of the three clusters and their small projected separation of ∼25 pc suggest that they may merge in the near future unless this is prevented by velocity shearing.

  13. Mathematical Description of Dendrimer Structure

    NASA Technical Reports Server (NTRS)

    Majoros, Istvan J.; Mehta, Chandan B.; Baker, James R., Jr.

    2004-01-01

    Characteristics of starburst dendrimers can be easily attributed to the multiplicity of the monomers used to synthesize them. The molecular weight, degree of polymerization, number of terminal groups and branch points for each generation of a dendrimer can be calculated using mathematical formulas incorporating these variables. Mathematical models for the calculation of degree of polymerization, molecular weight, and number of terminal groups and branching groups previously published were revised and elaborated on for poly(amidoamine) (PAMAM) dendrimers, and introduced for poly(propyleneimine) (POPAM) dendrimers and the novel POPAM-PAMAM hybrid, which we call the POMAM dendrimer. Experimental verification of the relationship between theoretical and actual structure for the PAMAM dendrimer was also established.

  14. Attosecond time-resolved imaging of molecular structure by photoelectron holography.

    PubMed

    Bian, Xue-Bin; Bandrauk, André D

    2012-06-29

    Dynamic imaging of the molecular structure of H(2)(+) is investigated by attosecond photoelectron holography. The interference between direct (reference) and backward rescattered (signal) photoelectrons in attosecond photoelectron holography reveals the birth time of both channels and the spatial information of molecular structure. This is confirmed by simulations with a semiclassical model and numerical solutions of the corresponding time-dependent Schrödinger equation, suggesting an attosecond time-resolved way of imaging molecular structure obtained from laser induced rescattering of ionized electrons. It is shown that both short and long rescattered electron trajectories can be imaged from the momentum distribution.

  15. Aspects of the interstellar medium in starburst galaxies

    NASA Technical Reports Server (NTRS)

    Fanelli, Michael N.

    1990-01-01

    Researchers are engaged in a multifaceted program to investigate the stellar content and star formation history of actively star-forming galaxies. A large body of stellar spectra have been examined to identify spectral features characteristic of specific stellar types. These spectral diagnostics are then calibrated in terms of temperature (spectral type), gravity (luminosity class) and metallicity. The spectral data is compiled into a stellar library whose members represent specific locations in the HR diagram. Through the use of population synthesis techniques, both optimizing and evolutionary approaches, the stellar luminosity function in composite populations can be determined by analysis of their integrated light. Researchers have concentrated on the ultraviolet wavelength region (lambda lambda 1200 to 3200), utilizing the International Ultraviolet Explorer (IUE) archives supplemented by additional observations. In the optical, virtually all stars will contribute to the integrated light. In the ultraviolet however, cool stars will produce negligible flux due to their steep ultraviolet-to-visual continua, greatly simplifying the investigation of the hot component in a composite population. The researchers' initial stellar library has been applied to several blue compact galaxies, (BCGs), a class of starburst galaxy which is UV luminous. BCGs possess a complex interstellar medium which affects the emergent stellar continuum in several ways. This presents a challenge to the stellar analysis but affords insight into the properties of the gas and dust from which the massive OB stars have formed. The optimizing synthesis method solves for the stellar luminosity function and extinction simultaneously. This therefore provides an independent measure of the extinction affecting the hot population component. Despite the rise of the reddening law towards the ultraviolet, BCGs are found to be brighter in the ultraviolet than expected.

  16. The multiphase starburst-driven galactic wind in NGC 5394

    NASA Astrophysics Data System (ADS)

    Martín-Fernández, Pablo; Jiménez-Vicente, Jorge; Zurita, Almudena; Mediavilla, Evencio; Castillo-Morales, África

    2016-09-01

    We present a detailed study of the neutral and ionized gas phases in the galactic wind for the nearby starburst galaxy NGC 5394 based on new integral field spectroscopy obtained with the INTEGRAL fibre system at the William Herschel Telescope. The neutral gas phase in the wind is detected via the interstellar Na I D doublet absorption. After a careful removal of the stellar contribution to these lines, a significant amount of neutral gas (˜107 M⊙) is detected in a central region of ˜1.75 kpc size. This neutral gas is blueshifted by ˜165 km s-1 with respect to the underlying galaxy. The mass outflow of neutral gas is comparable to the star formation rate of the host galaxy. Simultaneously, several emission lines (Hα, [N II], [S II]) are also analysed looking for the ionized warm phase counterpart of the wind. A careful kinematic decomposition of the line profiles reveals the presence of a secondary, broader, kinematic component. This component is found roughly in the same region where the Na I D absorption is detected. It presents higher [N II]/Hα and [S II]/Hα line ratios than the narrow component at the same locations, indicative of contamination by shock ionization. This secondary component also presents blueshifted velocities, although smaller than those measured for the neutral gas, averaging to ˜-30 km s-1. The mass and mass outflow rate of the wind is dominated by the neutral gas, of which a small fraction might be able to escape the gravitational potential of the host galaxy. The observations in this system can be readily understood within a bipolar gas flow scenario.

  17. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    NASA Astrophysics Data System (ADS)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  18. Molecular and crystal structures of noble gas compounds

    NASA Astrophysics Data System (ADS)

    Nabiev, Sh Sh; Sokolov (deceased, V. B.; Chaivanov, B. B.

    2014-12-01

    Data on the structures of xenon and krypton compounds in various physical states are analyzed and generalized. The structures of simple, coordination, polymeric and clathrate-like compounds of these elements with various types of bonds are considered. Characteristic features of their vibrational spectra are discussed in relation to structural transformations caused by cation-anion interactions, structurally non-rigid intramolecular rearrangements and other factors. The bibliography includes 332 references.

  19. Supersonic turbulence and structure of interstellar molecular clouds.

    PubMed

    Boldyrev, Stanislav; Nordlund, Ake; Padoan, Paolo

    2002-07-15

    The interstellar medium provides a unique laboratory for highly supersonic, driven hydrodynamic turbulence. We propose a theory of such turbulence, test it by numerical simulations, and use the results to explain observational scaling properties of interstellar molecular clouds, the regions where stars are born.

  20. Molecular structure of the number 21 chromosome and Down syndrome

    SciTech Connect

    Smith, G.F.

    1985-01-01

    This book contains 19 papers. Some of the titles are: The Biology of Down Syndrome, Human Chromosome Analysis, Expression of Genes on Human Chromosome 21, Comparative Gene Mapping of Human Chromosome 21 and Mouse Chromosome 16, and Relating Molecular Specificity to Normal and Abnormal Brain Development.

  1. Study on molecular structural characteristics of tea polysaccharide.

    PubMed

    Guo, Li; Du, Xianfeng; Lan, Jing; Liang, Qin

    2010-08-01

    Tea polysaccharide (TPS) is attracting more attention gradually due to its particular biological properties. However, molecular characteristics of TPS are unclear since appropriate method is still absent. So, study on the molecular characteristics of TPS was carried out by high-performance size-exclusion chromatography (HPSEC), multi-angle laser light scattering (MALLS) and viscosimetry. The results showed that the molar masses of TPS ranged from 2.287 x 10(5) to 2.762 x 10(5)gmol(-1), the RMS radii distributed from 132.1 to 145.9 nm, and M(w)/M(n) is 1.028. The Mark-Houwink equation was established as [eta]=0.5423 M(w)(0.5379), and the intrinsic viscosity and molecular chain parameters were as follows: [eta]=1.007 dL g(-1), k(H)=0.845, k(K)=0.387, alpha=0.5379, K=0.5423. In addition, based on the slope of the RMS radius versus molar mass conformational plot being 0.24+/-0.00, we suggest that the molecular morphology of TPS is a homogeneous and spherical polymer with branch in solution.

  2. Ionizing Photon Production and Escape in Extreme Starbursts: the Case of the Green Peas

    NASA Astrophysics Data System (ADS)

    Jaskot, Anne; Oey, Sally

    2015-08-01

    With similarities to high-redshift galaxies and potential Lyman continuum (LyC) escape, the low-redshift "Green Pea" (GP) galaxies represent an important test of ionizing photon production and feedback in young massive clusters. Using optical spectra and HST ACS emission-line imaging, we evaluate the ionizing sources, optical depths, and spatial variation of ionization in these unusual starbursts. The GPs’ spectra imply young starburst ages and possible low LyC optical depths. However, CLOUDY photoionization and Starburst99 models have difficulty reproducing all of the observed line ratios and suggest a need for additional hard ionizing sources. New ACS observations of four GPs highlight the extreme, compact nature of these bursts and reveal regions of low optical depth that are the likely sites of LyC escape.

  3. Chandra Observations of the Evening Core of the Starburst Galaxy NGC 253

    NASA Technical Reports Server (NTRS)

    Weaver, K. A.; Heckman, T. M.; Dahlem, M.; White, Nicholas E. (Technical Monitor)

    2002-01-01

    Chandra observations of the core of the nearby starburst galaxy NGC 253 reveal a heavily absorbed source of hard X-rays embedded within the nuclear starburst region. The source has an unabsorbed, 2 to 10 keV luminosity of greater than or equal to 10(exp 39) erg per s and photoionizes the surrounding gas. We observe this source through a dusty torus with a neutral absorbing column density of N(sub eta) approximately 2 x 10(exp 23)cm (exp -2). The torus is hundreds of pc across and collimates the starburst-driven nuclear outflow. We suggest that the ionizing source is an intermediate-mass black hole or a weakly accreting supermassive black hole, which may signal the beginnings or endings of AGN (active galactic nuclei) activity.

  4. Just-After THE FALL: Post-Starburst Galaxies and the E+B Phase

    NASA Astrophysics Data System (ADS)

    Smercina, Adam; Tremonti, Christina A.; Chisholm, John P.

    2015-01-01

    A key question in galaxy evolution is how star formation is quenched. Post-starburst galaxies, which can be identified by their distinctive optical spectra, are excellent laboratories for studying various quenching processes. However, canonical post-starbursts, called E+A's or K+A's, are several 100 Myr past the epoch of active quenching, making it challenging to measure quenching timescales and make inferences about the processes at work. To address this problem, we have identified a sample of 23 young, B-star dominated post-starbursts (E+B's) at z = 0.45 - 0.82 in SDSS-III's Baryon Oscillation Spectroscopic Survey (BOSS). In this new class of objects, we determine how abruptly star formation is truncated and probe the role of various possible feedback mechanisms.This work was supported by the National Science Foundation's REU program through NSF Award AST-1004881.

  5. A role for TREK1 in generating the slow afterhyperpolarization in developing starburst amacrine cells

    PubMed Central

    Ford, Kevin J.; Arroyo, David A.; Kay, Jeremy N.; Lloyd, Eric E.; Bryan, Robert M.; Sanes, Joshua R.

    2013-01-01

    Slow afterhyperpolarizations (sAHPs) play an important role in establishing the firing pattern of neurons that in turn influence network activity. sAHPs are mediated by calcium-activated potassium channels. However, the molecular identity of these channels and the mechanism linking calcium entry to their activation are still unknown. Here we present several lines of evidence suggesting that the sAHPs in developing starburst amacrine cells (SACs) are mediated by two-pore potassium channels. First, we use whole cell and perforated patch voltage clamp recordings to characterize the sAHP conductance under different pharmacological conditions. We find that this conductance was calcium dependent, reversed at EK, blocked by barium, insensitive to apamin and TEA, and activated by arachidonic acid. In addition, pharmacological inhibition of calcium-activated phosphodiesterase reduced the sAHP. Second, we performed gene profiling on isolated SACs and found that they showed strong preferential expression of the two-pore channel gene kcnk2 that encodes TREK1. Third, we demonstrated that TREK1 knockout animals exhibited an altered frequency of retinal waves, a frequency that is set by the sAHPs in SACs. With these results, we propose a model in which depolarization-induced decreases in cAMP lead to disinhibition of the two-pore potassium channels and in which the kinetics of this biochemical pathway dictate the slow activation and deactivation of the sAHP conductance. Our model offers a novel pathway for the activation of a conductance that is physiologically important. PMID:23390312

  6. Observations of the impact of starbursts on the interstellar medium in dwarf galaxies

    NASA Technical Reports Server (NTRS)

    Marlowe, Amanda T.; Heckman, Timothy M.; Wyse, Rosemary F. G.; Schommer, Robert

    1995-01-01

    Dwarf galaxies play a crucial role in our understanding of the formation and evolution of galaxies, and the concept of supernova-driven mass outflows is a vital ingredient in theories of the structure and evolution of dwarf galaxies. Despite the theoretical importance of these outflows, there is a very limited amount of direct observational evidence for their existence. We have therefore begun a detailed multi-wave-band search for outflows in dwarf (M(sub B) greater than or = -18) galaxies with extensive recent or ongoing centrally concentrated star formation. We report the first results of this search in the present paper. Observations of the ionized gas in dwarf amorphous galaxies with centrally concentrated populations of massive stars provide evidence for the large-scale expansion of their expansion of their ionized interstellar media. Fabry-Perot H alpha images reveal the presence of kiloparsec-scale 'superbubbles' and filaments which tend to be oriented along the galaxy minor axis. These structures are comparable in size to the chracteristic optical sizes of the galaxies, and dominate the morphology of the galaxies at low surface brightness in H alpha. Since expanding structure of this size and velocity are not observed in all low-mass galaxies with recent or ongoing star formation, we suggest that we are witnessing transient events that likely have a relatively low 'duty cycle' in such galaxies. That is, we argue that the particular galaxies in the present paper have had significantly elevated star formation rates over the past 10(exp 7)-10(exp 8) yr (i.e., these are starburst or young poststarburst systems). This interpretation is consistent with the optical colors and emission-line properties of these galaxies.

  7. The evolution of post-starburst galaxies from z=2 to 0.5

    NASA Astrophysics Data System (ADS)

    Wild, Vivienne; Almaini, Omar; Dunlop, Jim; Simpson, Chris; Rowlands, Kate; Bowler, Rebecca; Maltby, David; McLure, Ross

    2016-11-01

    We present the evolution in the number density and stellar mass functions of photometrically selected post-starburst galaxies in the UKIDSS Ultra Deep Survey, with redshifts of 0.5 < z < 2 and stellar masses log (M/M⊙) >10. We find that this transitionary species of galaxy is rare at all redshifts, contributing ˜5 per cent of the total population at z ˜ 2, to <1 per cent by z ˜ 0.5. By comparing the mass functions of quiescent galaxies to post-starburst galaxies at three cosmic epochs, we show that rapid quenching of star formation can account for 100 per cent of quiescent galaxy formation, if the post-starburst spectral features are visible for ˜250 Myr. The flattening of the low-mass end of the quiescent galaxy stellar mass function seen at z ˜ 1 can be entirely explained by the addition of rapidly quenched galaxies. Only if a significant fraction of post-starburst galaxies have features that are visible for longer than 250 Myr, or they acquire new gas and return to the star-forming sequence, can there be significant growth of the red sequence from a slower quenching route. The shape of the mass function of these transitory post-starburst galaxies resembles that of quiescent galaxies at z ˜ 2, with a preferred stellar mass of log (M/M⊙) ˜10.6, but evolves steadily to resemble that of star-forming galaxies at z < 1. This leads us to propose a dual origin for post-starburst galaxies: (1) at z ≳ 2 they are exclusively massive galaxies that have formed the bulk of their stars during a rapid assembly period, followed by complete quenching of further star formation; (2) at z ≲ 1 they are caused by the rapid quenching of gas-rich star-forming galaxies, independent of stellar mass, possibly due to environment and/or gas-rich major mergers.

  8. ALMA Reveals Weak [N ii] Emission in "Typical" Galaxies and Intense Starbursts at z = 5-6

    NASA Astrophysics Data System (ADS)

    Pavesi, Riccardo; Riechers, Dominik A.; Capak, Peter L.; Carilli, Christopher L.; Sharon, Chelsea E.; Stacey, Gordon J.; Karim, Alexander; Scoville, Nicholas Z.; Smolčić, Vernesa

    2016-12-01

    We report interferometric measurements of [N ii] 205 μm fine-structure line emission from a representative sample of three galaxies at z = 5-6 using the Atacama Large (sub)Millimeter Array (ALMA). These galaxies were previously detected in [C ii] and far-infrared continuum emission and span almost two orders of magnitude in star formation rate (SFR). Our results show at least two different regimes of ionized interstellar medium properties for galaxies in the first billion years of cosmic time, separated by their {L}[{{C}{{II}}]}/{L}[{{N}{{II}}]} ratio. We find extremely low [N ii] emission compared to [C ii] ({L}[{{C}{{II}}]}/{L}[{{N}{{II}}]}={68}-28+200) from a “typical” ˜ {L}{UV}* star-forming galaxy, likely directly or indirectly (by its effect on the radiation field) related to low dust abundance and low metallicity. The infrared-luminous modestly star-forming Lyman-break galaxy (LBG) in our sample is characterized by an ionized-gas fraction ({L}[{{C}{{II}}]}/{L}[{{N}{{II}}]}≲ 20) typical of local star-forming galaxies and shows evidence for spatial variations in its ionized-gas fraction across an extended gas reservoir. The extreme SFR, warm and compact dusty starburst AzTEC-3 shows an ionized fraction higher than expected given its SFR surface density ({L}[{{C}{{II}}]}/{L}[{{N}{{II}}]}=22+/- 8) suggesting that [N ii] dominantly traces a diffuse ionized medium rather than star-forming H ii regions in this type of galaxy. This highest redshift sample of [N ii] detections provides some of the first constraints on ionized and neutral gas modeling attempts and on the structure of the interstellar medium at z = 5-6 in “normal” galaxies and starbursts.

  9. [Cajal bodies and histone locus bodies: molecular structure and function].

    PubMed

    Khodiuchenko, T A; Krasikova, A V

    2014-01-01

    The review provides modern classification of evolutionarily conserved coilin-containing nuclear bodies of somatic and germ cells that is based on the characteristic features of their molecular composition and the nature of their functions. The main differences between Cajal bodies and histone locus bodies, which are involved in the biogenesis of small nuclear spliceosomal and nucleolar RNAs and in the 3'-end processing of histone precursor messenger RNA, respectively, are considered. It is shown that a significant contribution to the investigation of the diversity of coilin-containing bodies was made by the studies on the architecture of the RNA processing machinery in oocyte nuclei in a number of model organisms. The characteristics features of the molecular composition of coilin-containing bodies in the nuclei of growing oocytes (the so-called germinal vesicles) of vertebrates, including amphibians and birds, are described.

  10. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

    PubMed

    Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-lin; Du, Guan-hua

    2016-05-01

    A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives.

  11. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    SciTech Connect

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J.

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  12. [Structural and molecular origin of information recording/reading].

    PubMed

    Kuzurman, P A; Arkhipova, G V

    2002-01-01

    On the basis of experimental data on the thermoinduced state of water dispersions of natural and synthetic phospholipids in the presence of nootropic agents, a new phenomenological molecular mechanism of information recording/reading was proposed. The mechanism is based on the polymorphism of membrane lipids. A new approach, to the problem of memory was suggested, which considers memory as an information data bank and separates this concept from the concept of the mechanisms of information recording/reading.

  13. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract
    One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  14. ONTOGENETIC ALTERATIONS IN MOLECULAR AND STRUCTURAL CORRELATES OF DENDRITIC GROWTH FOLLOWING DEVELOPMENTAL EXPOSURE TO POLYCHLORINATED BIPHENYLS.

    EPA Science Inventory

    This is the first report showing both molecular and structural changes in brain following developmental exposure to a neurotoxicant. It is known that perinatal exposure to a neurotoxicant, polychlorinated biphenyls (PCBs), is associated with decreased IQ scores, impaired learnin...

  15. Ultra-low-molecular-weight heparins: precise structural features impacting specific anticoagulant activities.

    PubMed

    Lima, Marcelo A; Viskov, Christian; Herman, Frederic; Gray, Angel L; de Farias, Eduardo H C; Cavalheiro, Renan P; Sassaki, Guilherme L; Hoppensteadt, Debra; Fareed, Jawed; Nader, Helena B

    2013-03-01

    Ultra-low-molecular-weight heparins (ULMWHs) with better efficacy and safety ratios are under development; however, there are few structural data available. The main structural features and molecular weight of ULMWHs were studied and compared to enoxaparin. Their monosaccharide composition and average molecular weights were determined and preparations studied by nuclear magnetic resonance spectroscopy, scanning ultraviolet spectroscopy, circular dichroism and gel permeation chromatography. In general, ULMWHs presented higher 3-O-sulphated glucosamine and unsaturated uronic acid residues, the latter being comparable with their higher degree of depolymerisation. The analysis showed that ULMWHs are structurally related to LMWHs; however, their monosaccharide/oligosaccharide compositions and average molecular weights differed considerably explaining their different anticoagulant activities. The results relate structural features to activity, assisting the development of new and improved therapeutic agents, based on depolymerised heparin, for the prophylaxis and treatment of thrombotic disorders.

  16. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  17. Molecular structures and functional relationships in clostridial neurotoxins.

    PubMed

    Swaminathan, Subramanyam

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  18. Molecular Structures and Functional Relationships in Clostridial Neurotoxins

    SciTech Connect

    Swaminathan S.

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  19. Molecular Structure and Transport Dynamics in Perfluoro Sulfonyl Imide Membranes

    SciTech Connect

    Idupulapati, Nagesh B.; Devanathan, Ramaswami; Dupuis, Michel

    2011-05-25

    We report a detailed and comprehensive analysis of the nanostructure, transport dynamics of water and hydronium and water percolation in hydrated perfluoro sulfonyl imides (PFSI), a polymer considered for proton transport in PEM fuel cells, using classical molecular dynamics simulations. The dynamical changes are related to the changes in the membrane nanostructure. Water network percolation threshold, the level at which a consistent spanning water network starts to develop in the membrane, lies between hydration level (λ) 6 and 7. The higher acidity of the sulfonyl imide acid group of PFSI compared to Nafion reported in our earlier ab initio study, translates into more free hydronium ions at low hydration levels. Nevertheless, the calculated diffusion coefficients of the H3O+ ions and H2O molecules as a function the hydration level were observed to be almost the same as that of Nafion, indicating similar conductivity and consistent with the experimental observations. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, a U.S. Department of Energy (DOE) national scientific user facility located at the Pacific Northwest National Laboratory (PNNL). This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  20. IRAS 23532+2513: a compact group including a Seyfert 1 and a starburst galaxy.

    NASA Astrophysics Data System (ADS)

    Zou, Z.-L.; Xia, X.-Y.; Deng, Z.-G.; Wu, H.

    1995-12-01

    The very luminous infrared source IRAS 23532 coincides with a compact group of galaxies including MCG 04-01-002, MCG 04-01-003 and MCG 04-01-004. Spectroscopic observations show that the bright-nucleus galaxy MCG 04-01-002 is a Seyfert 1 and the disturbed spiral galaxy MCG 04-01-003 is a starburst galaxy. CCD images in V band reveal that clear tidal interaction exists between those two objects. This is another example of tidal interaction triggering starburst and Seyfert activity.

  1. High energy (gamma)-ray emission from the starburst nucleus of NGC 253

    SciTech Connect

    Domingo-Santamaria, E; Torres, D F

    2005-06-15

    The high density medium that characterizes the central regions of starburst galaxies and its power to accelerate particles up to relativistic energies make these objects good candidates as {gamma}-rays sources. In this paper, a self-consistent model of the multifrequency emission of the starburst galaxy NGC 253, from radio to gamma-rays, is presented. The model is in agreement with all current measurements and provides predictions for the high energy behavior of the NGC 253 central region. Prospects for observations with the HESS array and GLAST satellite are especially discussed.

  2. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    PubMed

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  3. Discovery of a Galaxy Cluster with a Violently Starbursting Core at z = 2.506

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Elbaz, David; Daddi, Emanuele; Finoguenov, Alexis; Liu, Daizhong; Schreiber, Corentin; Martín, Sergio; Strazzullo, Veronica; Valentino, Francesco; van der Burg, Remco; Zanella, Anita; Ciesla, Laure; Gobat, Raphael; Le Brun, Amandine; Pannella, Maurilio; Sargent, Mark; Shu, Xinwen; Tan, Qinghua; Cappelluti, Nico; Li, Yanxia

    2016-09-01

    We report the discovery of a remarkable concentration of massive galaxies with extended X-ray emission at z spec = 2.506, which contains 11 massive (M * ≳ 1011 M ⊙) galaxies in the central 80 kpc region (11.6σ overdensity). We have spectroscopically confirmed 17 member galaxies with 11 from CO and the remaining ones from Hα. The X-ray luminosity, stellar mass content, and velocity dispersion all point to a collapsed, cluster-sized dark matter halo with mass M 200c = 1013.9±0.2 M ⊙, making it the most distant X-ray-detected cluster known to date. Unlike other clusters discovered so far, this structure is dominated by star-forming galaxies (SFGs) in the core with only 2 out of the 11 massive galaxies classified as quiescent. The star formation rate (SFR) in the 80 kpc core reaches ˜3400 M ⊙ yr-1 with a gas depletion time of ˜200 Myr, suggesting that we caught this cluster in rapid build-up of a dense core. The high SFR is driven by both a high abundance of SFGs and a higher starburst fraction (˜25%, compared to 3%-5% in the field). The presence of both a collapsed, cluster-sized halo and a predominant population of massive SFGs suggests that this structure could represent an important transition phase between protoclusters and mature clusters. It provides evidence that the main phase of massive galaxy passivization will take place after galaxies accrete onto the cluster, providing new insights into massive cluster formation at early epochs. The large integrated stellar mass at such high redshift challenges our understanding of massive cluster formation.

  4. VAMMPIRE: a matched molecular pairs database for structure-based drug design and optimization.

    PubMed

    Weber, Julia; Achenbach, Janosch; Moser, Daniel; Proschak, Ewgenij

    2013-06-27

    Structure-based optimization to improve the affinity of a lead compound is an established approach in drug discovery. Knowledge-based databases holding molecular replacements can be supportive in the optimization process. We introduce a strategy to relate the substitution effect within matched molecular pairs (MMPs) to the atom environment within the cocrystallized protein-ligand complex. Virtually Aligned Matched Molecular Pairs Including Receptor Environment (VAMMPIRE) database and the supplementary web interface ( http://vammpire.pharmchem.uni-frankfurt.de ) provide valuable information for structure-based lead optimization.

  5. Molecular structure of the coalescence of liquid interfaces

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1992-01-01

    When two bodies of liquid merge, their interfaces must also rupture and rearrange into one. Virtually no information is available concerning the small-scale dynamics of this process. Molecular dynamics simulations of coalescence in systems of about 10,000 Lennard-Jones particles have been performed, arranged so as to mimic laboratory experiments on dense liquids. The coalescence event begins when molecules near the boundary of one liquid body thermally fluctuate into the range of attraction of the other, forming a string of mutually attracting molecules. These molecules gradually thicken into a tendril, which continues to thicken as the bodies smoothly combine in a zipper-like merger.

  6. Protein structure in context: The molecular landscape of angiogenesis

    PubMed Central

    Span, Elise A.; Goodsell, David S.; Ramchandran, Ramani; Franzen, Margaret; Herman, Timothy; Sem, Daniel S.

    2014-01-01

    A team of students, educators, and researchers has developed new materials to teach cell signaling within its cellular context. Two non-traditional modalities are employed: physical models, to explore the atomic details of several of the proteins in the angiogenesis signaling cascade, and illustrations of the proteins in their cellular environment, to give an intuitive understanding of the cellular context of the pathway. The experiences of the team underscore the utility of these types of materials as an effective mode for fostering students’ understanding of the molecular world, and the scientific method used to define it. PMID:23868376

  7. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    PubMed

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-07

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches.

  8. THE ANATOMY OF AN EXTREME STARBURST WITHIN 1.3 Gyr OF THE BIG BANG REVEALED BY ALMA

    SciTech Connect

    Carilli, C. L.; Riechers, D.; Walter, F.; Maiolino, R.; Lentati, L.; Wagg, J.; McMahon, R.; Wolfe, A.

    2013-02-15

    We present further analysis of the [C II] 158 {mu}m fine structure line and thermal dust continuum emission from the archetype extreme starburst/active galactic nucleus (AGN) group of galaxies in the early universe, BRI 1202-0725 at z = 4.7, using the Atacama Large Millimeter Array. The group has long been noted for having a closely separated (26 kpc in projection) FIR-hyperluminous quasar host galaxy and an optically obscured submillimeter galaxy (SMG). A short ALMA test observation reveals a rich laboratory for the study of the myriad processes involved in clustered massive galaxy formation in the early universe. Strong [C II] emission from the SMG and the quasar have been reported earlier by Wagg et al. based on these observations. In this paper, we examine in more detail the imaging results from the ALMA observations, including velocity channel images, position-velocity plots, and line moment images. We present detections of [C II] emission from two Ly{alpha}-selected galaxies in the group, demonstrating the relative ease with which ALMA can detect the [C II] emission from lower star formation rate galaxies at high redshift. Imaging of the [C II] emission shows a clear velocity gradient across the SMG, possibly indicating rotation or a more complex dynamical system on a scale {approx}10 kpc. There is evidence in the quasar spectrum and images for a possible outflow toward the southwest, as well as more extended emission (a {sup b}ridge{sup )}, between the quasar and the SMG, although the latter could simply be emission from Ly{alpha}-1 blending with that of the quasar at the limited spatial resolution of the current observations. These results provide an unprecedented view of a major merger of gas-rich galaxies driving extreme starbursts and AGN accretion during the formation of massive galaxies and supermassive black holes within 1.3 Gyr of the big bang.

  9. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    SciTech Connect

    Marcia, Marco Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-11-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

  10. The Molecular Structure of the Liquid Ordered Phase

    NASA Astrophysics Data System (ADS)

    Lyman, Edward

    2014-03-01

    Molecular dynamics simulations reveal substructures within the liquid-ordered phase of lipid bilayers. These substructures, identified in a 10 μsec all-atom trajectory of liquid-ordered/liquid-disordered coexistence (Lo/Ld) , are composed of saturated hydrocarbon chains packed with local hexagonal order, and separated by interstitial regions enriched in cholesterol and unsaturated chains. Lipid hydrocarbon chain order parameters calculated from the Lo phase are in excellent agreement with 2H NMR measurements; the local hexagonal packing is also consistent with 1H-MAS NMR spectra of the Lo phase, NMR diffusion experiments, and small angle X-ray- and neutron scattering. The balance of cholesterol-rich to local hexagonal order is proposed to control the partitioning of membrane components into the Lo regions. The latter have been frequently associated with formation of so-called rafts, platforms in the plasma membranes of cells that facilitate interaction between components of signaling pathways.

  11. Molecular structure, functionality and applications of oxidized starches: A review.

    PubMed

    Vanier, Nathan Levien; El Halal, Shanise Lisie Mello; Dias, Alvaro Renato Guerra; da Rosa Zavareze, Elessandra

    2017-04-15

    During oxidation, the hydroxyl groups of starch molecules are first oxidized to carbonyl groups, then to carboxyl groups. The contents of the carbonyl and carboxyl groups in a starch molecule therefore indicate the extent of starch oxidation. The mechanisms of starch oxidation with different oxidizing agents, including sodium hypochlorite, hydrogen peroxide, ozone and sodium periodate, are described in this review. The effects of these oxidizing agents on the molecular, physicochemical, thermal, pasting and morphological properties of starch are described as well. In addition, the main industrial applications of oxidized starches are presented. The present review is important for understanding the effects of oxidation on starch properties, and this information may facilitate the development of novel oxidized starches for both food and non-food applications.

  12. Microwave spectrum, molecular structure, and quadrupole coupling of vinyl chloroformate

    NASA Astrophysics Data System (ADS)

    Bimler, Jonathan; Broadbent, Stacy; Utzat, Karissa A.; Bohn, Robert K.; Restrepo, Albeiro; Harvey Michels, H.; True, Nancy S.

    2012-09-01

    Vinyl chloroformate is confirmed to have the planar structure reported in an earlier study [1]. Our study uses much higher resolution microwave rotational spectra and ab initio calculations have been extended to a higher level. Naturally abundant isotopologs with single substitution of 37Cl, 13C, and 18O isotopes have also been measured and a substitution structure obtained. The quadrupole coupling constants of the 35Cl and 37Cl isotopologs have been determined. The potential energy profiles of internal rotation about the Odbnd Csbnd Osbnd C and Csbnd Osbnd Cdbnd C dihedral angles have been calculated.

  13. Cosmic-ray induced gamma-ray emission from the starburst galaxy NGC 253

    SciTech Connect

    Wang, Xilu; Fields, Brian D.

    2014-05-09

    Cosmic rays in galaxies interact with the interstellar medium and give us a direct view of nuclear and particle interactions in the cosmos. For example, cosmic-ray proton interactions with interstellar hydrogen produce gamma rays via PcrPism→π{sup 0}→γγ. For a 'normal' star-forming galaxy like the Milky Way, most cosmic rays escape the Galaxy before such collisions, but in starburst galaxies with dense gas and huge star formation rate, most cosmic rays do suffer these interactions [1,2]. We construct a 'thick-target' model for starburst galaxies, in which cosmic rays are accelerated by supernovae, and escape is neglected. This model gives an upper limit to the gamma-ray emission. Only two free parameters are involved in the model: cosmic-ray proton acceleration energy rate from supernova and the proton injection spectral index. The pionic gamma-radiation is calculated from 10 MeV to 10 TeV for the starburst galaxy NGC 253, and compared to Fermi and HESS data. Our model fits NGC 253 well, suggesting that cosmic rays in this starburst are in the thick target limit, and that this galaxy is a gamma-ray calorimeter.

  14. A connection between star formation activity and cosmic rays in the starburst galaxy M82.

    PubMed

    2009-12-10

    Although Galactic cosmic rays (protons and nuclei) are widely believed to be mainly accelerated by the winds and supernovae of massive stars, definitive evidence of this origin remains elusive nearly a century after their discovery. The active regions of starburst galaxies have exceptionally high rates of star formation, and their large size-more than 50 times the diameter of similar Galactic regions-uniquely enables reliable calorimetric measurements of their potentially high cosmic-ray density. The cosmic rays produced in the formation, life and death of massive stars in these regions are expected to produce diffuse gamma-ray emission through interactions with interstellar gas and radiation. M82, the prototype small starburst galaxy, is predicted to be the brightest starburst galaxy in terms of gamma-ray emission. Here we report the detection of >700-GeV gamma-rays from M82. From these data we determine a cosmic-ray density of 250 eV cm(-3) in the starburst core, which is about 500 times the average Galactic density. This links cosmic-ray acceleration to star formation activity, and suggests that supernovae and massive-star winds are the dominant accelerators.

  15. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

  16. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant.

    PubMed

    Li, Hongyan; Fitzgerald, Melissa A; Prakash, Sangeeta; Nicholson, Timothy M; Gilbert, Robert G

    2017-03-06

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch.

  17. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant

    PubMed Central

    Li, Hongyan; Fitzgerald, Melissa A.; Prakash, Sangeeta; Nicholson, Timothy M.; Gilbert, Robert G.

    2017-01-01

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch. PMID:28262830

  18. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant

    NASA Astrophysics Data System (ADS)

    Li, Hongyan; Fitzgerald, Melissa A.; Prakash, Sangeeta; Nicholson, Timothy M.; Gilbert, Robert G.

    2017-03-01

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch.

  19. Molecular cloning of the 8000-base thyroglobulin structural gene.

    PubMed

    Christophe, D; Mercken, L; Brocas, H; Pohl, V; Vassart, G

    1982-03-01

    Bovine thyroglobulin mRNA was reverse-transcribed into full-length double-stranded cDNA. The existence of three HindIII restriction endonuclease sites in the 8000-base thyroglobulin structural gene had allowed the easy cloning of the two internal HindIII fragments [Christophe et al. (1980) Eur. J. Biochem. 111, 419-423]. In the present study, the central portion of the structural gene was cloned in Escherichia coli as two individual recombinant plasmids containing 2000-base-pair and 4700-base-pair segments located respectively 5' and 3' relative to the unique BamHI site of the cDNA. BamHI linkers were added to the double-stranded cDNA and, following restriction with HindIII, selective cloning of the 5' (2600-base-pair) and 3' (1000-base-pair) terminal HindIII fragments was achieved by inserting them between the HindIII and BamHI sites of the plasmid pBR322. Partial sequencing of the 1000-base-pair 3'-terminal fragment demonstrated the presence of an A-A-U-A-A-A sequence in the mRNA 14 bases upstream from a poly(A) tract corresponding to the 3' end of the mRNA. Together, the four clones represent about 99% of the thyroglobulin structural gene and provide the starting material for the determination of thyroglobulin primary structure.

  20. The Mid-Infrared Spectrum of the Galactic Center: A Starburst Nucleus

    NASA Technical Reports Server (NTRS)

    Simpson, J. P.; Witteborn, F. C.; Cohen, M.; Price, S. D.

    1998-01-01

    Using the Michelson interferometer on the Midcourse Space Experiment (MSX), we have taken spectra of many positions in the central 25 min of the Galactic Center (GC) with a 6 min x 9 min FOV. The spectral coverage was 380 to 1700/ cm (6 to 26 microns) and the resolution was approx. 21/cm. The spectra exhibit strong UIR/PAH features at 6.2, 7.7, 8.6 and 11.3 microns, in addition to the ionic lines of (Ne II), at 12.8 microns, (S III) 18.7 microns, and (Ar II) 6.98 microns. There are deep silicate absorption features at 10 and 18 microns and a cold continuum increasing at the longest wavelengths. Additional weak features are present in the spectra. We discuss the variation in the extinction at 10 microns as a function of location in the GC. Compared to the MSX spectrum of the Orion nebula, smoothed to the same resolution and multiplied by the estimated GC extinction, the GC spectra have similar PAH features, but the Orion Nebula also has strong lines of (He III) 15.6 microns, (S IV) 10.5 microns, and (Ar III) 8.99 microns and its 25 microns continuum is stronger (colder). Thus, the GC exhibits the mid-IR spectrum of a low excitation H II region and a nearby molecular cloud with a surface photodissociation region (PDR). This is in excellent agreement with the canonical model of a starburst nucleus in which the hot stars and molecular clouds are randomly distributed. The outer surfaces of the clouds are photodissociated and ionized by the photons from the stars located outside the clouds. The PAH molecules are transiently heated by the stellar photons. Since the exciting stars are located well outside the clouds, the radiation field is dilute compared to a newly-formed blister H II region like Orion; this dilute radiation field causes the relatively low excitation of the ionic lines.

  1. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    PubMed

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers.

  2. The Scent of Roses and beyond: Molecular Structures, Analysis, and Practical Applications of Odorants

    ERIC Educational Resources Information Center

    Mannschreck, Albrecht; von Angerer, Erwin

    2011-01-01

    A few odorous compounds found in roses are chosen to arouse the reader's interest in their molecular structures. This article differs from some similar reports on odorants mainly by combining the structural description with the presentation of the following types of isomers: constitutional isomers, enantiomers, and diastereomers. The preparation…

  3. Teaching the Structure of Immunoglobulins by Molecular Visualization and SDS-PAGE Analysis

    ERIC Educational Resources Information Center

    Rižner, Tea Lanišnik

    2014-01-01

    This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG…

  4. Relationships between molecular structure and chromosomal aberrations in virto human lymphocytes induced by substituted nitrobenzenes

    SciTech Connect

    Huang, Q.G.; Kong, L.R.; Liu, Y.B.; Wang, L.S.

    1996-12-31

    Most nitrated aromatics are genotoxic, some structure-activity relationship (SAR) studies have been done about their mutagenicity, but most studies are concerned with the nitrated polycyclic aromatic hydrocarbons. This report studied the substituted nitrobenzenes and the relationship between molecular structure and genotoxicity of these compounds. 8 refs., 1 tab.

  5. Photoexcited State Molecular Structures in Solution Studied by Pump-Probe XAFS

    NASA Astrophysics Data System (ADS)

    Chen, Lin

    2002-03-01

    The photoexcitation causes displacement of electron densities within or among molecules, which consequently leads to nuclear movements. Such nuclear displacements often occur in transient states with short lifetimes. Knowing transient molecular structures during photochemical reactions is important for understanding fundamental aspects of solar energy conversion and storage. Fast x-ray techniques provide direct probes for these transient structures. Using x-ray pulses from the Advanced Photon Source at Argonne, a laser pulse pump, x-ray pulse probe XAFS technique has been developed to capture transient molecular structures in disordered media with nanosecond time resolution. We have carried out several pump-probe XAFS measurements on 1)identifying a transient molecular structure of the photodissociation product of nickel-tetraphenylporphyrin with piperidine axial ligands (NiTPP-L2); 2)determination of the MLCT state structure of Bis(2,9-dimethyl-1,10-phenanthroline) Copper(I) [Cu(I)(dmp)2]+, and 3) triplet state molecular structures of metalloporphyrins. These studies not only prove the feasibility of the technique, but also gain structural information that otherwise will not be available. Future studies include probing transient structures in electron donor-acceptor complexes and optical polarization selected XAFS (OPS-XAFS) using the same technique with a 100-ps time resolution. This work is supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, U. S. Department of Energy, under contract W-31-109-Eng-38.

  6. Guided folding takes a start from the molecular imprinting of structured epitopes.

    PubMed

    Cenci, L; Guella, G; Andreetto, E; Ambrosi, E; Anesi, A; Bossi, A M

    2016-08-25

    A biomimetic route towards assisted folding was explored. Molecularly imprinted polymeric nanoparticles (MIP NPs), i.e. biomimetics with entailed molecular recognition properties made by a template assisted synthesis, were prepared to target a structured epitope: the cystine containing peptide CC9ox, which corresponds to the apical portion of the β-hairpin hormone Hepcidin-25. The structural selection was achieved by the MIP NPs; moreover, the MIP NPs demonstrated favouring the folding of the linear random peptide (CC9red) into the structured one (CC9ox), anticipating the future role of the MIP NPs as in situ nanomachines to counteract folding defects.

  7. The observation of correlated velocity structures in a translucent molecular cloud and implications for turbulence

    NASA Technical Reports Server (NTRS)

    Magnani, L.; Larosa, T. N.; Shore, S. N.

    1993-01-01

    We present a formaldehyde map of the translucent high-latitude molecular cloud MBM 16. The molecular gas traced by the H2CO is located in spatially distinct large structures that exhibit velocity coherence on a scale of 0.5 pc. These structures are not pressure-confined and are probably not self-gravitating. They may be transient structures. If so, we suggest that they are produced by shear flows whose scale length is of order the size of the cloud.

  8. STAR FORMATION RATES FOR STARBURST GALAXIES FROM ULTRAVIOLET, INFRARED, AND RADIO LUMINOSITIES

    SciTech Connect

    Sargsyan, Lusine A.; Weedman, Daniel W. E-mail: dweedman@isc.astro.cornell.edu

    2009-08-20

    We present a comparison of star formation rates (SFR) determined from mid-infrared 7.7 {mu}m polycyclic aromatic hydrocarbon (PAH) luminosity [SFR(PAH)], from 1.4 GHz radio luminosity [SFR(radio)], and from far-ultraviolet luminosity [SFR(UV)] for a sample of 287 starburst galaxies with z < 0.5 having Spitzer IRS observations. The previously adopted relation log [SFR(PAH)] = log [{nu}L {sub {nu}}(7.7 {mu}m)] - 42.57 {+-} 0.2, for SFR in M{sub sun} yr{sup -1} and {nu}L {sub {nu}}(7.7 {mu}m) the luminosity at the peak of the 7.7 {mu}m PAH feature in erg s{sup -1}, is found to agree with SFR(radio). Comparing with SFR(UV) determined independently from ultraviolet observations of the same sources with the Galaxy Evolution Explorer mission (not corrected for dust extinction), the median log [SFR(PAH)/SFR(UV)] = 1.67, indicating that only 2% of the ultraviolet continuum typically escapes extinction by dust within a starburst. This ratio SFR(PAH)/SFR(UV) depends on infrared luminosity, with the form log [SFR(PAH)/SFR(UV)] = (0.53 {+-} 0.05)log [{nu}L{sub {nu}}(7.7 {mu}m)] - 21.5 {+-} 0.18, indicating that more luminous starbursts are also dustier. Using our adopted relation between {nu}L{sub {nu}}(7.7 {mu}m) and L {sub ir}, this becomes log [SFR(PAH)/SFR(UV)]= (0.53 {+-} 0.05)log L{sub ir} - 4.11 {+-} 0.18, for L{sub ir} in L{sub sun}. Only blue compact dwarf galaxies show comparable or greater SFR(UV) compared to SFR(PAH). We also find that the ratio SFR(PAH)/SFR(UV) is similar to that in infrared-selected starbursts for a sample of Markarian starburst galaxies originally selected using optical classification, which implies that there is no significant selection effect in SFR(PAH)/SFR(UV) using starburst galaxies discovered by Spitzer. These results indicate that SFRs determined with ultraviolet luminosities require dust corrections by a factor of {approx}10 for typical local starbursts but this factor increases to >700 for the most luminous starbursts at z {approx} 2

  9. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    NASA Astrophysics Data System (ADS)

    Owens, Jonathan R.

    properties of the IV curves of single molecule nano-junctions. Specifically, these systems consist of a zinc-porphyrin molecule coupled between two gold electrodes, i.e., a nano-gap. The first observation we want to explain is the asymmetric nature of the experimental IV curve for this porphyrin system, where the IV curve is skewed heavily to the negative bias region. Using a plane-wave DFT calculation, we present the density of states of the porphyrin molecule (both in the presence and absence of the electrodes) and indeed see highly delocalized states (as confirmed by site-projection of the DOS) only in the negative bias region, meaning that the channels with high transmission probability reside there, in agreement with experimental observation. The next problem studied pertains to observed switching in an experimentally-measured IV curve, this time of a longer zinc porphyrin molecule, still within a gold nano-gap. The switching behavior is observed only at 300K, not at 4.2K. The temperature-dependance of this problem renders our previous toolset of DFT calculations void; DFT is a ground-state theory. Instead, we employ a density functional-based tight-binding (DFTB) approach in a molecular dynamics simulation. Basically, the structural configuration evaluated at each time step is based on a tight-binding electronic structure calculation, instead of a typical MD force field. Trajectories are presented at varying temperatures and electric field strengths. Indeed, we observe a conformation of the porphyrin molecule between two configurations of the dihedral angle of the central nitrogen ring, ±15. {o} at 300K, but not 4.2K. These confirmations are equally likely, i.e., the structure assumes these configurations an equal number of teams, meaning the average structure has an angle of 0. {o}. After computing the DOS of all three aforementioned configurations (0. {text{o}} and ±15. {text{o}}), we indeed see a difference between the DOS curves at ±15. {text{o}} (which are

  10. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    SciTech Connect

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  11. Molecular and supra-molecular structure of waxy starches developed from cassava (Manihot esculenta Crantz).

    PubMed

    Rolland-Sabaté, Agnès; Sanchez, Teresa; Buléon, Alain; Colonna, Paul; Ceballos, Hernan; Zhao, Shan-Shan; Zhang, Peng; Dufour, Dominique

    2013-02-15

    The aim of this work was to characterize the amylopectin of low amylose content cassava starches obtained from transgenesis comparatively with a natural waxy cassava starch (WXN) discovered recently in CIAT (International Center for Tropical Agriculture). Macromolecular features, starch granule morphology, crystallinity and thermal properties of these starches were determined. M¯(w) of amylopectin from the transgenic varieties are lower than WXN. Branched and debranched chain distributions analyses revealed slight differences in the branching degree and structure of these amylopectins, principally on DP 6-9 and DP>37. For the first time, a deep structural characterization of a series of transgenic lines of waxy cassava was carried out and the link between structural features and the mutated gene expression approached. The transgenesis allows to silenced partially or totally the GBSSI, without changing deeply the starch granule ultrastructure and allows to produce clones with similar amylopectin as parental cassava clone.

  12. Molecular structures of porphyrin-quinone models for electron transfer

    SciTech Connect

    Fajer, J.; Barkigia, K.M.; Melamed, D.; Sweet, R.M.; Kurreck, H.; Gersdorff, J. von; Plato, M.; Rohland, H.C.; Elger, G.; Moebius, K.

    1996-08-15

    Synthetic porphyrin-quinone complexes are commonly used to mimic electron transport in photosynthetic reaction centers and to probe the effects of energetics, distances, and relative orientations on rates of electron transfer between donor-acceptor couples. The structures of two such models have been determined by X-ray diffraction. The redox pairs consist of a zinc porphyrin covalently linked to benzoquinone in cis and trans configurations via a cyclohexanediyl bridge. The crystallographic studies were undertaken to provide a structural foundation for the extensive body of experimental and theoretical results that exists for these compounds in both the ground and photoinduced charge-separated states. The results validate conclusions reached from theoretical calculations, EPR and two-dimensional NMR results for these states. 15 refs., 6 figs., 2 tabs.

  13. Laboratory spectra of C60 and related molecular structures

    NASA Technical Reports Server (NTRS)

    Janca, J.; Solc, M.; Vetesnik, M.

    1994-01-01

    The electronic spectra of fullerene structures in high frequency discharge are studied in the plasma chemistry laboratory of the Faculty of Science of Masaryk University in Brno. The ultraviolet and visual spectra are investigated in order to be compared with the diffuse interstellar bands and interpreted within the theory of quantum mechanics. The preliminary results of the study are presented here in the form of a poster.

  14. Structure of molecular liquids: hard rod-disk mixtures.

    PubMed

    Cheung, David L; Anton, Lucian; Allen, Michael P; Masters, Andrew J

    2008-01-01

    The structure of hard rod-disk mixtures is studied using Monte Carlo simulations and integral equation theory, for a range of densities in the isotropic phase. By extension of methods used in single component fluids, the pair correlation functions of the molecules are calculated and comparisons between simulation and integral equation theory, using a number of different closure relations, are made. Comparison is also made for thermodynamic data and phase behavior.

  15. Rattlesnake Neurotoxin Structure, Mechanism of Action, Immunology and Molecular Biology

    DTIC Science & Technology

    1992-09-10

    Revised 1985). For the protection of human subjects, the investigator(s) adhered to policies of applicable Federal Law 45 CFR 46. condurting research...trial crystallization studies. Sequencing of the basic subunit of Mojave toxin was also proposed in this application , to facilitate our x-ray structural...hydroxysuccinimidyl-4-azidobenzoate ( HSAB ), to synaptosomes and synaptosomal membranes yielded bands on SDS-PAGE migrating at 102kD, equating to a 88kD

  16. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations

    PubMed Central

    Pérez, Jesús M.; Soriguer, Ramón C.; Granados, José E.

    2017-01-01

    Background Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. Methodology/Principal Findings We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Conclusions Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies. PMID:28135293

  17. Molecular structure and transport dynamics in perfluoro sulfonyl imide membranes.

    PubMed

    Idupulapati, Nagesh; Devanathan, Ram; Dupuis, Michel

    2011-06-15

    We report a detailed and comprehensive analysis from classical molecular dynamics simulations of the nanostructure of a model of hydrated perfluoro sulfonyl imide (PFSI) membrane, a polymeric system of interest as a proton conductor in polymer electrolyte membrane fuel cells. We also report on the transport dynamics of water and hydronium ions, and water network percolation in this system. We find that the water network percolation threshold for PFSI, i.e. the threshold at which a consistent spanning water network starts to develop in the membrane, is found to occur between hydration levels (λ) 6 and 7. The higher acidity of the sulfonyl imide acid group of PFSI compared to the sulfonic acid group in Nafion, as computationally characterized in our earlier ab initio study (Idupulapati et al 2010 J. Phys. Chem. A 114 6904-12), results in a larger fraction of 'free' hydronium ions at low hydration levels in PFSI compared to Nafion. However, the calculated diffusion coefficients of the H(3)O(+) ions and H(2)O molecules as a function the hydration level are observed to be almost the same as that of Nafion, indicating similar conductivity and consistent with experimental data.

  18. Quantitative structure-hydrophobicity relationships of molecular fragments and beyond.

    PubMed

    Zou, Jian-Wei; Huang, Meilan; Huang, Jian-Xiang; Hu, Gui-Xiang; Jiang, Yong-Jun

    2016-03-01

    Quantitative structure-property relationship (QSPR) models were firstly established for the hydrophobic substituent constant (πX) using the theoretical descriptors derived solely from electrostatic potentials (EPSs) at the substituent atoms. The descriptors introduced are found to be related to hydrogen-bond basicity, hydrogen-bond acidity, cavity, or dipolarity/polarizability terms in linear solvation energy relationship, which endows the models good interpretability. The predictive capabilities of the models constructed were also verified by rigorous Monte Carlo cross-validation. Then, eight groups of meta- or para-disubstituted benzenes and one group of substituted pyridines were investigated. QSPR models for individual systems were achieved with the ESP-derived descriptors. Additionally, two QSPR models were also established for Rekker's fragment constants (foct), which is a secondary-treatment quantity and reflects average contribution of the fragment to logP. It has been demonstrated that the descriptors derived from ESPs at the fragments, can be well used to quantitatively express the relationship between fragment structures and their hydrophobic properties, regardless of the attached parent structure or the valence state. Finally, the relations of Hammett σ constant and ESP quantities were explored. It implies that σ and π, which are essential in classic QSAR and represent different type of contributions to biological activities, are also complementary in interaction site.

  19. HST WFPC2 Images and CFHT Fabry-Perot Optical Spectra of the Starburst Disk and Energetic Superbubble in NGC 3079

    NASA Astrophysics Data System (ADS)

    Cecil, G.; Veilleux, S.; Filippenko, A. V.; Bland-Hawthorn, J.

    1999-12-01

    The nearly edge-on spiral LINER/Seyfert galaxy NGC 3079 (17 Mpc) has a ``boxy" bulge, stellar bar, and contains the most energetic known example of a windblown superbubble (ionized mass 107/ne Msun & KE 2x1056/ne erg) that extends 12" (1 kpc) above the disk. We have mapped emission-line profiles across the galaxy disk and superbubble with an imaging Fabry-Perot spectrophotometer. We have also obtained dithered WFPC2 658N Hα +[N II]λ 6583 and 814W continuum images of the inner 13-kpc diameter. We find that gas within 9-kpc diameter is lofted into narrow filaments that project up to 2 kpc above the disk, and which are usually unresolved in their narrow dimensions at 0\\farcs1 resolution. The superbubble is the most striking of these structures. The brightest filaments are organized into 4 distinct streams in azimuth that all fragment 0.7 kpc above the disk. The top of the superbubble is composed of numerous resolved droplets, each comprising 104/ne Msun of ionized gas, that resemble the ``cometary" blobs of stredded, dense clumps of disk material generated in the dense-disk+tenuous-halo hydro model of Suchkov et al (1994 ApJ, 430, 511). This morphology supports the presence of a free-streaming, blowout superwind, whose origin (AGN or starburst driven) and energetics we will discuss. The starburst disk is composed of diffuse filaments, along with numerous H II regions that are often ruptured on their top sides. A striking spray of linear filaments that trail for ⪆ 0.6 kpc behind unresolved ``bullets" is found outside the main starburst region. They emerge from a bright star-forming complex at ⪆ 7 kpc radius that lies well beyond the ends of the stellar bar, and which has X-ray luminosity 7*E38 erg/s in the ROSAT bands. This program is supported by NASA HST grant GO-6674

  20. Structure and photochromic properties of molybdenum-containing silica gels obtained by molecular-lamination method

    SciTech Connect

    Belotserkovskaya, N.G.; Dobychin, D.P.; Pak, V.N.

    1992-05-10

    The structure and physicochemical properties of molybdenum-containing silica gels obtained by molecular lamination have been studied quite extensively. Up to the present, however, no studies have been made of the influence of the pore structure of the original silica gel on the structure and properties of molybdenum-containing silica gels (MSG). The problem is quite important, since molybdenum silicas obtained by molecular lamination may find applications in catalysis and as sensors of UV radiation. In either case, the structure of the support is not a factor to be ignored. Here, the authors are reporting on an investigation of the structure of MSG materials with different pore structures and their susceptibility to reduction of the Mo(VI) oxide groupings when exposed to UV radiation. 16 refs., 2 figs., 2 tabs.

  1. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    SciTech Connect

    Yu,P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  2. A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

    NASA Technical Reports Server (NTRS)

    Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

    1993-01-01

    We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

  3. Charge-distribution effect of imaging molecular structure by high-order above-threshold ionization

    SciTech Connect

    Wang Bingbing; Fu Panming; Guo Yingchun; Zhang Bin; Zhao Zengxiu; Yan Zongchao

    2010-10-15

    Using a triatomic molecular model, we show that the interference pattern in the high-order above-threshold ionization (HATI) spectrum depends dramatically on the charge distribution of the molecular ion. Therefore the charge distribution can be considered a crucial factor for imaging a molecular geometric structure. Based on this study, a general destructive interference formula for each above-threshold ionization channel is obtained for a polyatomic molecule concerning the positions and charge values of each nuclei. Comparisons are made for the HATI spectra of CO{sub 2}, O{sub 2}, NO{sub 2}, and N{sub 2}. These results may shed light on imaging complex molecular structure by the HATI spectrum.

  4. Shaken, Not Stirred: The Disrupted Disk of the Starburst Galaxy NGC 253

    NASA Astrophysics Data System (ADS)

    Davidge, T. J.

    2010-12-01

    Near-infrared images obtained with WIRCam on the Canada-France-Hawaii Telescope are used to investigate the recent history of the nearby Sculptor Group spiral NGC 253, which is one of the nearest starburst galaxies. Bright asymptotic giant branch (AGB) stars are traced out to projected distances of ~22-26 kpc (~13-15 disk scale lengths) along the major axis. The distribution of stars in the disk is lopsided, in the sense that the projected density of AGB stars in the northeast portion of the disk between 10 and 20 kpc from the galaxy center is ~0.5 dex higher than on the opposite side of the galaxy. A large population of red supergiants is also found in the northeast portion of the disk and, with the exception of the central 2 kpc, this area appears to have been the site of the highest levels of star-forming activity in the galaxy during the past ~0.1 Gyr. It is argued that such high levels of localized star formation may have produced a fountain that ejected material from the disk, and the extraplanar H I detected by Boomsma et al. may be one manifestation of such activity. Diffuse stellar structures are found in the periphery of the disk, and the most prominent of these is to the south and east of the galaxy. Bright AGB stars, including cool C stars that are identified based on their J - K colors, are detected out to 15 kpc above the disk plane, and these are part of a diffusely distributed, flattened extraplanar component. Comparisons between observed and model luminosity functions suggest that the extraplanar regions contain stars that formed throughout much of the age of the universe. Additional evidence of a diffuse, extraplanar stellar component that contains moderately young stars comes from archival Galaxy Evolution Explorer images. It is suggested that the disk of NGC 253 was disrupted by a tidal encounter with a now defunct companion. This encounter introduced asymmetries that remain to this day, and the projected distribution of stars in and around NGC

  5. SHAKEN, NOT STIRRED: THE DISRUPTED DISK OF THE STARBURST GALAXY NGC 253

    SciTech Connect

    Davidge, T. J.

    2010-12-10

    Near-infrared images obtained with WIRCam on the Canada-France-Hawaii Telescope are used to investigate the recent history of the nearby Sculptor Group spiral NGC 253, which is one of the nearest starburst galaxies. Bright asymptotic giant branch (AGB) stars are traced out to projected distances of {approx}22-26 kpc ({approx}13-15 disk scale lengths) along the major axis. The distribution of stars in the disk is lopsided, in the sense that the projected density of AGB stars in the northeast portion of the disk between 10 and 20 kpc from the galaxy center is {approx}0.5 dex higher than on the opposite side of the galaxy. A large population of red supergiants is also found in the northeast portion of the disk and, with the exception of the central 2 kpc, this area appears to have been the site of the highest levels of star-forming activity in the galaxy during the past {approx}0.1 Gyr. It is argued that such high levels of localized star formation may have produced a fountain that ejected material from the disk, and the extraplanar H I detected by Boomsma et al. may be one manifestation of such activity. Diffuse stellar structures are found in the periphery of the disk, and the most prominent of these is to the south and east of the galaxy. Bright AGB stars, including cool C stars that are identified based on their J - K colors, are detected out to 15 kpc above the disk plane, and these are part of a diffusely distributed, flattened extraplanar component. Comparisons between observed and model luminosity functions suggest that the extraplanar regions contain stars that formed throughout much of the age of the universe. Additional evidence of a diffuse, extraplanar stellar component that contains moderately young stars comes from archival Galaxy Evolution Explorer images. It is suggested that the disk of NGC 253 was disrupted by a tidal encounter with a now defunct companion. This encounter introduced asymmetries that remain to this day, and the projected distribution

  6. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  7. Crystal and molecular structure of barley alpha-amylase.

    PubMed

    Kadziola, A; Abe, J; Svensson, B; Haser, R

    1994-05-27

    The three-dimensional structure of barley malt alpha-amylase (isoform AMY2-2) was determined by multiple isomorphous replacement using three heavy-atom derivatives and solvent flattening. The model was refined using a combination of simulated annealing and conventional restrained least-squares crystallographic refinement to an R-factor of 0.153 based on 18,303 independent reflections with F(o) > sigma(F(o)) between 10 and 2.8 A resolution, with root-mean-square deviations of 0.016 A and 3.3 degrees from ideal bond lengths and bond angles, respectively. The final model consists of 403 amino acid residues, three calcium ions and 153 water molecules. The polypeptide chain folds into three domains: a central domain forming a (beta alpha)8-barrel of 286 residues, with a protruding irregular structured loop domain of 64 residues (domain B) connecting strand beta 3 and helix alpha 3 of the barrel, and a C-terminal domain of 53 residues forming a five stranded anti-parallel beta-sheet. Unlike the previously known alpha-amylase structures, AMY2-2 contains three Ca2+ binding sites co-ordinated by seven or eight oxygen atoms from carboxylate groups, main-chain carbonyl atoms and water molecules, all calcium ions being bound to domain B and therefore essential for the structural integrity of that domain. Two of the Ca2+ sites are located only 7.0 A apart with one Asp residue serving as ligand for both. One Ca2+ site located at about 20 A from the other two was found to be exchangeable with Eu3+. By homology with other alpha-amylases, some important active site residues are identified as Asp179, Glu204 and Asp289, and are situated at the C-terminal end of the central beta-barrel. A starch granule binding site, previously identified as Trp276 and Trp277, is situated on alpha-helix 6 in the central (beta alpha)8-barrel, at the surface of the enzyme. This binding site region is associated with a considerable disruption of the (beta alpha)8-barrel 8-fold symmetry.

  8. The liquid structure of tetrachloroethene: Molecular dynamics simulations and reverse Monte Carlo modeling with interatomic potentials

    NASA Astrophysics Data System (ADS)

    Gereben, Orsolya; Pusztai, László

    2013-10-01

    The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ˜11 Å and a very small third one at ˜16 Å can be found as well, without preference for any axis or plane orientation.

  9. DFT study of the effect of substitution on the molecular structure of copper phthalocyanine

    NASA Astrophysics Data System (ADS)

    Kaur, Prabhjot; Sachdeva, Ritika; Singh, Sukhwinder; Saini, G. S. S.

    2016-05-01

    To study the effect of sulfonic acid group as substituent on the molecular structure of an organic compound copper Phthalocyanine, the optimized geometry, mulliken charges, energies and dipole momemts of copper phthalocyanine and copper phthalocyaninetetrasulfonic acid tetra sodium salt have been investigated using density functional theory. Also to predict the change in reactive sites after substitution, molecular electrostatic potential maps for both the molecules have been calculated.

  10. The Molecular and Morphologic Structures That Make Saltatory Conduction Possible in Peripheral Nerve.

    PubMed

    Carroll, Steven L

    2017-03-14

    Saltatory conduction is the process by which action potentials are rapidly and efficiently propagated along myelinated axons. In the peripheral nervous system, saltatory conduction is made possible by a series of morphologically and molecularly distinct subdomains in both axons and their associated myelinating Schwann cells. This review briefly summarizes current knowledge on the molecular structure and physiology of the node of Ranvier and adjacent regions of the axoglial unit in peripheral nerve.

  11. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders.

    PubMed

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-07

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  12. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders

    NASA Astrophysics Data System (ADS)

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-01

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  13. Molecular and crystal structure of anhydrous zirconium perchlorate

    SciTech Connect

    Genkina, E.A.; Babaeva, V.P.; Rosolovskii, V.Ya.

    1985-08-01

    An x-ray diffraction investigation (diffractometer, Mo K..cap alpha.., graphite monochromator, omega scan technique, Theta less than or equal to 30/sup 0/, 1060 reflections, least-squares method in the anisotropic approximation to R = 0.058) of anhydrous zirconium perchlorate has been carried out. The crystals of Zr(Cl0/sub 4/)/sub 4/ are monoclinic: ..cap alpha.. = 12.899(3), b = 13.188(7), c = 7.937(3) A, ..gamma.. = 107.91/sup 0/, Z = 4, space group Bb. The structure has an island character and is built up from isolated Zr(ClO/sub 4/)/sub 4/ molecules. The Zr atom is surrounded by eight O atoms in four bidentate perchlorato groups. The Zr-O distances lie in the range from 2.13 to 2.23 A, averaging 2.19 A. The eight-vertex polyhedron around Zr is the mmmm steroisomer of a dodecahedron. The centers of the perchlorato groups are located at the vertices of flattened tetrahedron. The ClO/sub 4/ groups have a distorted tetrahedral structure, and the mean length of the Cl-O/sub b/ bonds (1.50 A) is 0.11 A greater than the mean length of the Cl-O/sub t/ bonds, pointing out the essentially covalent character of the bonds of the perchlorato groups with the central Zr atom.

  14. Molecular determinants of staphylococcal biofilm dispersal and structuring

    PubMed Central

    Le, Katherine Y.; Dastgheyb, Sana; Ho, Trung V.; Otto, Michael

    2014-01-01

    Staphylococci are frequently implicated in human infections, and continue to pose a therapeutic dilemma due to their ability to form deeply seated microbial communities, known as biofilms, on the surfaces of implanted medical devices and host tissues. Biofilm development has been proposed to occur in three stages: (1) attachment, (2) proliferation/structuring, and (3) detachment/dispersal. Although research within the last several decades has implicated multiple molecules in the roles as effectors of staphylococcal biofilm proliferation/structuring and detachment/dispersal, to date, only phenol soluble modulins (PSMs) have been consistently demonstrated to serve in this role under both in vitro and in vivo settings. PSMs are regulated directly through a density-dependent manner by the accessory gene regulator (Agr) system. They disrupt the non-covalent forces holding the biofilm extracellular matrix together, which is necessary for the formation of channels, a process essential for the delivery of nutrients to deeper biofilm layers, and for dispersal/dissemination of clusters of biofilm to distal organs in acute infection. Given their relevance in both acute and chronic biofilm-associated infections, the Agr system and the psm genes hold promise as potential therapeutic targets. PMID:25505739

  15. Current and emerging opportunities for molecular simulations in structure-based drug design

    PubMed Central

    Michel, Julien

    2014-01-01

    An overview of the current capabilities and limitations of molecular simulation of biomolecular complexes in the context of computer-aided drug design is provided. Steady improvements in computer hardware coupled with more refined representations of energetics are leading to a new appreciation of the driving forces of molecular recognition. Molecular simulations are poised to more frequently guide the interpretation of biophysical measurements of biomolecular complexes. Ligand design strategies emerge from detailed analyses of computed structural ensembles. The feasibility of routine applications to ligand optimization problems hinges upon successful extensive large scale validation studies and the development of protocols to intelligently automate computations. PMID:24469595

  16. Structural and dipolar fluctuations in liquid water: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Skarmoutsos, Ioannis; Masia, Marco; Guardia, Elvira

    2016-03-01

    A Car-Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order and hydrogen bonding. The average dipole moment of water molecules with a strong tetrahedral order around them comes in excellent agreement with previous estimations of the dipole moment of ice Ih molecules.

  17. Exploring Molecular and Mechanical Gradients in Structural Bioscaffolds†

    PubMed Central

    Waite, J. Herbert; Lichtenegger, Helga C.; Stucky, Galen D.; Hansma, Paul

    2007-01-01

    Most organisms consist of a functionally adaptive assemblage of hard and soft tissues. Despite the obvious advantages of reinforcing soft protoplasm with a hard scaffold, such composites can lead to tremendous mechanical stresses where the two meet. Although little is known about how nature relieves these stresses, it is generally agreed that fundamental insights about molecular adaptation at hard/soft interfaces could profoundly influence how we think about biomaterials. Based on two noncellular tissues, mussel byssus and polychaete jaws, recent studies suggest that one natural strategy to minimize interfacial stresses between adjoining stiff and soft tissue appears to be the creation of a “fuzzy” boundary, which avoids abrupt changes in mechanical properties. Instead there is a gradual mechanical change that accompanies the transcendence from stiff to soft and vice versa. In byssal threads, the biochemical medium for achieving such a gradual mechanical change involves the elegant use of collagen-based self-assembling block copolymers. There are three distinct diblock copolymer types in which one block is always collagenous, whereas the other can be either elastin-like (soft), amorphous polyglycine (intermediate), or silk-like (stiff). Gradients of these are made by an incrementally titrated expression of the three proteins in secretory cells the titration phenotype of which is linked to their location. Thus, reflecting exactly the composition of each thread, the distal cells secrete primarily the silk– and polyglycine–collagen diblocks, whereas the proximal cells secrete the elastin– and polyglycine–collagen diblocks. Those cells in between exhibit gradations of collagens with silk or elastin blocks. Spontaneous self-assembly appears to be by pH triggered metal binding by histidine (HIS)-rich sequences at both the amino and carboxy termini of the diblocks. In the polychaete jaws, HIS-rich sequences are expanded into a major block domain. Histidine

  18. Spectral molecular line surveys of active galaxies

    NASA Astrophysics Data System (ADS)

    Villicana Pedraza, Ilhuiyolitzin

    The enormous mass of molecular gas and dust found in the nuclei of active galaxies has a major role in feeding the activity (either starburst or AGN) and therefore in the galactic evolution. Thus, observations of the molecular can provide clues to identify and analyze the type of activity in very deeply obscured galactic nuclei. Indeed, studies of the chemical composition in starburst galaxies via wide band spectral has shown the potential of molecular spectroscopy to trace the physical and chemical propierties of their central ISM material. In this work we present the analysis of the emission of molecules such as HCN, CCH, CN,CS,HCO+, HNC, CH3OH, among others obtained from the survey of spectra of the 3 near seyfert galaxies observed with the APEX Telescope. We have also found that one of the molecules is not at LTE conditions- H3O+ molecule. Whether radiatively pumped or maser enhanced, the emission of H3O+ is emerging from a different region from most other molecules (distributed in two molecular lobes seen as the two velocity components). H3O+ emission peaks close to the systemic velocity of the system, particularly clear in NGC 253, which suggest the emission to be centrally peaked towards the nuclear engine, It is common in the same kind of galaxies? In adition, preliminar conclusions show isotopic ratio 12C/13C in starburst galaxies is higher than nuclei of the Milky Way indicating that interestelar matter in starburst nuclei is less processed than in the nucleus of the Milky Way .There are two possible explanations for this effect in starburst, nucleosynthesis differences due stellar population history and acretion of matter from halo.

  19. Molecular tools for investigating ANME community structure and function

    SciTech Connect

    Hallam, Steven J.; Page, Antoine P.; Constan, Lea; Song, Young C.; Norbeck, Angela D.; Brewer, Heather M.; Pasa-Tolic, Ljiljana

    2011-05-20

    Methane production and consumption in anaerobic marine sediments 1 is catalyzed by a series of reversible tetramethanopterin (H4MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabolism. These include reactions catalyzed by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase and methyl coenzyme M reductase. The latter enzyme is central to C-H bond formation and cleavage underlying methanogenic and reverse methanogenic phenotypes. Here we describe a set of novel tools for the detection and functional analysis of H4MPT-linked C1 transfer reactions mediated by uncultivated anaerobic methane oxidizing archaea (ANME). These tools include polymerase chain reaction primers targeting ANME methyl coenzyme M reductase subunit A subgroups and protein extraction methods from marine sediments compatible with high-resolution mass spectrometry for profiling population structure and functional dynamics. [910, 1,043

  20. Molecular Structure and Reactivity in the Pyrolysis of Aldehydes

    NASA Astrophysics Data System (ADS)

    Sias, Eric; Cole, Sarah; Sowards, John; Warner, Brian; Wright, Emily; McCunn, Laura R.

    2016-06-01

    The effect of alkyl chain structure on pyrolysis mechanisms has been investigated in a series of aldehydes. Isovaleraldehyde, CH_3CH(CH_3)CH_2CHO, and pivaldehyde, (CH_3)_3CCHO, were subject to thermal decomposition in a resistively heated SiC tubular reactor at 800-1200 °C. Matrix-isolation FTIR spectroscopy was used to identify pyrolysis products. Carbon monoxide and isobutene were major products from each of the aldehydes, which is consistent with what is known from previous studies of unbranched alkyl-chain aldehydes. Other products observed include vinyl alcohol, propene, acetylene, and ethylene, revealing complexities to be considered in the pyrolysis of large, branched-chain aldehydes.

  1. Crystal and molecular structure of sodium paratungstate 26 hydrate

    SciTech Connect

    Cruywagen, J.J.; Nassibemi, L.R.; Niven, M.L.; Vander Merwe, I.F.

    1986-08-01

    On standing, an acid solution of tungstate yields single crystals of the paratungstate salt Na/sub 10/(H/sub 2/W/sub 12/O/sub 42/ /SUB sd/ /SUP ./ 26H/sub 2/O. The space group is P1, (No. 2), a 11.811(2), b = 12.486(2), c = 12.206(2) A, ..cap alpha.. = 82.29(1), ..beta.. = 115.12(1), ..gamma.. = 113.76(1) /sup 0/, V = 1485.6 A/sup 3/, Z = 1. The structure was solved by direct methods and refined to R = 0.0397, R /SUB w/ = 0.0403 (w = (sigma/sup 2/F)/sup -1/). The 12 WO/sub 6/ octahedra (shared edges and vertices) are distorted from regular geometry; one of the sodium ions exhibits disorder and there is extensive hydrogen bonding between the water molecules and the oxygens of the paratungstate anion.

  2. Searching molecular structure databases with tandem mass spectra using CSI:FingerID

    PubMed Central

    Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

    2015-01-01

    Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

  3. Molecular dynamics of protein kinase-inhibitor complexes: a valid structural information.

    PubMed

    Caballero, Julio; Alzate-Morales, Jans H

    2012-01-01

    Protein kinases (PKs) are key components of protein phosphorylation based signaling networks in eukaryotic cells. They have been identified as being implicated in many diseases. High-resolution X-ray crystallographic data exist for many PKs and, in many cases, these structures are co-complexed with inhibitors. Although this valuable information confirms the precise structure of PKs and their complexes, it ignores the dynamic movements of the structures which are relevant to explain the affinities and selectivity of the ligands, to characterize the thermodynamics of the solvated complexes, and to derive predictive models. Atomistic molecular dynamics (MD) simulations present a convenient way to study PK-inhibitor complexes and have been increasingly used in recent years in structure-based drug design. MD is a very useful computational method and a great counterpart for experimentalists, which helps them to derive important additional molecular information. That enables them to follow and understand structure and dynamics of protein-ligand systems with extreme molecular detail on scales where motion of individual atoms can be tracked. MD can be used to sample dynamic molecular processes, and can be complemented with more advanced computational methods (e.g., free energy calculations, structure-activity relationship analysis). This review focuses on the most commonly applications to study PK-inhibitor complexes using MD simulations. Our aim is that researchers working in the design of PK inhibitors be aware of the benefits of this powerful tool in the design of potent and selective PK inhibitors.

  4. The state of the warm and cold gas in the extreme starburst at the core of the Phoenix galaxy cluster (SPT-CLJ2344-4243)

    SciTech Connect

    McDonald, Michael; Bautz, Marshall W.; Swinbank, Mark; Edge, Alastair C.; Hogan, Michael T.; Wilner, David J.; Bayliss, Matthew B.; Veilleux, Sylvain; Benson, Bradford A.; Marrone, Daniel P.; McNamara, Brian R.; Wei, Lisa H.

    2014-03-20

    We present new optical integral field spectroscopy (Gemini South) and submillimeter spectroscopy (Submillimeter Array) of the central galaxy in the Phoenix cluster (SPT-CLJ2344-4243). This cluster was previously reported to have a massive starburst (∼800 M {sub ☉} yr{sup –1}) in the central, brightest cluster galaxy, most likely fueled by the rapidly cooling intracluster medium. These new data reveal a complex emission-line nebula, extending for >30 kpc from the central galaxy, detected at [O II]λλ3726, 3729, [O III]λλ4959, 5007, Hβ, Hγ, Hδ, [Ne III]λ3869, and He II λ4686. The total Hα luminosity, assuming Hα/Hβ = 2.85, is L {sub Hα} = 7.6 ± 0.4 ×10{sup 43} erg s{sup –1}, making this the most luminous emission-line nebula detected in the center of a cool core cluster. Overall, the relative fluxes of the low-ionization lines (e.g., [O II], Hβ) to the UV continuum are consistent with photoionization by young stars. In both the center of the galaxy and in a newly discovered highly ionized plume to the north of the galaxy, the ionization ratios are consistent with both shocks and active galactic nucleus (AGN) photoionization. We speculate that this extended plume may be a galactic wind, driven and partially photoionized by both the starburst and central AGN. Throughout the cluster we measure elevated high-ionization line ratios (e.g., He II/Hβ, [O III]/Hβ), coupled with an overall high-velocity width (FWHM ≳ 500 km s{sup –1}), suggesting that shocks are likely important throughout the interstellar medium of the central galaxy. These shocks are most likely driven by a combination of stellar winds from massive young stars, core-collapse supernovae, and the central AGN. In addition to the warm, ionized gas, we detect a substantial amount of cold, molecular gas via the CO(3-2) transition, coincident in position with the galaxy center. We infer a molecular gas mass of M{sub H{sub 2}} = 2.2 ± 0.6 × 10{sup 10} M {sub ☉}, which implies that

  5. The State of the Warm and Cold Gas in the Extreme Starburst at the Core of the Phoenix Galaxy Cluster (SPT-CLJ2344-4243)

    NASA Astrophysics Data System (ADS)

    McDonald, Michael; Swinbank, Mark; Edge, Alastair C.; Wilner, David J.; Veilleux, Sylvain; Benson, Bradford A.; Hogan, Michael T.; Marrone, Daniel P.; McNamara, Brian R.; Wei, Lisa H.; Bayliss, Matthew B.; Bautz, Marshall W.

    2014-03-01

    We present new optical integral field spectroscopy (Gemini South) and submillimeter spectroscopy (Submillimeter Array) of the central galaxy in the Phoenix cluster (SPT-CLJ2344-4243). This cluster was previously reported to have a massive starburst (~800 M ⊙ yr-1) in the central, brightest cluster galaxy, most likely fueled by the rapidly cooling intracluster medium. These new data reveal a complex emission-line nebula, extending for >30 kpc from the central galaxy, detected at [O II]λλ3726, 3729, [O III]λλ4959, 5007, Hβ, Hγ, Hδ, [Ne III]λ3869, and He II λ4686. The total Hα luminosity, assuming Hα/Hβ = 2.85, is L Hα = 7.6 ± 0.4 ×1043 erg s-1, making this the most luminous emission-line nebula detected in the center of a cool core cluster. Overall, the relative fluxes of the low-ionization lines (e.g., [O II], Hβ) to the UV continuum are consistent with photoionization by young stars. In both the center of the galaxy and in a newly discovered highly ionized plume to the north of the galaxy, the ionization ratios are consistent with both shocks and active galactic nucleus (AGN) photoionization. We speculate that this extended plume may be a galactic wind, driven and partially photoionized by both the starburst and central AGN. Throughout the cluster we measure elevated high-ionization line ratios (e.g., He II/Hβ, [O III]/Hβ), coupled with an overall high-velocity width (FWHM gsim 500 km s-1), suggesting that shocks are likely important throughout the interstellar medium of the central galaxy. These shocks are most likely driven by a combination of stellar winds from massive young stars, core-collapse supernovae, and the central AGN. In addition to the warm, ionized gas, we detect a substantial amount of cold, molecular gas via the CO(3-2) transition, coincident in position with the galaxy center. We infer a molecular gas mass of M_{H_2} = 2.2 ± 0.6 × 1010 M ⊙, which implies that the starburst will consume its fuel in ~30 Myr if it is not

  6. Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.

    PubMed Central

    Woolf, T B

    1997-01-01

    Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments. Images FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 Figure 6 PMID:9370432

  7. Hierarchical QSAR technology based on the Simplex representation of molecular structure

    NASA Astrophysics Data System (ADS)

    Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N.

    2008-06-01

    This article is about the hierarchical quantitative structure-activity relationship technology (HiT QSAR) based on the Simplex representation of molecular structure (SiRMS) and its application for different QSAR/QSP(property)R tasks. The essence of this technology is a sequential solution (with the use of the information obtained on the previous steps) to the QSAR problem by the series of enhanced models of molecular structure description [from one dimensional (1D) to four dimensional (4D)]. It is a system of permanently improved solutions. In the SiRMS approach, every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality and symmetry). The level of simplex descriptors detailing increases consecutively from the 1D to 4D representation of the molecular structure. The advantages of the approach reported here are the absence of "molecular alignment" problems, consideration of different physical-chemical properties of atoms (e.g. charge, lipophilicity, etc.), the high adequacy and good interpretability of obtained models and clear ways for molecular design. The efficiency of the HiT QSAR approach is demonstrated by comparing it with the most popular modern QSAR approaches on two representative examination sets. The examples of successful application of the HiT QSAR for various QSAR/QSPR investigations on the different levels (1D-4D) of the molecular structure description are also highlighted. The reliability of developed QSAR models as predictive virtual screening tools and their ability to serve as the base of directed drug design was validated by subsequent synthetic and biological experiments, among others. The HiT QSAR is realized as a complex of computer programs known as HiT QSAR software that also includes a powerful statistical block and a number of useful utilities.

  8. Molecular Structure of Aggregated Amyloid-β: Insights from Solid State Nuclear Magnetic Resonance

    PubMed Central

    Tycko, Robert

    2016-01-01

    Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made on characterization of the molecular structures of Aβ aggregates. Full molecular structural models that are based primarily on data from solid state nuclear magnetic resonance measurements have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates. PMID:27481836

  9. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

    PubMed

    Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

    2017-04-04

    Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology.

  10. Molecular structure and liquid-crystalline characteristics of chitosan phenylcarbamate.

    PubMed

    Kuse, Yasunori; Asahina, Daisuke; Nishio, Yoshiyuki

    2009-01-12

    Chitosan phenylcarbamate (CtsPC) samples were synthesized to have different degrees of substitution (DS) ranging from approximately 2.7 to approximately 3.7, and the lyotropic liquid crystallinity was mainly characterized by spectrophotometry. The products of DS>2.8 formed a cholesteric type of mesophase in concentrated solutions of >44 wt % with polar aprotic solvents such as N,N-dimethylformamide (DMF), N,N-dimethylacetamide (DMAc), and dimethyl sulfoxide (DMSO), and some of the solutions imparted vivid colorations because of selective visible light reflection. The cholesteric helical pitch increased with increasing temperature and with decreasing polymer concentration, but the helical sense remained left-handed under the adopted measurement conditions. It was also found that the helical pitch increased in proportion to the increment of DS, whereas an average degree of phenylcarbamoyl polyaddition in the side chains (DPs) rather affected the pitch distribution measuring an orderliness in the cholesteric structure. With a small increase in DPs (e.g., from 1.01 to 1.04), the cholesteric orderliness decreased and the temperature sensitivity of the pitch turned sluggish. Wide-angle X-ray diffractometry was also used for evaluating the distance and azimuth difference between adjacent nematic thin layers in the cholesteric mesophase.

  11. Microwave Spectroscopy and Molecular Structure of Isonitrosyl Hydroxide (hoon)

    NASA Astrophysics Data System (ADS)

    Crabtree, Kyle N.; Talipov, Marat R.; O'Connor, Gerard; Martinez, Oscar, Jr.; Khursan, Sergey L.; McCarthy, Michael C.

    2014-06-01

    Nitrous acid (HONO) is an important member of the atmospheric nitrogen cycle whose chemistry involves a variety of gas-phase, photochemical, and heterogeneous processes. Among its formation pathways in the atmosphere is the ternary association of hydroxyl (OH) with nitric oxide (NO), but the formation of the isonitrosyl hydroxide (HOON) isomer has largely been ignored owing to early theoretical studies that questioned its stability. Guided by new high-level ab initio calculations, we have detected the rotational spectrum of trans-HOON in an electrical discharge of a dilute mixture of NO and water vapor by a combination of Fourier transform microwave spectroscopy and double resonance methods. No evidence for the cis isomer was found in any of our spectroscopic surveys between 15.4--17.0 GHz. A semi-experimental equilibrium structure for trans-HOON has been derived to high precision from isotopic substitution (DOON, H18OON, HO18ON, HOO15N) along with zero-point vibrational corrections calculated at the CCSD(T)/aug-cc-pVTZ level of theory. Most notably, the central O--O bond in trans-HOON is found to be 1.9149 ± 0.0005 Å in length, which is the longest known O--O bond in a molecule (nearly 20% longer than the analogous bond in the HOOO radical).

  12. Crystal and mol-ecular structure of aflatrem.

    PubMed

    Lenta, Bruno N; Ngatchou, Jules; Kenfack, Patrice T; Neumann, Beate; Stammler, Hans-Georg; Sewald, Norbert

    2015-11-01

    The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the mol-ecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabi-cyclo-[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabi-cyclo-[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the mol-ecule exhibits a tilt of 2.02 (1)° between its two rings. In the crystal, O-H⋯O hydrogen bonds connect mol-ecules into chains along [010]. Weak N-H⋯π inter-actions connect these chains, forming sheets parallel to (10-1).

  13. Modification of LDPE molecular structure by gamma irradiation for bioapplications

    NASA Astrophysics Data System (ADS)

    Ferreira, L. M.; Falcão, A. N.; Gil, M. H.

    2005-07-01

    The surface properties of low-density polyethylene (LDPE) can be modified by the grafting of 2-hydroxyethyl methacrylate (HEMA). This was done aiming at the production of new materials suitable for bioapplications. Samples with different monomer concentrations were prepared from LDPE particles by gamma irradiation, following different irradiation protocols, including irradiation in presence and absence of air. The samples were characterized by thermal analysis techniques (DSC and TGA) and by Fourier transform infrared spectroscopy (FTIR). The results obtained show a decrease in the crystallinity of the supporting matrix for copolymers with high yields of grafting. However, the new materials prepared maintain good structural order resulting from the protective effect of polyHEMA grafted onto LDPE backbone. These effects can improve the diffusion of other species deeper inside the matrix and increase the material hydrophilicity. The studies performed made possible the selection of experimental protocols adequate for the production of new copolymeric materials with high grafting yield. These were used in the production of new LDPE films with enhanced hydrophilic properties.

  14. Computational nanochemistry study of the molecular structure and properties of ethambutol.

    PubMed

    Salgado-Morán, Guillermo; Ruiz-Nieto, Samuel; Gerli-Candia, Lorena; Flores-Holguín, Norma; Favila-Pérez, Alejandra; Glossman-Mitnik, Daniel

    2013-09-01

    The M06 family of density functionals was employed to calculate the molecular structure and properties of the ethambutol molecule. Besides determination of molecular structures, UV-vis spectra were computed using TD-DFT in the presence of a solvent and the results compared with available experimental data. The chemical reactivity descriptors were calculated through conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to Fukui function indices. A comparison between the descriptors calculated through vertical energy values and those arising from Koopmans' theorem approximation were performed in order to check the validity of the latter procedure.

  15. Spectroscopic study of molecular structure, antioxidant activity and biological effects of metal hydroxyflavonol complexes

    NASA Astrophysics Data System (ADS)

    Samsonowicz, Mariola; Regulska, Ewa

    2017-02-01

    Flavonols with varied hydroxyl substitution can act as strong antioxidants. Thanks to their ability to chelate metals as well as to donate hydrogen atoms they have capacity to scavenge free radicals. Their metal complexes are often more active in comparison with free ligands. They exhibit interesting biological properties, e.g. anticancer, antiphlogistic and antibacterial. The relationship between molecular structure and their biological properties was intensively studied using spectroscopic methods (UV-Vis, IR, Raman, NMR, ESI-MS). The aim of this paper is review on spectroscopic analyses of molecular structure and biological activity of hydroxyflavonol metal complexes.

  16. Modulated structure and molecular dissociation of solid chlorine at high pressures

    NASA Astrophysics Data System (ADS)

    Li, Peifang; Gao, Guoying; Ma, Yanming

    2012-08-01

    Among diatomic molecular halogen solids, high pressure structures of solid chlorine (Cl2) remain elusive and least studied. We here report first-principles structural search on solid Cl2 at high pressures through our developed particle-swarm optimization algorithm. We successfully reproduced the known molecular Cmca phase (phase I) at low pressure and found that it remains stable up to a high pressure 142 GPa. At 150 GPa, our structural searches identified several energetically competitive, structurally similar, and modulated structures. Analysis of the structural results and their similarity with those in solid Br2 and I2, it was suggested that solid Cl2 adopts an incommensurate modulated structure with a modulation wave close to 2/7 in a narrow pressure range 142-157 GPa. Eventually, our simulations at >157 GPa were able to predict the molecular dissociation of solid Cl2 into monatomic phases having body centered orthorhombic (bco) and face-centered cubic (fcc) structures, respectively. One unique monatomic structural feature of solid Cl2 is the absence of intermediate body centered tetragonal (bct) structure during the bco → fcc transition, which however has been observed or theoretically predicted in solid Br2 and I2. Electron-phonon coupling calculations revealed that solid Cl2 becomes superconductors within bco and fcc phases possessing a highest superconducting temperature of 13.03 K at 380 GPa. We further probed the molecular Cmca → incommensurate phase transition mechanism and found that the softening of the Ag vibrational (rotational) Raman mode in the Cmca phase might be the driving force to initiate the transition.

  17. The anharmonic force field and equilibrium molecular structure of ketene

    NASA Astrophysics Data System (ADS)

    East, Allan L. L.; Allen, Wesley D.; Klippenstein, Stephen J.

    1995-06-01

    A comprehensive anharmonic vibrational analysis of isotopic ketenes has been performed on the basis of a complete ab initio quartic force field constructed by means of second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles and doubles (CCSD) approach, augmented for structural optimizations by a contribution for connected triple excitations [CCSD(T)]. The atomic-orbital basis sets of the study entailed C,O(10s6p/5s4p) and H(6s/4s) spaces multiply polarized in the valence region to give QZ(2d,2p) and QZ(2d1f,2p1d) sets. An iterative anharmonic vibrational refinement of a limited set of quadratic scaling parameters on 27 fundamentals of H2CCO, HDCCO, D2CCO, and H2C13CO generates a final quartic force field which reproduces the empirical νi data with an average absolute error of only 1.1 cm-1. This force field yields a complete and self-consistent set of Coriolis (ζij), vibrational anharmonic (χij), vibration-rotation interaction (αi), and quartic and sextic centrifugal distortion constants, providing a critical assessment of the assorted spectroscopic constants determined over many years and also facilitating future computations of vibrational state densities for detailed tests of unimolecular dissociation theories. The harmonic frequencies ascertained for H2CCO (in cm-1), with associated anharmonicities in parentheses, are ω1(a1)=3202.2(-129.2), ω2(a1)=2197.2(-44.4), ω3(a1)=1415.2(-25.9), ω4(a1)=1146.0(-29.7), ω5(b1)=581.9(+7.1), ω6(b1)=502.6(+26.3), ω7(b2)=3308.2(-141.3), ω8(b2)=996.0(-17.9), and ω9(b2)=433.6(+5.0). The large positive anharmonicity for the ν6(b1) C=C=O bending mode, which is principally a Coriolis effect, warrants continued investigation. Explicit first-order treatments of the strong Fermi interactions within the (ν4,2ν5,ν5+ν6,2ν6) manifold reveal resonance shifts for ν4(H2CCO, HDCCO, D2CCO) of (-12.1, -10.0, +12.2) cm-1, in order. The experimental assignments for this Fermi tetrad are confirmed to

  18. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

    PubMed Central

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-01-01

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

  19. Molecular structure and dynamics in bacterial mercury resistance

    SciTech Connect

    Johs, Alexander; Shi, Liang; Miller, Susan M; Summers, Anne O; Liang, Liyuan

    2008-01-01

    Bacteria participate significantly in mercury transformation in natural and industrial environments. Previous studies have shown that bacterial mercury resistance is mediated by the mer operon, typically located on transposons or plasmids. It encodes specific genes that facilitate uptake of mercury species, cleavage of organomercurials, and reduction of Hg(II) to Hg(0). Expression of mer operon genes is regulated by MerR, a metal-responsive regulator protein on the level of transcription. In vitro studies have shown that MerR forms a non-transcribing pre-initiation complex with RNA polymerase and the promoter DNA. Binding of Hg(II) induces conformational changes in MerR and other components of the complex resulting in the transcription of mer operon genes. As part of ongoing investigations on allosteric conformational changes induced by Hg(II) in dimeric MerR, and the implications on the binding of RNA polymerase to the promoter of the mer operon, we applied small angle scattering to study the regulatory mechanism of MerR in the presence and absence of Hg(II). Our results show that in the presence of Hg(II) the MerR dimer undergoes a significant reorientation from a compact state to a conformation revealing two distinct domains. Bacterial reduction of Hg(II) can also occur at concentrations too low to induce mer operon functions. Dissimilatory metal reducing bacteria, such as Shewanella and Geobacter are able to reduce Hg(II) in the presence of mineral oxides. This process has been linked to the activity of outer membrane multiheme cytochromes. We isolated and purified a decaheme outer membrane cytochrome OmcA from Shewanella oneidensis MR-1 and characterized its envelope shape in solution by small angle x-ray scattering. Structural features were identified and compared to homology models. These results show that OmcA is an elongated macromolecule consisting of separate modules, which may be connected by flexible linkers.

  20. Molecular Structures of Isolevuglandin-Protein Cross-Links.

    PubMed

    Bi, Wenzhao; Jang, Geeng-Fu; Zhang, Lei; Crabb, John W; Laird, James; Linetsky, Mikhail; Salomon, Robert G

    2016-10-17

    Isolevuglandins (isoLGs) are stereo and structurally isomeric γ-ketoaldehydes produced through free radical-induced oxidation of arachidonates. Some isoLG isomers are also generated through enzymatic cyclooxygenation. Post-translational modification of proteins by isoLGs is associated with loss-of-function, cross-linking and aggregation. We now report that a low level of modification by one or two molecules of isoLG has a profound effect on the activity of a multi subunit protease, calpain-1. Modification of one or two key lysyl residues apparently suffices to abolish catalytic activity. Covalent modification of calpain-1 led to intersubunit cross-linking. Hetero- and homo-oligomers of the catalytic and regulatory subunits of calpain-1 were detected by SDS-PAGE with Western blotting. N-Acetyl-glycyl-lysine methyl ester and β-amyloid(11-17) peptide EVHHQKL were used as models for characterizing the cross-linking of protein lysyl residues resulting from adduction of iso[4]LGE2. Aminal, bispyrrole, and trispyrrole cross-links of these two peptides were identified and fully characterized by mass spectrometry. Aminal and bispyrrole dimers were both detected. Furthermore, a complex mixture of derivatives of the bispyrrole cross-link containing one or more additional atoms of oxygen was found. Interesting differences are evident in the predominant cross-link type generated in the reaction of iso[4]LGE2 with these peptides. More aminal cross-links versus bispyrrole are formed during the reaction of the dipeptide with iso[4]LGE2. In contrast, more bispyrrole versus aminal cross-links are formed during the reaction of EVHHQKL with iso[4]LGE2. It is tempting to speculate that the EVHHQKL peptide-pyrrole modification forms noncovalent aggregates that favor the production of covalent bispyrrole cross-links because β-amyloid(11-17) tends to spontaneously oligomerize.

  1. Starbursts in dwarf galaxies: A multiwavelength case study of NGC 625

    NASA Astrophysics Data System (ADS)

    Cannon, John Michael

    The results of a multiwavelength case study of the nearby dwarf starburst galaxy NGC 625 are presented. This low- mass galaxy hosts a massive starburst comparable in luminosity to 30 Doradus in the Large Magellanic Cloud; its proximity and high galactic latitude provide an ideal opportunity to investigate the starburst phenomenon and its impact on the ISM and IGM. We use Chandra, FUSE, HST, CTIO, ATCA, and VLA data to investigate the nature of the stellar population and multi-phase ISM. Our principal findings are summarized as follows: (1)Ground-based optical spectroscopy finds a prominent Wolf-Rayet (W-R) feature arising from the major starburst region, implying a brief burst duration (4 6 Myr); (2)A spatially resolved star formation history analysis using HST/WFPC2 data shows that the duration of the burst is actually much longer than the W-R features would imply (duration ≳ 50 Myr), and that the star formation has been widespread throughout the disk over this interval; (3)This extended starburst has input sufficient kinetic energy into the ISM to create a large-scale outflow; (4)H I observations from the ATCA show complex kinematics that are consistent with a minor-axis outflow of large amounts of neutral gas; (5)This outflow is verified by FUSE spectroscopy, where strong O VI coronal gas absorption is blueshifted with respect to the neutral and diffuse H2 absorption lines; (6)FUSE spectra also reveal an abundance offset between the neutral and nebular gas regions that may be a common component of the ISM of low-metallicity dwarf galaxies; (7)The ROSAT detection of diffuse soft x-ray emission is verified by new Chandra imaging of NGC 625; (8)VLA radio continuum data shows a thermal global spectral index and a mix of thermal and nonthermal indices for the individual major star formation regions, suggesting vigorous and (temporally and spatially) extended star formation throughout the disk. We interpret these results in the context of low-mass galaxy evolution

  2. Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Rankin, David W H

    2007-07-05

    A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).

  3. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  4. Assessing protein conformational sampling and structural stability via de novo design and molecular dynamics simulations.

    PubMed

    Cunha, Keila C; Rusu, Victor H; Viana, Isabelle F T; Marques, Ernesto T A; Dhalia, Rafael; Lins, Roberto D

    2015-06-01

    Molecular dynamics and de novo techniques, associated to quality parameter sets, have excelled at determining the structure of small proteins with high accuracy. To achieve a detailed description of protein conformations, these methods must critically assess the thermodynamic features of the molecular ensembles. Here, a comparison of the conformational ensemble generated by molecular dynamics and de novo techniques were carried out for six Top7-based proteins carrying gp41 HIV-1 epitopes. The native Top7, a highly stable computationally designed protein, was used as benchmark. Structural stability, flexibility, and secondary structure content were assessed. The consistency of the latter was compared to experimental circular dichroism spectra for all proteins. While both methods are capable to identify the stable from unstable chimeric proteins, the sampled conformational space and flexibility differ significantly in both methods. Molecular dynamics simulations seem to better describe secondary structure content and identify regions responsible for conformational instability. The de novo method, as implemented in Rosetta-a prime tool for protein design, overestimates secondary structure content. On the other hand, its empirical energy function is capable to predict the threshold for protein stability.

  5. Using Molecular Replacement Phasing to Study the Structure and Function of RNA.

    PubMed

    Marcia, Marco

    2016-01-01

    In recent years a wide variety of RNA molecules regulating fundamental cellular processes has been discovered. Therefore, RNA structure determination is experiencing a boost and many more RNA structures are likely to be determined in the years to come. The broader availability of experimentally determined RNA structures implies that molecular replacement (MR) will be used more and more frequently as a method for phasing future crystallographic structures. In this report we describe various aspects relative to RNA structure determination by MR. First, we describe how to select and create MR search models for nucleic acids. Second, we describe how to perform MR searches on RNA using available crystallographic software. Finally, we describe how to refine and interpret the successful MR solutions. These protocols are applicable to determine novel RNA structures as well as to establish structural-functional relationships on existing RNA structures.

  6. Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

    PubMed

    Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

    2015-01-16

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  7. A unique role for Kv3 voltage-gated potassium channels in starburst amacrine cell signaling in mouse retina.

    PubMed

    Ozaita, Ander; Petit-Jacques, Jerome; Völgyi, Béla; Ho, Chi Shun; Joho, Rolf H; Bloomfield, Stewart A; Rudy, Bernardo

    2004-08-18

    Direction-selective retinal ganglion cells show an increased activity evoked by light stimuli moving in the preferred direction. This selectivity is governed by direction-selective inhibition from starburst amacrine cells occurring during stimulus movement in the opposite or null direction. To understand the intrinsic membrane properties of starburst cells responsible for direction-selective GABA release, we performed whole-cell recordings from starburst cells in mouse retina. Voltage-clamp recordings revealed prominent voltage-dependent K(+) currents. The currents were mostly blocked by 1 mm TEA, activated rapidly at voltages more positive than -20 mV, and deactivated quickly, properties reminiscent of the currents carried by the Kv3 subfamily of K+ channels. Immunoblots confirmed the presence of Kv3.1 and Kv3.2 proteins in retina and immunohistochemistry revealed their expression in starburst cell somata and dendrites. The Kv3-like current in starburst cells was absent in Kv3.1-Kv3.2 knock-out mice. Current-clamp recordings showed that the fast activation of the Kv3 channels provides a voltage-dependent shunt that limits depolarization of the soma to potentials more positive than -20 mV. This provides a mechanism likely to contribute to the electrical isolation of individual starburst cell dendrites, a property thought essential for direction selectivity. This function of Kv3 channels differs from that in other neurons where they facilitate high-frequency repetitive firing. Moreover, we found a gradient in the intensity of Kv3.1b immunolabeling favoring proximal regions of starburst cells. We hypothesize that this Kv3 channel gradient contributes to the preference for centrifugal signal flow in dendrites underlying direction-selective GABA release from starburst amacrine cells

  8. Evolving molecular cloud structure and the column density probability distribution function

    NASA Astrophysics Data System (ADS)

    Ward, Rachel L.; Wadsley, James; Sills, Alison

    2014-12-01

    The structure of molecular clouds can be characterized with the probability distribution function (PDF) of the mass surface density. In particular, the properties of the distribution can reveal the nature of the turbulence and star formation present inside the molecular cloud. In this paper, we explore how these structural characteristics evolve with time and also how they relate to various cloud properties as measured from a sample of synthetic column density maps of molecular clouds. We find that, as a cloud evolves, the peak of its column density PDF will shift to surface densities below the observational threshold for detection, resulting in an underlying lognormal distribution which has been effectively lost at late times. Our results explain why certain observations of actively star-forming, dynamically older clouds, such as the Orion molecular cloud, do not appear to have any evidence of a lognormal distribution in their column density PDFs. We also study the evolution of the slope and deviation point of the power-law tails for our sample of simulated clouds and show that both properties trend towards constant values, thus linking the column density structure of the molecular cloud to the surface density threshold for star formation.

  9. Molecular dynamics simulations of soliton-like structures in a dusty plasma medium

    SciTech Connect

    Tiwari, Sanat Kumar Das, Amita; Sen, Abhijit; Kaw, Predhiman

    2015-03-15

    The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.

  10. The Vertex Version of Weighted Wiener Number for Bicyclic Molecular Structures

    PubMed Central

    Gao, Wei; Wang, Weifan

    2015-01-01

    Graphs are used to model chemical compounds and drugs. In the graphs, each vertex represents an atom of molecule and edges between the corresponding vertices are used to represent covalent bounds between atoms. We call such a graph, which is derived from a chemical compound, a molecular graph. Evidence shows that the vertex-weighted Wiener number, which is defined over this molecular graph, is strongly correlated to both the melting point and boiling point of the compounds. In this paper, we report the extremal vertex-weighted Wiener number of bicyclic molecular graph in terms of molecular structural analysis and graph transformations. The promising prospects of the application for the chemical and pharmacy engineering are illustrated by theoretical results achieved in this paper. PMID:26640513

  11. Determination of molecular-ion structures through the use of accelerated beams

    SciTech Connect

    Gemmell, D.S.

    1987-01-01

    In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the ''Coulomb-explosion'' technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, has been termed a ''Coulomb explosion.'' 4 refs., 2 figs.

  12. Molecular structure and dynamical properties of niosome bilayers with and without cholesterol incorporation: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Ritwiset, Aksornnarong; Krongsuk, Sriprajak; Johns, Jeffrey Roy

    2016-09-01

    Niosomes are non-ionic surfactant vesicles having a bilayer structure formed by self-assembly of hydrated surfactants, usually with cholesterol incorporation. Stability and mechanical properties of niosomes strongly depend on type of non-ionic surfactants and compositions used. In this study we present the structural and dynamical properties of niosome bilayers composed of sorbitan monostearate (Span60) with 0% and 50% cholesterol compositions which are investigated by using molecular dynamics simulations. The simulations reveal that niosome bilayer without cholesterol prefer to form in the gel phase with a higher order structure, while in the presence of cholesterol the bilayer exhibits more fluidity having a less ordered structure. The niosome bilayer with 50% cholesterol inclusion shows an increase of area per lipid (∼11%) and thickness (∼39%) compared with the niosome bilayer without cholesterol. The Span60 tailgroup orientation of the niosome bilayers without cholesterol exhibits more tilt (34.5o ± 0.5) than that of the bilayer with 50% cholesterol (15.4o ± 0.8). Additionally, our results show that the addition of cholesterol to the bilayer causes the higher in lateral and transverse diffusion, as well as an increase in the hydrogen bond number between Span60 and water. Such characteristics not only enhance the niosome stability but also increase the fluidity, which are necessary for the niosomal drug delivery.

  13. Crystal structure and molecular dynamics studies of L-amino acid oxidase from Bothrops atrox.

    PubMed

    Feliciano, Patricia R; Rustiguel, Joane K; Soares, Ricardo O S; Sampaio, Suely V; Cristina Nonato, M

    2017-03-15

    L-amino acid oxidases (LAAOs) are dimeric flavoproteins that catalyze the deamination of L-amino acid to α-keto acid, producing ammonia and hydrogen peroxide. In this study, we report the crystal structure and molecular dynamics simulations of LAAO from the venom of Bothrops atrox (BatroxLAAO). BatroxLAAO presents several biological and pharmacological properties with promising biomedical applications. BatroxLAAO structure contains the highly conserved structural pattern of LAAOs comprising a FAD-binding domain, substrate-binding domain and helical domain, and a dimeric arrangement that can be stabilized by zinc. Also, molecular dynamics results show an asymmetric behavior, and a direct communication between FAD- and substrate-binding domains of counterpart subunits. These findings shed light on the structural role of dimerization to catalytic mechanism of SV-LAAOs.

  14. Structure and behavior of human α-thrombin upon ligand recognition: thermodynamic and molecular dynamics studies.

    PubMed

    Silva, Vivian de Almeira; Cargnelutti, Maria Thereza; Giesel, Guilherme M; Palmieri, Leonardo C; Monteiro, Robson Q; Verli, Hugo; Lima, Luis Mauricio T R

    2011-01-01

    Thrombin is a serine proteinase that plays a fundamental role in coagulation. In this study, we address the effects of ligand site recognition by alpha-thrombin on conformation and energetics in solution. Active site occupation induces large changes in secondary structure content in thrombin as shown by circular dichroism. Thrombin-D-Phe-Pro-Arg-chloromethyl ketone (PPACK) exhibits enhanced equilibrium and kinetic stability compared to free thrombin, whose difference is rooted in the unfolding step. Small-angle X-ray scattering (SAXS) measurements in solution reveal an overall similarity in the molecular envelope of thrombin and thrombin-PPACK, which differs from the crystal structure of thrombin. Molecular dynamics simulations performed with thrombin lead to different conformations than the one observed in the crystal structure. These data shed light on the diversity of thrombin conformers not previously observed in crystal structures with distinguished catalytic and conformational behaviors, which might have direct implications on novel strategies to design direct thrombin inhibitors.

  15. Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

    NASA Astrophysics Data System (ADS)

    Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

    2017-02-01

    Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

  16. Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

    NASA Astrophysics Data System (ADS)

    Kluber, Alexander; Hayre, Robert; Cox, Daniel

    2012-02-01

    Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

  17. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Whitfield, T. W.; Crain, J.; Martyna, G. J.

    2006-03-01

    In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

  18. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    PubMed Central

    Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-01-01

    Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts. PMID:24189228

  19. De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation

    PubMed Central

    Maffeo, Christopher; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-01-01

    The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures. PMID:26980283

  20. Computational characterization of the molecular structure and properties of Dye 7 for organic photovoltaics.

    PubMed

    Baldenebro-López, Jesús; Castorena-González, José; Flores-Holguin, Norma; Calderón-Guillén, Joel; Glossman-Mitnik, Daniel

    2012-03-01

    Organic dyes have great potential for its use in solar cells. In this recent work, the molecular structure and properties of Dye 7 were obtained using density functional theory (DFT) and different levels of calculation. Upon comparing the molecular structure and the ultraviolet visible spectrum with experimental data reported in the literature, it was found that the M05-2X/6-31G(d) level of calculation gave the best approximation. Once the appropriate methodology had been obtained, the molecule was characterized by obtaining the infrared spectrum, dipole moment, total energy, isotropic polarizability, molecular orbital energies, free energy of solvation in different solvents, and the chemical reactivity sites using the condensed Fukui functions.

  1. CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

    PubMed Central

    2011-01-01

    CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity. PMID:21214931

  2. Molecular structure of poly(methyl methacrylate) surface II: Effect of stereoregularity examined through all-atom molecular dynamics.

    PubMed

    Jha, Kshitij C; Zhu, He; Dhinojwala, Ali; Tsige, Mesfin

    2014-11-04

    Utilizing all-atom molecular dynamics (MD), we have analyzed the effect of tacticity and temperature on the surface structure of poly(methyl methacrylate) (PMMA) at the polymer-vacuum interface. We quantify these effects primarily through orientation, measured as the tilt with respect to the surface normal, and the surface number densities of the α-methyl, ester-methyl, carbonyl, and backbone methylene groups. Molecular structure on the surface is a complex interplay between orientation and number densities and is challenging to capture through sum frequency generation (SFG) spectroscopy alone. Independent quantification of the number density and orientation of chemical groups through all-atom MD presents a comprehensive model of stereoregular PMMA on the surface. SFG analysis presented in part I of this joint publication measures the orientation of molecules that are in agreement with MD results. We observe the ester-methyl groups as preferentially oriented, irrespective of tacticity, followed by the α-methyl and carbonyl groups. SFG spectroscopy also points to ester-methyl being dominant on the surface. The backbone methylene groups show a very broad angular distribution, centered along the surface plane. The surface number density ratios of ester-methyl to α-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to α-methyl. These subtle trends in the relative angular orientation and number densities that influence the variation of surface structure with tacticity are highlighted in this article. A more planar conformation of the syndiotactic PMMA along the surface (x-y plane) can be visualized through the trajectories from all-atom MD. Results from conformation tensor calculations for chains with any of their segments contributing to the surface validate the visual observation.

  3. Optimization of large amorphous silicon and silica structures for molecular dynamics simulations of energetic impacts

    NASA Astrophysics Data System (ADS)

    Samela, Juha; Norris, Scott A.; Nordlund, Kai; Aziz, Michael J.

    2011-07-01

    A practical method to create optimized amorphous silicon and silica structures for molecular dynamics simulations is developed and tested. The method is based on the Wooten, Winer, and Weaire algorithm and combination of small optimized blocks to larger structures. The method makes possible to perform simulations of either very large cluster hypervelocity impacts on amorphous targets or small displacements induced by low energy ion impacts in silicon.

  4. From Molecular Structure to Global Processes : NMR Spectroscopy in Analytical/Environmental Chemistry

    NASA Astrophysics Data System (ADS)

    Simpson, A.

    2009-04-01

    NMR Spectroscopy is arguably the most powerful tool to elucidate structure and probe molecular interactions. A range of NMR approaches will be introduced with emphasis on addressing and understanding structure and reactivity of soil organic matter at the molecular level. The presentation will be split into three main sections. The first section will look at evidence from advanced NMR based approaches that when considered synergistically describes the major structural components in soil organic matter. Multidimensional NMR spectroscopy (1-3D NMR), automated pattern matching, spectral simulations, diffusion NMR and hybrid-diffusion NMR will be introduced in context of molecular structure. Finally the structural components in soil will be contrasted to those found in aquatic dissolved organic matter. Secondly molecular interactions of natural organic matter will be considered. Advanced structural studies have provided detailed spectral assignments which in turn permit the reactivity of various soil components to be elucidated. Aggregation and self-association of soil and dissolved organic matter will be discussed along with the structural components likely responsible for aggregation/colloid formation. Interactions of soil organic matter with anthropogenic chemicals will also be considered and NMR techniques based on "Saturation Transfer Difference" introduced. These techniques are extremely powerful and can be used to both; describe mechanistically how anthropogenic chemicals sorb to whole soils and identify the structural components (lignin, protein, cellulose, etc..) that are responsible for the binding/sorption in soil. In the last section, the "big questions" and challenges facing the field will be considered along with some novel experimental NMR based approaches that should, in future, assist in providing answers to these questions.

  5. Conformation of the umifenovir cation in the molecular and crystal structures of four carboxylic acid salts

    NASA Astrophysics Data System (ADS)

    Orola, Liana; Sarcevica, Inese; Kons, Artis; Actins, Andris; Veidis, Mikelis V.

    2014-01-01

    The umifenovir salts of maleic, salicylic, glutaric, and gentisic acid as well as the chloroform solvate of the salicylate were prepared. Single crystals of the five compounds were obtained and their molecular and crystal structures determined by X-ray diffraction. In each structure the conformation of phenyl ring with respect to the indole group of the umifenovir moiety is different. The water solubility and melting points of the studied umifenovir salts have been determined.

  6. Molecular Modeling of Rigid-Rod Polymers Structures Dominated by Electrostatic Interactions

    DTIC Science & Technology

    2005-11-01

    the structure in solutions of PBO in strong acids . The role of the dielectric properties of the medium ( dielectric constant) and counterions. 1...morphology which the polymer adopts. We propose to undertake a molecular modeling study of the effect of strong acids on the structure and properties of PBO...methane sulphonic and chlorine sulphonic acids [5], (protons are connected with oxygen atoms as well). Besides we have considered also patially protonated

  7. A very deep IRAS survey - Constraints on the evolution of starburst galaxies

    NASA Astrophysics Data System (ADS)

    Hacking, Perry; Condon, J. J.; Houck, J. R.

    1987-05-01

    Counts of sources (primarily starburst galaxies) from a deep 60 microns IRAS survey published by Hacking and Houck (1987) are compared with four evolutionary models. The counts below 100 mJy are higher than expected if no evolution has taken place out to a redshift of approximately 0.2. Redshift measurements of the survey sources should be able to distinguish between luminosity-evolution and density-evolution models and detect as little as a 20 percent brightening or increase in density of infrared sources per billion years ago (H/0/ = 100 km/s per Mpc). Starburst galaxies cannot account for the reported 100 microns background without extreme evolution at high redshifts.

  8. Crystallization of silicates in massive young star cluster Westerlund 1: a nearby starburst analog

    NASA Astrophysics Data System (ADS)

    Kemper, Francisca

    2014-10-01

    We propose to observe dust forming stars in massive young cluster Westerlund 1 with the FORCASTgrism modes. The objective of this proposal is to determine the crystalline fraction of the silicates formed by the brightest mid-infrared point sources in this cluster, by disentangling the crystalline and amorphous silicate contributions to the infrared spectroscopy. This research is motivated by the discovery of large amounts of crystalline silicate dust in starburst galaxies (Spoon et al. 2006), while the silicates in the interstellar medium of our own galaxies are completely amorphous (Kemper et al. 2004). Spoon et al. explain the high crystallinity by the production by massive stars, although models show this may not be sufficient (Kemper et al. 2011). With these observations we hope to accurately pin down the crystalline silicate production by massive stars in a starburst environment.

  9. Very deep IRAS survey - constraints on the evolution of starburst galaxies

    SciTech Connect

    Hacking, P.; Houck, J.R.; Condon, J.J.

    1987-05-01

    Counts of sources (primarily starburst galaxies) from a deep 60 microns IRAS survey published by Hacking and Houck (1987) are compared with four evolutionary models. The counts below 100 mJy are higher than expected if no evolution has taken place out to a redshift of approximately 0.2. Redshift measurements of the survey sources should be able to distinguish between luminosity-evolution and density-evolution models and detect as little as a 20 percent brightening or increase in density of infrared sources per billion years ago (H/0/ = 100 km/s per Mpc). Starburst galaxies cannot account for the reported 100 microns background without extreme evolution at high redshifts. 21 references.

  10. Correlates across the Structural, Functional, and Molecular Phenotypes of Fragile X Syndrome

    ERIC Educational Resources Information Center

    Beckel-Mitchener, Andrea; Greenough, William T.

    2004-01-01

    Fragile X syndrome (FXS) is characterized by a pattern of morphological, functional, and molecular characteristics with, in at least some cases, apparent relationships among phenotypic features at different levels. Gross morphology differences in the sizes of some human brain regions are accompanied by fine structural alterations in the shapes and…

  11. The History of Molecular Structure Determination Viewed through the Nobel Prizes.

    ERIC Educational Resources Information Center

    Jensen, William P.; Palenik, Gus J.; Suh, Il-Hwan

    2003-01-01

    Discusses the importance of complex molecular structures. Emphasizes their individual significance through examination of the Nobel Prizes of the 20th century. Highlights prizes awarded to Conrad Rontgen, Francis H.C. Crick, James D. Watson, Maurice H.F. Wilkins, and others. (SOE)

  12. Development and Assessment of a Molecular Structure and Properties Learning Progression

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Underwood, Sonia M.; Hilley, Caleb Z.; Klymkowsky, Michael W.

    2012-01-01

    Previously, we found that: (i) many students were unable to construct representations of simple molecular structures; (ii) a majority of students fail to make the important connection between these representations and macroscopic properties of the material; and (iii) they were unable to decode the information contained in such representations.…

  13. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    ERIC Educational Resources Information Center

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

    2010-01-01

    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  14. Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations

    NASA Astrophysics Data System (ADS)

    Marques, Helder M.; Egan, Timothy J.; de Villiers, Katherine A.

    The use of empirical force field methods for modeling important systems in bioinorganic chemistry, including the cobalt corrins (derivatives of vitamin B12) and the iron porphyrins, is described. Particular attention is given to the use of molecular dynamics and simulated annealing calculations in exploring the solution structures of corrin, and those of likely complexes between the ferriprotoporphyrin-IX and the arylmethanol antimalarials.

  15. Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

    ERIC Educational Resources Information Center

    Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

    2011-01-01

    We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

  16. Structural Order in Water: Comparison between the Spectral Analysis of Raman Data and Molecular Dynamics Results

    NASA Astrophysics Data System (ADS)

    Faginas Lago, N.; Paolantoni, M.; Laganá, A.; Alberti, M.

    2007-12-01

    We utilize molecular dynamics calculations performed using the DL_POLY suite of programs to test the validity of two popular water interaction models and to better understand the structural order of its liquid phase by comparing calculated properties with the Raman spectrum.

  17. Molecular Docking of Enzyme Inhibitors: A Computational Tool for Structure-Based Drug Design

    ERIC Educational Resources Information Center

    Rudnitskaya, Aleksandra; Torok, Bela; Torok, Marianna

    2010-01-01

    Molecular docking is a frequently used method in structure-based rational drug design. It is used for evaluating the complex formation of small ligands with large biomolecules, predicting the strength of the bonding forces and finding the best geometrical arrangements. The major goal of this advanced undergraduate biochemistry laboratory exercise…

  18. Biological and Molecular Structure Analyses of the Controls on Soil Organic Matter Dynamics.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A combination of biological analysis, such as incubation and microbial biomass determination, 13C and 14C tracers, soil fractionation, and matrix analysis (LF, POM, silt, and clay) with molecular structure analysis (py-MBMS) on long-term sites with a C3 ' C4 crop switch provided the tools for determ...

  19. Well-ordered monolayers of alkali-doped coronene and picene: Molecular arrangements and electronic structures

    SciTech Connect

    Yano, M.; Endo, M.; Hasegawa, Y.; Okada, R.; Yamada, Y. Sasaki, M.

    2014-07-21

    Adsorptions of alkali metals (such as K and Li) on monolayers of coronene and picene realize the formation of ordered phases, which serve as well-defined model systems for metal-intercalated aromatic superconductors. Upon alkali-doping of the monolayers of coronene and picene, scanning tunneling microscopy and X-ray absorption spectroscopy revealed the rearrangement of the entire molecular layer. The K-induced reconstruction of both monolayers resulted in the formation of a structure with a herringbone-like arrangement of molecules, suggesting the intercalation of alkali metals between molecular planes. Upon reconstruction, a shift in both the vacuum level and core levels of coronene was observed as a result of a charge transfer from alkali metals to coronene. In addition, a new density of states near the Fermi level was formed in both the doped coronene and the doped picene monolayers. This characteristic electronic feature of the ordered monolayer has been also reported in the multilayer picene films, ensuring that the present monolayer can model the properties of the metal-intercalated aromatic hydrocarbons. It is suggested that the electronic structure near the Fermi level is sensitive to the molecular arrangement, and that both the strict control and determinations of the molecular structure in the doped phase should be important for the determination of the electronic structure of these materials.

  20. Study of Starburst/Activity/Interaction Phenomena based on the Multiple Byurakan-IRAS Galaxies

    NASA Astrophysics Data System (ADS)

    Harutyunyan, Gohar S.; Mickaelian, Areg M.

    2014-07-01

    The Byurakan-IRAS Galaxy (BIG) sample is the result of optical identifications of IRAS PSC sources at high-galactic latitudes using the First Byurakan Survey (FBS) low-dispersion spectra. Among the 1178 objects most are spiral galaxies and many have been proved to be AGN and starburst by spectroscopic observations, as well as there is a number of ULIRGs among these objects. BIG objects contain galaxy pairs, multiples, and small groups that are subject for study on the matter of the real IR-emitter in these systems. Given that these objects are powerful IR sources, they are considered as young systems indicating high rate of evolution and starburst activity exceeding 100 M o /yr. Spectroscopic observations show that all these systems are physical ones and we were able to measure the mutual distances and sizes for all components. Cross-correlations with the recent more accurate IR catalogues, such as 2MASS and WISE, as well as radio ones (NVSS, FIRST), provided accurate coordinates of the IR source and possibility to find the individual galaxy responsible for the IR. However, in almost half of the cases, IR position indicates the intermediate region between the components, which means that it comes from the system as a whole. Some more MW data have been matched to IR and radio to have an overall understanding on these systems. Given that these systems are mostly interacting/merging ones often containing AGN and most of them may be considered as powerful starbursts, it is possible to study starburst/activity/interaction phenomena and their interrelationship.

  1. The Post-starburst Evolution of Tidal Disruption Event Host Galaxies

    NASA Astrophysics Data System (ADS)

    French, K. Decker; Arcavi, Iair; Zabludoff, Ann

    2017-02-01

    We constrain the recent star formation histories of the host galaxies of eight optical/UV-detected tidal disruption events (TDEs). Six hosts had quick starbursts of <200 Myr duration that ended 10–1000 Myr ago, indicating that TDEs arise at different times in their hosts’ post-starburst evolution. If the disrupted star formed in the burst or before, the post-burst age constrains its mass, generally excluding O, most B, and highly massive A stars. If the starburst arose from a galaxy merger, the time since the starburst began limits the coalescence timescale and thus the merger mass ratio to more equal than 12:1 in most hosts. This uncommon ratio, if also that of the central supermassive black hole (SMBH) binary, disfavors the scenario in which the TDE rate is boosted by the binary but is insensitive to its mass ratio. The stellar mass fraction created in the burst is 0.5%–10% for most hosts, not enough to explain the observed 30–200× boost in TDE rates, suggesting that the host’s core stellar concentration is more important. TDE hosts have stellar masses 109.4–1010.3 M⊙, consistent with the Sloan Digital Sky Survey volume-corrected, quiescent Balmer-strong comparison sample and implying SMBH masses of 105.5–107.5 M⊙. Subtracting the host absorption line spectrum, we uncover emission lines; at least five hosts have ionization sources inconsistent with star formation that instead may be related to circumnuclear gas, merger shocks, or post-AGB stars.

  2. New constraints on the escape of ionizing photons from starburst galaxies using ionization-parameter mapping

    SciTech Connect

    Zastrow, Jordan; Oey, M. S.; Veilleux, Sylvain; McDonald, Michael

    2013-12-10

    The fate of ionizing radiation in starburst galaxies is key to understanding cosmic reionization. However, the galactic parameters on which the escape fraction of ionizing radiation depend are not well understood. Ionization-parameter mapping provides a simple, yet effective, way to study the radiative transfer in starburst galaxies. We obtain emission-line ratio maps of [S III]/[S II] for six, nearby, dwarf starbursts: NGC 178, NGC 1482, NGC 1705, NGC 3125, NGC 7126, and He 2-10. The narrowband images are obtained with the Maryland-Magellan Tunable Filter at Las Campanas Observatory. Using these data, we previously reported the discovery of an optically thin ionization cone in NGC 5253, and here we also discover a similar ionization cone in NGC 3125. This latter cone has an opening angle of 40° ± 5° (0.4 sr), indicating that the passageways through which ionizing radiation may travel correspond to a small solid angle. Additionally, there are three sample galaxies that have winds and/or superbubble activity, which should be conducive to escaping radiation, yet they are optically thick. These results support the scenario that an orientation bias limits our ability to directly detect escaping Lyman continuum in many starburst galaxies. A comparison of the star formation properties and histories of the optically thin and thick galaxies is consistent with the model that high escape fractions are limited to galaxies that are old enough (≳3 Myr) for mechanical feedback to have cleared optically thin passageways in the interstellar medium, but young enough (≲5 Myr) that the ionizing stars are still present.

  3. Optical spectroscopy of the radio-loud nuclei of spiral galaxies: Starbursts or monsters

    SciTech Connect

    Heckman, T.M.; Van Breugel, W.; Miley, G.K.; Butcher, H.R.

    1983-08-01

    We present optical spectroscopic data pertaining to the physical state, kinematics, and spatial extent of the emission-line gas near the radio-loud nuclei of spiral galaxies. These data are combined with published optical, radio, and infrared data to evaluate the suggestions by Condon et al. (1982) that the nuclear radio emission in this class of galaxy is produced by multiple supernova remnants generated as a consequence of a nuclear starburst. As a whole, the radio-loud nuclei have stronger emission lines than radio-quiet nuclei of galaxies of similar Hubble/de Vaucouleurs type. This emission-line gas is generally at least as spatially extended as the radio continuum emission. However, we find that only about 1/3 of the spiral galaxies examined have optical spectroscopic properties consistent with those of ''extranuclear starbursts'' (i.e., giant H II regions). The majority of the nuclei seem to require a form of energy input to the ionized gas which is ''harder'' than the Lyman continuum radiation of OB stars, as their emission-line spectra are of the Seyfert or Liner variety. The nuclei with H II region spectra are distinct from the nuclei with Seyfert spectra in terms of radio morphology and radio spectral index, and tend to occur in spiral galaxies of much later Hubble type than do the Seyfert or Liner nuclei (Sc vs Sa). Moreover, the most luminous nuclear radio sources in our sample (PMHz> or =10/sup 22/ Watts Hz/sup -1/ Sr/sup -1/) are not associated with H II region nuclei. We summarize evidence that the putative nuclear starbursts must differ significantly from extranuclear starbursts.

  4. Search for post-starburst (E+A) galaxies in the cluster Abell 3266

    NASA Astrophysics Data System (ADS)

    Zhang, Zhongyu

    The objective of this work is to use spectroscopic techniques to further the understanding of the dynamical state of the galaxy cluster Abell 3266. This is a very rich cluster in the southern skies that has been extensively studied by many groups. The cluster shows evidence of a merger of substructure in its midst, but the geometry, dynamics, and age of this merger remain uncertain. Low resolution, fiber spectra of galaxies in Abell 3266 were analyzed and searched for “E+A” (post-starburst) galaxies, from which we selected two candidate “E+A” galaxies for follow-up high-resolution spectroscopy. The 2 candidate galaxies are confirmed as “E+A” galaxies with high-resolution, slit spectra. The ages of these “E+A” galaxies (i.e. time since their starburst occurred) are determined with the method developed by Leonardi & Rose (1996). We find that both galaxies had a major starburst in the past, but they occurred at significantly different epochs. If the starbursts are related to the recent merger history of Abell 3266, instead of being just isolated events, they would indicate that there may have been more than one merger in this cluster in the past 3 Gyr or so. This might explain the rather disparate conclusions that have been obtained in the past about the merger history of this cluster. To compare with other nearby clusters, “E+A” galaxies were also searched for among nearly 2400 galaxies in 26 clusters fields. Only 4 candidates are found. This result is consistent with the general observational fact that there are substantially fewer spectroscopically disturbed galaxies in nearby clusters than in distant clusters. The result is also in quantitative agreement with the findings in the larger, more homogeneous Las Campanas Redshift Survey, confirming the reliability of our identification in Abell 3266. The impact of these statistical analyses on the understanding of galaxy evolution in cluster environment is also discussed.

  5. Physical properties of young stellar populations in 24 starburst galaxies observed with FUSE

    NASA Astrophysics Data System (ADS)

    Pellerin, Anne; Robert, Carmelle

    2007-10-01

    We present the main physical properties of very young stellar populations seen with the Far Ultraviolet Spectroscopic Explorer in 24 individual starbursts. These characteristics have been obtained using the evolutionary spectral synthesis technique in the far-ultraviolet range with the LAVALSB code. For each starburst, quantitative values for age, metallicity, initial mass function slope, stellar mass and internal extinction have been obtained and discussed in details. Limits of the code have been tested. One main conclusion is that most starbursts (and probably all of them) cannot be represented by any continuous star formation burst in the far ultraviolet. Also, quantitative values of various optical diagnostics related to these stellar populations have been predicted. Underlying stellar populations, dominated by B-type stars, have been detected in NGC1140, NGC4449 and possibly NGC3991. We characterized the young stellar populations of less than 5Myr in Seyfert2 nuclei. Based on observations made with the NASA-CNES-CSA Far Ultraviolet Spectroscopic Explorer. Far Ultraviolet Spectroscopic Explorer (FUSE) is operated for NASA by the Johns Hopkins University under NASA contract NAS5-32985. E-mail: pellerin@stsci.edu (AP); carobert@phy.ulaval.ca (CR)

  6. VizieR Online Data Catalog: IR spectroscopy of AGN & starbursts (Samsonyan+, 2016)

    NASA Astrophysics Data System (ADS)

    Samsonyan, A.; Weedman, D.; Lebouteiller, V.; Barry, D.; Sargsyan, L.

    2016-10-01

    A sample of 379 extragalactic sources is presented that has mid-infrared, high-resolution spectroscopy from the Spitzer Infrared Spectrograph (IRS) and also spectroscopy of the [CII]158μm line from the Herschel Photodetector Array Camera and Spectrometer (PACS). The emission line profiles of [NeII]12.81μm, [NeIII]15.55μm, and [CII]158μm are presented, and intrinsic line widths are determined (full width half maximum of Gaussian profiles after instrumental correction). All line profiles, together with overlays comparing the positions of PACS and IRS observations, are made available in the Cornell Atlas of Spitzer IRS Sources (CASSIS). Sources are classified from active galactic nucleus (AGN) to starburst based on equivalent widths of the 6.2μm polycyclic aromatic hydrocarbon feature. It is found that intrinsic line widths do not change among classifications for [CII], with median widths of 207km/s for AGNs, 248km/s for composites, and 233km/s for starbursts. The [NeII] line widths also do not change with classification, but [NeIII] lines are progressively broader from starburst to AGN. A few objects with unusually broad lines or unusual redshift differences in any feature are identified. (1 data file).

  7. THE PANCHROMATIC STARBURST IRREGULAR DWARF SURVEY (STARBIRDS): OBSERVATIONS AND DATA ARCHIVE

    SciTech Connect

    McQuinn, Kristen B. W.; Mitchell, Noah P.; Skillman, Evan D.

    2015-06-22

    Understanding star formation in resolved low mass systems requires the integration of information obtained from observations at different wavelengths. We have combined new and archival multi-wavelength observations on a set of 20 nearby starburst and post-starburst dwarf galaxies to create a data archive of calibrated, homogeneously reduced images. Named the panchromatic “STARBurst IRregular Dwarf Survey” archive, the data are publicly accessible through the Mikulski Archive for Space Telescopes. This first release of the archive includes images from the Galaxy Evolution Explorer Telescope (GALEX), the Hubble Space Telescope (HST), and the Spitzer Space Telescope (Spitzer) Multiband Imaging Photometer instrument. The data sets include flux calibrated, background subtracted images, that are registered to the same world coordinate system. Additionally, a set of images are available that are all cropped to match the HST field of view. The GALEX and Spitzer images are available with foreground and background contamination masked. Larger GALEX images extending to 4 times the optical extent of the galaxies are also available. Finally, HST images convolved with a 5″ point spread function and rebinned to the larger pixel scale of the GALEX and Spitzer 24 μm images are provided. Future additions are planned that will include data at other wavelengths such as Spitzer IRAC, ground-based Hα, Chandra X-ray, and Green Bank Telescope H i imaging.

  8. Young Super Star Clusters in the Starburst of M82: The Catalog

    NASA Astrophysics Data System (ADS)

    Melo, V. P.; Muñoz-Tuñón, C.; Maíz-Apellániz, J.; Tenorio-Tagle, G.

    2005-01-01

    Recent results from the Hubble Space Telescope (HST) have resolved starbursts as collections of compact young stellar clusters. Here we present a photometric catalog of the young stellar clusters in the nuclear star