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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

    2016-08-01

    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 disk with mid-plane density n0 ˜ 200-1000 cm-3 and scale height 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 a SFR surface density of 10 ≤ ΣSFR ≤ 50 M⊙ yr-1 kpc-2 favours the production of molecular outflows, consistent with observed values.

  2. Dense circumnuclear molecular gas in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Green, C.-E.; Cunningham, M. R.; Green, J. A.; Dawson, J. R.; Jones, P. A.; López-Sánchez, Á. R.; Verdes-Montenegro, L.; Henkel, C.; Baan, W. A.; Martín, S.

    2016-04-01

    We present results from a study of the dense circumnuclear molecular gas of starburst galaxies. The study aims to investigate the interplay between starbursts, active galactic nuclei and molecular gas. We characterize the dense gas traced by HCN, HCO+ and HNC and examine its kinematics in the circumnuclear regions of nine starburst galaxies observed with the Australia Telescope Compact Array. We detect HCN (1-0) and HCO+ (1-0) in seven of the nine galaxies and HNC (1-0) in four. Approximately 7 arcsec resolution maps of the circumnuclear molecular gas are presented. The velocity-integrated intensity ratios, HCO+ (1-0)/HCN (1-0) and HNC (1-0)/HCN (1-0), are calculated. Using these integrated intensity ratios and spatial intensity ratio maps, we identify photon-dominated regions (PDRs) in NGC 1097, NGC 1365 and NGC 1808. We find no galaxy which shows the PDR signature in only one part of the observed nuclear region. We also observe unusually strong HNC emission in NGC 5236, but it is not strong enough to be consistent with X-ray-dominated region chemistry. Rotation curves are derived for five of the galaxies and dynamical mass estimates of the inner regions of three of the galaxies are made.

  3. 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.

  4. Starburst at the Expanding Molecular Superbubble in M82: Self-induced Starburst at the Inner Edge of the Superbubble

    NASA Astrophysics Data System (ADS)

    Matsushita, Satoki; Kawabe, Ryohei; Kohno, Kotaro; Matsumoto, Hironori; Tsuru, Takeshi G.; Vila-Vilaró, Baltasar

    2005-01-01

    We present high spatial resolution (2.3"×1.9" or 43pc×36pc at D=3.9 Mpc) 100 GHz millimeter-wave continuum emission observations with the Nobeyama Millimeter Array toward an expanding molecular superbubble in the central region of M82. The 100 GHz continuum image, which is dominated by free-free emission, revealed that the four strongest peaks are concentrated at the inner edge of the superbubble along the galactic disk. The production rates of Lyman continuum photons calculated from 100 GHz continuum flux at these peaks are an order of magnitude higher than those from the most massive star-forming regions in our Galaxy. At these regions, high-velocity ionized gas (traced by H41α and [Ne II]) can be seen, and H2O and OH masers are also concentrated. The center of the superbubble, on the other hand, is weak in molecular and free-free emissions and strong in diffuse hard X-ray emission. These observations suggest that a strong starburst produced energetic explosions and the resulting plasma and superbubble expansions and induced the present starburst regions traced by our 100 GHz continuum observations at the inner edge of the molecular superbubble. These results, therefore, provide the first clear evidence of self-induced starburst in external galaxies. The starburst at the center of the superbubble, on the other hand, is beginning to cease because of a lack of molecular gas. This kind of intense starburst seems to have occurred several times within 106-107 yr in the central region of M82.

  5. 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

    2014-12-01

    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. PMID:25471881

  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. PMID:23887428

  7. The Vertical Structure of Nuclear Starburst Disks: Testing a Model of AGN Obscuration

    NASA Astrophysics Data System (ADS)

    Ballantyne, David R.; Gohil, Raj

    2016-04-01

    Nuclear starburst disks are Eddington-limited, radiation pressure supported disks that may be active in the nuclear environment of active galaxies (ULIRGS and AGNs). Earlier analytical models suggested that, under certain conditions, these disks may be geometrically thick on pc-scales, and thus could be a viable source for AGN obscuration, partcularly at z≤1, when gas factions in galaxies are still significant. Here, we present early results from numerical 2D models of nuclear starburst disks where the vertical structure is calculated explicitly from solving the hydrostatic balance and radiative transfer equations. We quantitatively assess under which conditions the starburst disk may present substantial obscuring columns for AGN observations.

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

    NASA Astrophysics Data System (ADS)

    Warren, Steven R.; Bolatto, A. D.; Leroy, A. K.; Walter, F.; Veilleux, S.; Ostriker, E. C.; Ott, J.; Zwaan, M.; Fisher, D. B.; Weiss, A.; Rosolowsky, E.; Hodge, J.

    2014-01-01

    We present Atacama Large (Sub)Millimeter Array (ALMA) CO (J=1-0) observations of the nearby, nuclear starburst galaxy NGC 253. NGC 253 is host to a "superwind" emanating from the central ~200 pc. Galaxy superwinds are thought to help shape the galactic mass function, play a critical role in galaxy evolution, and pollute the intergalactic medium with heavy metals. Detailed studies of nearby systems frequently focus on the warm or hot phases of the wind, visible in X-ray or Halpha emission. However, most of the mass in the outflowing material is thought to be in the form of neutral atomic and molecular gas. We use the observed CO luminosities and velocities to estimate the mass, mass loss rate, and energetics of the molecular wind. We compute an outflow mass of M_mo 6.6x10^6 Msun. The observed projected velocities of the CO filaments range from ~30-60 km s^-1 resulting in a mass loss rate of ~9 Msun yr^-1. The nuclear region of NGC 253 has a star formation rate of ~3 Msun yr^-1 resulting in a mass loading parameter 1-3. It is not immediately clear if the outflowing gas will escape the halo or eventually rain back onto the disk. What is clear is that NGC 253 will exhaust its nuclear star forming gas in ~60-120 Myr at its current mass loss rate, cementing the superwind as an important contributor in the evolution of NGC 253.

  10. Molecular Gas Heating Mechanisms, and Star Formation Feedback in Merger/Starbursts: NGC 6240 and Arp 193 as Case Studies

    NASA Astrophysics Data System (ADS)

    Papadopoulos, Padelis P.; Zhang, Zhi-Yu; Xilouris, E. M.; Weiss, Axel; van der Werf, Paul; Israel, F. P.; Greve, T. R.; Isaak, Kate G.; Gao, Y.

    2014-06-01

    We used the SPIRE/FTS instrument aboard the Herschel Space Observatory to obtain the Spectral Line Energy Distributions (SLEDs) of CO from J = 4-3 to J = 13-12 of Arp 193 and NGC 6240, two classical merger/starbursts selected from our molecular line survey of local Luminous Infrared Galaxies (L IR >= 1011 L ⊙). The high-J CO SLEDs are then combined with ground-based low-J CO, 13CO, HCN, HCO+, CS line data and used to probe the thermal and dynamical states of their large molecular gas reservoirs. We find the two CO SLEDs strongly diverging from J = 4-3 onward, with NGC 6240 having a much higher CO line excitation than Arp 193, despite their similar low-J CO SLEDs and L FIR/L CO, 1 - 0, L HCN/L CO (J = 1-0) ratios (proxies of star formation efficiency and dense gas mass fraction). In Arp 193, one of the three most extreme starbursts in the local universe, the molecular SLEDs indicate a small amount (~5%-15%) of dense gas (n >= 104 cm-3) unlike NGC 6240 where most of the molecular gas (~60%-70%) is dense (n ~ (104-105) cm-3). Strong star-formation feedback can drive this disparity in their dense gas mass fractions, and also induce extreme thermal and dynamical states for the molecular gas. In NGC 6240, and to a lesser degree in Arp 193, we find large molecular gas masses whose thermal states cannot be maintained by FUV photons from Photon-Dominated Regions. We argue that this may happen often in metal-rich merger/starbursts, strongly altering the initial conditions of star formation. ALMA can now directly probe these conditions across cosmic epoch, and even probe their deeply dust-enshrouded outcome, the stellar initial mass function averaged over galactic evolution.

  11. Molecular gas heating mechanisms, and star formation feedback in merger/starbursts: NGC 6240 and Arp 193 as case studies

    SciTech Connect

    Papadopoulos, Padelis P.; Zhang, Zhi-Yu; Weiss, Axel; Van der Werf, Paul; Israel, F. P.; Greve, T. R.; Isaak, Kate G.; Gao, Y. E-mail: zyzhang@pmo.ac.cn E-mail: aweiss@mpifr-bonn.mpg.de E-mail: israel@strw.leidenuniv.nl E-mail: kisaak@rssd.esa.int

    2014-06-20

    We used the SPIRE/FTS instrument aboard the Herschel Space Observatory to obtain the Spectral Line Energy Distributions (SLEDs) of CO from J = 4-3 to J = 13-12 of Arp 193 and NGC 6240, two classical merger/starbursts selected from our molecular line survey of local Luminous Infrared Galaxies (L {sub IR} ≥ 10{sup 11} L {sub ☉}). The high-J CO SLEDs are then combined with ground-based low-J CO, {sup 13}CO, HCN, HCO{sup +}, CS line data and used to probe the thermal and dynamical states of their large molecular gas reservoirs. We find the two CO SLEDs strongly diverging from J = 4-3 onward, with NGC 6240 having a much higher CO line excitation than Arp 193, despite their similar low-J CO SLEDs and L {sub FIR}/L {sub CO,} {sub 1} {sub –0}, L {sub HCN}/L {sub CO} (J = 1-0) ratios (proxies of star formation efficiency and dense gas mass fraction). In Arp 193, one of the three most extreme starbursts in the local universe, the molecular SLEDs indicate a small amount (∼5%-15%) of dense gas (n ≥ 10{sup 4} cm{sup –3}) unlike NGC 6240 where most of the molecular gas (∼60%-70%) is dense (n ∼ (10{sup 4}-10{sup 5}) cm{sup –3}). Strong star-formation feedback can drive this disparity in their dense gas mass fractions, and also induce extreme thermal and dynamical states for the molecular gas. In NGC 6240, and to a lesser degree in Arp 193, we find large molecular gas masses whose thermal states cannot be maintained by FUV photons from Photon-Dominated Regions. We argue that this may happen often in metal-rich merger/starbursts, strongly altering the initial conditions of star formation. ALMA can now directly probe these conditions across cosmic epoch, and even probe their deeply dust-enshrouded outcome, the stellar initial mass function averaged over galactic evolution.

  12. The Role of Radiation Feedback in Starburst Environments

    NASA Astrophysics Data System (ADS)

    Yeh, Sherry; Matzner, C. D.; Seaquist, E. R.

    2012-01-01

    Massive bursts of stellar activity in starburst environments feed prodigious amount of energy and momentum into the surrounding neutral clouds. With sufficiently intense irradiation from starbursts, the structure of an HII region will be dominated by radiation pressure rather than ionized gas pressure, and radiative energy input in photodissociation regions (PDRs) becomes more important. This state is of considerable interest because of its role in the formation of massive stars, the disruption of giant molecular clouds, and the evolution of starburst galaxies. We study the role of radiation feedback in starburst environments via both theoretical and observational approaches. We argue that radiation pressure is the underlying mechanism for the remarkable constancy of ionization parameters in starburst environments. We also point out that clumping in the neutral material and compression by stellar wind pressure can act to reduce ionization parameters. We use the Cloudy code to determine effective ionization parameters for a population of static dusty HII regions compressed by both radiation pressure and stellar winds. We conclude that the inner starburst region of M82 and the Antennae Galaxies HII regions are both dominated by a combination of radiation pressure and shocked winds. We investigate radiative energy feedback in starburst environments by observing the nearest starburst region 30 Doradus in the LMC. We observe 30 Doradus using NOAO Extremely Wide-Field Infrared Imager (NEWFIRM) with H2 1-0 S(1), Brγ, and [FeII] lines. While H2 can be either radiative or shock excited, the near infrared [FeII] emission line traces shock activities, and the hydrogen recombination line Brγ arises from regions ionized by UV radiation. Therefore ratios of the three emission lines form very useful diagnostics to assess the fraction of radiative and shock feedback. We preliminarily suggest that radiative energy input in the 30 Doradus PDRs is non-negligible.

  13. 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

  14. 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.

  15. 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}ȯ {({{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.

  16. A molecular Einstein ring: imaging a starburst disk surrounding a quasi-stellar object.

    PubMed

    Carilli, C L; Lewis, G F; Djorgovski, S G; Mahabal, A; Cox, P; Bertoldi, F; Omont, A

    2003-05-01

    Images of the molecular CO 2-1 line emission and the radio continuum emission from the redshift 4.12 gravitationally lensed quasi-stellar object (QSO) PSS J2322+1944 reveal an Einstein ring with a diameter of 1.5". These observations are modeled as a star-forming disk surrounding the QSO nucleus with a radius of 2 kiloparsecs. The implied massive star formation rate is 900 solar masses per year. At this rate, a substantial fraction of the stars in a large elliptical galaxy could form on a dynamical time scale of 108 years. The observation of active star formation in the host galaxy of a high-redshift QSO supports the hypothesis of coeval formation of supermassive black holes and stars in spheroidal galaxies. PMID:12677071

  17. 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.

  18. 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.

  19. 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.

  20. A dust-obscured massive maximum-starburst galaxy at a redshift of 6.34.

    PubMed

    Riechers, Dominik A; Bradford, C M; Clements, D L; Dowell, C D; Pérez-Fournon, I; Ivison, R J; Bridge, C; Conley, A; Fu, Hai; Vieira, J D; Wardlow, J; Calanog, J; Cooray, A; Hurley, P; Neri, R; Kamenetzky, J; Aguirre, J E; Altieri, B; Arumugam, V; Benford, D J; Béthermin, M; Bock, J; Burgarella, D; Cabrera-Lavers, A; Chapman, S C; Cox, P; Dunlop, J S; Earle, L; Farrah, D; Ferrero, P; Franceschini, A; Gavazzi, R; Glenn, J; Solares, E A Gonzalez; Gurwell, M A; Halpern, M; Hatziminaoglou, E; Hyde, A; Ibar, E; Kovács, A; Krips, M; Lupu, R E; Maloney, P R; Martinez-Navajas, P; Matsuhara, H; Murphy, E J; Naylor, B J; Nguyen, H T; Oliver, S J; Omont, A; Page, M J; Petitpas, G; Rangwala, N; Roseboom, I G; Scott, D; Smith, A J; Staguhn, J G; Streblyanska, A; Thomson, A P; Valtchanov, I; Viero, M; Wang, L; Zemcov, M; Zmuidzinas, J

    2013-04-18

    Massive present-day early-type (elliptical and lenticular) galaxies probably gained the bulk of their stellar mass and heavy elements through intense, dust-enshrouded starbursts--that is, increased rates of star formation--in the most massive dark-matter haloes at early epochs. However, it remains unknown how soon after the Big Bang massive starburst progenitors exist. The measured redshift (z) distribution of dusty, massive starbursts has long been suspected to be biased low in z owing to selection effects, as confirmed by recent findings of systems with redshifts as high as ~5 (refs 2-4). Here we report the identification of a massive starburst galaxy at z = 6.34 through a submillimetre colour-selection technique. We unambiguously determined the redshift from a suite of molecular and atomic fine-structure cooling lines. These measurements reveal a hundred billion solar masses of highly excited, chemically evolved interstellar medium in this galaxy, which constitutes at least 40 per cent of the baryonic mass. A 'maximum starburst' converts the gas into stars at a rate more than 2,000 times that of the Milky Way, a rate among the highest observed at any epoch. Despite the overall downturn in cosmic star formation towards the highest redshifts, it seems that environments mature enough to form the most massive, intense starbursts existed at least as early as 880 million years after the Big Bang. PMID:23598341

  1. 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.

  2. 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.

  3. 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.

  4. High mass stars: starbursts

    NASA Astrophysics Data System (ADS)

    González Delgado, R. M.

    2006-08-01

    Starbursts are the preferred place where massive stars form; the main source of thermal and mechanical heating in the interstellar medium, and the factory where the heavy elements form. Thus, starbursts play an important role in the origin and evolution of galaxies. Starbursts are bright at ultraviolet (UV) wavelengths, and after the pioneering IUE program, high spatial and spectral resolution UV observations of local starburst galaxies, mainly taken with HST and FUSE, have made relevant contributions to the following issues: a) The determination of the initial mass function in violent star forming systems in low and high metallicity environments, and in dense (e.g. in stellar clusters) and diffuse environments. b) The modes of star formation: Starburst clusters are an important mode of star formation. c) The role of starbursts in AGN. d) The interaction between massive stars and the interstellar and intergalactic media. e) The contribution of starbursts to the reionization of the universe. Despite the very significant progress obtained over the past two decades of UV observations of starbursts, there are important problems that still need to be solved. High-spatial resolution UV observations of nearby starbursts are crucial to further progress in understanding the violent star formation processes in galaxies, the interaction between the stellar clusters and the interstellar medium, and the variation of the IMF. Thus, a new UV mission furnished with an intermediate spectral resolution long-slit spectrograph with high spatial resolution and high UV sensitivity is required to further progress in the study of starburst galaxies and their impact on the evolution of galaxies.

  5. 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

  6. Starbursts in colliding galaxies.

    NASA Astrophysics Data System (ADS)

    Mirabel, I. F.; Duc, P. A.

    Global starbursts are a consequence of rapid changes in the dynamics of the interstellar gas. The most violent starbursts take place in the nuclear regions of galaxies, when galaxy-galaxy encounters cause a sudden reduction of angular momentum, with the subsequent infall to the central regions of a large fraction of the overall interstellar gas. Although starbursts are also observed in the central regions of isolated barred spiral galaxies, most of the starbursts with bolometric luminosities above 1012Lsun occur in mergers. Super-starbursts in galactic nuclei seem to require high infall rates of interstellar gas that can only be produced during mergers. The authors discuss the phenomenon of extranuclear starbursts in relation to the formation of dwarf galaxies during galaxy-galaxy collisions. As a consequence of tidal interactions a fraction of the less gravitationally bound atomic hydrogen that populates the outskirts of disk galaxies may escape into the intergalactic medium. It is found that the ejected gas may assemble again and collapse, leading to the formation of intergalactic starbursts, namely, tidal dwarf galaxies.

  7. Massive stars: Starbursts

    NASA Astrophysics Data System (ADS)

    González Delgado, Rosa María

    2007-07-01

    Starbursts are the preferred place where massive stars form; the main source of thermal and mechanical heating in the interstellar medium, and the factory where the heavy elements form. Thus, starbursts play an important role in the origin and evolution of galaxies. Starbursts are bright at ultraviolet (UV) wavelengths, and after the pioneering IUE program, high spatial and spectral resolution UV observations of local starburst galaxies, mainly taken with HST and FUSE, have made relevant contributions to the following issues: a) The determination of the initial mass function (IMF) in violent star forming systems in low and high metallicity environments, and in dense (e.g. in stellar clusters) and diffuse environments: A Salpeter IMF with high-mass stars constrains well the UV properties. b) Stellar clusters are an important mode of star formation in starbursts. c) The role of starbursts in AGN: Nuclear starbursts can dominate the UV light in Seyfert 2 galaxies, having bolometric luminosities similar to the estimated bolometric luminosities of the obscured AGN. d) The interaction between massive stars and the interstellar medium: Outflows in cold, warm and coronal phases leave their imprints on the UV interstellar lines. Outflows of a few hundred km s%u22121 are ubiquitous phenomena in starbursts. Despite the very significant progress obtained over the past two decades of UV observations of starbursts, there are important problems that still need to be solved. High-spatial resolution UV observations of nearby starbursts are crucial to further progress in understanding the violent star formation processes in galaxies, the interaction between the stellar clusters and the interstellar medium, and the variation of the IMF. High-spatial resolution spectra are also needed to isolate the light from the center to the disk in UV luminous galaxies found by GALEX. Thus, a new UV mission furnished with an intermediate spectral resolution spectrograph with high spatial

  8. 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

  9. 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.

  10. 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%.

  11. THE IMACS CLUSTER BUILDING SURVEY. V. FURTHER EVIDENCE FOR STARBURST RECYCLING FROM QUANTITATIVE GALAXY MORPHOLOGIES

    SciTech Connect

    Abramson, Louis E.; Gladders, Michael D.; Dressler, Alan; Oemler, Augustus Jr.; Monson, Andrew; Persson, Eric; Poggianti, Bianca M.; Vulcani, Benedetta

    2013-11-10

    Using J- and K{sub s}-band imaging obtained as part of the IMACS Cluster Building Survey (ICBS), we measure Sérsic indices for 2160 field and cluster galaxies at 0.31 < z < 0.54. Using both mass- and magnitude-limited samples, we compare the distributions for spectroscopically determined passive, continuously star-forming, starburst, and post-starburst systems and show that previously established spatial and statistical connections between these types extend to their gross morphologies. Outside of cluster cores, we find close structural ties between starburst and continuously star-forming, as well as post-starburst and passive types, but not between starbursts and post-starbursts. These results independently support two conclusions presented in Paper II of this series: (1) most starbursts are the product of a non-disruptive triggering mechanism that is insensitive to global environment, such as minor mergers; (2) starbursts and post-starbursts generally represent transient phases in the lives of 'normal' star-forming and quiescent galaxies, respectively, originating from and returning to these systems in closed 'recycling' loops. In this picture, spectroscopically identified post-starbursts constitute a minority of all recently terminated starbursts, largely ruling out the typical starburst as a quenching event in all but the densest environments.

  12. Cosmic ray interactions in starbursting galaxies

    NASA Astrophysics Data System (ADS)

    Yoast-Hull, Tova M.

    High quality gamma-ray and radio observations of nearby galaxies offer an unprecedented opportunity to quantitatively study the properties of their cosmic ray populations. Accounting for various interactions and energy losses, I developed a multi-component, single-zone model of the cosmic ray populations in the central molecular zones of star-forming galaxies. Using observational knowledge of the interstellar medium and star formation, I successfully predicted the radio, gamma-ray, and neutrino spectra for nearby starbursts. Using chi-squared tests to compare the models with observational radio and gamma-ray data, I placed constraints on magnetic field strengths, cosmic ray energy densities, and galactic wind (advection) speeds. The initial models were applied to and tested on the prototypical starburst galaxy M82. To further test the model and to explore the differences in environment between starbursts and active galactic nuclei, I studied NGC 253 and NGC 1068, both nearby giant spiral galaxies which have been detected in gamma-rays. Additionally, I demonstrated that the excess GeV energy gamma-ray emission in the Galactic Center is likely not diffuse emission from an additional population of cosmic rays accelerated in supernova remnants. Lastly, I investigated cosmic ray populations in the starburst nuclei of Arp 220, a nearby ultraluminous infrared galaxy which displays a high-intensity mode of star formation more common in young galaxies, and I showed that the nuclei are efficient cosmic-ray proton calorimeters.

  13. A Spitzer High-resolution Mid-Infrared Spectral Atlas of Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Bernard-Salas, J.; Spoon, H. W. W.; Charmandaris, V.; Lebouteiller, V.; Farrah, D.; Devost, D.; Brandl, B. R.; Wu, Yanling; Armus, L.; Hao, L.; Sloan, G. C.; Weedman, D.; Houck, J. R.

    2009-10-01

    We present an atlas of Spitzer/IRS high-resolution (R ~ 600) 10-37 μm spectra for 24 well known starburst galaxies. The spectra are dominated by fine-structure lines, molecular hydrogen lines, and emission bands of polycyclic aromatic hydrocarbons (PAHs). Six out of the eight objects with a known active galactic nucleus (AGN) component show emission of the high excitation [Ne V] line. This line is also seen in one other object (NGC 4194) with, a priori, no known AGN component. In addition to strong PAH emission features in this wavelength range (11.3, 12.7, 16.4 μm), the spectra reveal other weak hydrocarbon features at 10.6, 13.5, 14.2 μm, and a previously unreported emission feature at 10.75 μm. An unidentified absorption feature at 13.7 μm is detected in many of the starbursts. We use the fine-structure lines to derive the abundance of neon and sulfur for 14 objects where the H I 7-6 line is detected. We further use the molecular hydrogen lines to sample the properties of the warm molecular gas. Several basic diagrams characterizing the properties of the sample are also shown. We have combined the spectra of all the pure starburst objects to create a high signal-to-noise ratio template, which is available to the community.

  14. A SPITZER HIGH-RESOLUTION MID-INFRARED SPECTRAL ATLAS OF STARBURST GALAXIES

    SciTech Connect

    Bernard-Salas, J.; Spoon, H. W. W.; Lebouteiller, V.; Farrah, D.; Wu, Yanling; Hao, L.; Sloan, G. C.; Weedman, D.; Houck, J. R.; Charmandaris, V.; Devost, D.; Brandl, B. R.; Armus, L.

    2009-10-01

    We present an atlas of Spitzer/IRS high-resolution (R {approx} 600) 10-37 {mu}m spectra for 24 well known starburst galaxies. The spectra are dominated by fine-structure lines, molecular hydrogen lines, and emission bands of polycyclic aromatic hydrocarbons (PAHs). Six out of the eight objects with a known active galactic nucleus (AGN) component show emission of the high excitation [Ne V] line. This line is also seen in one other object (NGC 4194) with, a priori, no known AGN component. In addition to strong PAH emission features in this wavelength range (11.3, 12.7, 16.4 {mu}m), the spectra reveal other weak hydrocarbon features at 10.6, 13.5, 14.2 {mu}m, and a previously unreported emission feature at 10.75 {mu}m. An unidentified absorption feature at 13.7 {mu}m is detected in many of the starbursts. We use the fine-structure lines to derive the abundance of neon and sulfur for 14 objects where the H I 7-6 line is detected. We further use the molecular hydrogen lines to sample the properties of the warm molecular gas. Several basic diagrams characterizing the properties of the sample are also shown. We have combined the spectra of all the pure starburst objects to create a high signal-to-noise ratio template, which is available to the community.

  15. Starburst Galaxy NGC 3310

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Scientists using NASA's Hubble Space Telescope are studying the colors of star clusters to determine the age and history of starburst galaxies, a technique somewhat similar to the process of learning the age of a tree by counting its rings.

    This month's Hubble Heritage image showcases the galaxy NGC 3310. It is one of several starburst galaxies, which are hotbeds of star formation, being studied by Dr. Gerhardt Meurer and a team of scientists at Johns Hopkins University, Laurel, Md.

    The picture, taken by Hubble's Wide Field and Planetary Camera 2, is online at http://heritage.stsci.edu and http://oposite.stsci.edu/pubinfo/pr/2001/26 and http://www.jpl.nasa.gov/images/wfpc . The camera was designed and built by NASA's Jet Propulsion Laboratory, Pasadena, Calif.

    Most galaxies form new stars at a fairly slow rate, but starburst galaxies blaze with extremely active star formation. Measuring the clusters' colors yields information about stellar temperatures. Since young stars are blue and older stars redder, the colors relate to their ages.

    NGC 3310 is forming clusters of new stars at a prodigious rate. The new image shows several hundred star clusters, visible as the bright blue, diffuse objects that trace the galaxy's spiral arms. Each of these star clusters represents the formation of up to about a million stars, a process that takes less than 100,000 years. In addition, hundreds of individual young, luminous stars can be seen throughout the galaxy.

    The star clusters become redder with age as the most massive and bluest stars exhaust their fuel and burn out. Measurements in this image of the wide range of cluster colors show their ages range between about one million and more than one hundred million years. This suggests that the starburst 'turned on' more than 100 million years ago. It may have been triggered when NGC 3310 collided with a companion galaxy.

    These observations may change astronomers' view of starbursts. Starbursts were once

  16. The evolution of the cold interstellar medium in galaxies following a starburst

    NASA Astrophysics Data System (ADS)

    Rowlands, K.; Wild, V.; Nesvadba, N.; Sibthorpe, B.; Mortier, A.; Lehnert, M.; da Cunha, E.

    2015-03-01

    We present the evolution of dust and molecular gas properties in a sample of 11 z ˜ 0.03 starburst to post-starburst (PSB) galaxies selected to span an age sequence from ongoing starburst to 1 Gyr after the starburst ended. All PSBs harbour significant molecular gas and dust reservoirs and residual star formation, indicating that complete quenching of the starburst due to exhaustion or expulsion of gas has not occurred during this timespan. As the starburst ages, we observe a clear decrease in the star formation efficiency, molecular gas and star formation rate (SFR) surface density, and effective dust temperature, from levels coincident with starburst galaxies to those of normal star-forming galaxies. These trends are consistent with a natural decrease in the SFR following consumption of molecular gas by the starburst, and corresponding decrease in the interstellar radiation field strength as the starburst ages. The gas and dust contents of the PSBs are coincident with those of star-forming galaxies and molecular gas-rich early-type galaxies, and are not consistent with galaxies on the red sequence. We find no evidence that the global gas reservoir is expelled by stellar winds or active galactic nuclei feedback. Our results show that although a strong starburst in a low-redshift galaxy may cause the galaxy to ultimately have a lower specific SFR and be of an earlier morphological type, the galaxy will remain in the `green valley' for an extended time. Multiple such episodes may be needed to complete migration of the galaxy from the blue- to red sequence.

  17. Ionized Gas Observation Toward a Nearby Starburst Galaxy NGC 253

    NASA Astrophysics Data System (ADS)

    Nakanishi, K.; Sorai, K.; Nakai, N.; Kuno, N.; Matsubayashi, K.; Sugai, H.; Takano, S.; Kohno, K.; Nakajima, T.

    2015-12-01

    ALMA observation of a hydrogen recombination emission line toward NGC 253 was performed. NGC 253 is a prototypical starburst galaxy in the nearby universe. The recombination line was clearly detected in the central region of NGC 253 with a spatial resolution of few dozens of parsecs at the galaxy. The line and thermal free-free continuum emission show quite similar spatial distribution, and this fact shows the recombination line certainly traces ionized gas formed by young massive stars. Estimated electron temperature (6500-9000K) from the data are similar to those of Galactic HII regions. The recombination line has large velocity width at the center of the galaxy, and the velocity structure is quite different from that of molecular emission line.

  18. Starbursts at space ultraviolet wavelengths

    NASA Astrophysics Data System (ADS)

    González Delgado, Rosa M.

    2006-06-01

    Starbursts are systems with very high star formation rate per unit area. They are the preferred place where massive stars form; the main source of thermal and mechanical heating in the interstellar medium, and the factory where the heavy elements form. Thus, starbursts play an important role in the origin and evolution of galaxies. The similarities between the physical properties of local starbursts and high-z star-forming galaxies, highlight the cosmological relevance of starbursts. On the other hand, nearby starbursts are laboratories where to study violent star formation processes and their interaction with the interstellar and intergalactic media, in detail and deeply. Starbursts are bright at ultraviolet (UV) wavelengths, as they are in the far-infrared, due to the ‘picket-fence’ interstellar dust distribution. After the pioneering IUE program, high spatial and spectral resolution UV observations of local starburst galaxies, mainly taken with HST and FUSE, have made relevant contributions to the following issues: The determination of the initial mass function (IMF) in violent star forming systems in low and high metallicity environments, and in dense (e.g. in stellar clusters) and diffuse environments: A Salpeter IMF with high-mass stars constrains well the UV properties. The modes of star formation: Starburst clusters are an important mode of star formation. Super-stellar clusters have properties similar to globular clusters. The role of starbursts in AGN: Nuclear starbursts can dominate the UV light in Seyfert 2 galaxies, having bolometric luminosities similar to the estimated bolometric luminosities of the obscured AGN. The interaction between massive stars and the interstellar and intergalactic media: Outflows in cold, warm and coronal phases leave their imprints on the UV

  19. (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.

  20. Interactive Modelling of Molecular Structures

    NASA Astrophysics Data System (ADS)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  1. Imaging the most extreme starbursts in the early Universe

    NASA Astrophysics Data System (ADS)

    Conley, Alexander; Bremer, Malcolm; Bock, Jamie; Oliver, Sebastien; Ivison, Rob; Farrah, Duncan; Cooray, Asantha; Clements, Dave; Schulz, Bernhard; Riechers, Dominik; Ibar, Edo; Vaccari, Mattia; Glenn, Jason; Omont, Alain; Valiente, Elisabetta; Dannerbauer, Helmut

    2012-12-01

    The HerMES and H-ATLAS projects, using Herschel/SPIRE data, have discovered a population of ultra-red (hence high-z), faint (hence unlensed), dusty extreme star forming galaxies, which are likely among the most distant, luminous and massive known. Follow up of the first few sources has confirmed that they predominantly lie above z > 4, including one souce at z=6.3. However, current observations of these sources can only probe their young, starbursting stellar populations. In order to form a complete picture of their stellar content, as well as place the starburst within the context of the history of these systems, we request Spitzer observations of 20 such sources. In addition, this data will be sensitive to un-obscured starbursts (LBGs) associated with the same overdensity, allowing us to test whether our targets serve as signposts to high-z protoclusters as suggested by structure formation models.

  2. PHOTODISSOCIATION CHEMISTRY FOOTPRINTS IN THE STARBURST GALAXY NGC 253

    SciTech Connect

    MartIn, Sergio; MartIn-Pintado, J.; Viti, S.

    2009-12-01

    UV radiation from massive stars is thought to be the dominant heating mechanism of the nuclear interstellar medium (ISM) in the late stages of evolution of starburst galaxies, creating large photodissociation regions (PDRs) and driving a very specific chemistry. We report the first detection of PDR molecular tracers, namely HOC{sup +} and CO{sup +}, and also confirm the detection of the PDR tracer HCO toward the starburst galaxy NGC 253, claimed to be mainly dominated by shock heating and in an earlier stage of evolution than M 82, the prototypical extragalactic PDR. Our CO{sup +} detection suffers from significant blending to a group of transitions of {sup 13}CH{sub 3}OH, tentatively detected for the first time in the extragalactic ISM. These species are efficiently formed in the highly UV-irradiated outer layers of molecular clouds, as observed in the late stage nuclear starburst in M 82. The molecular abundance ratios we derive for these molecules are very similar to those found in M 82. This strongly supports the idea that these molecules are tracing the PDR component associated with the starburst in the nuclear region of NGC 253. The presence of large abundances of PDR molecules in the ISM of NGC 253, which is dominated by shock chemistry, clearly illustrates the potential of chemical complexity studies to establish the evolutionary state of starbursts in galaxies. A comparison with the predictions of chemical models for PDRs shows that the observed molecular ratios are tracing the outer layers of UV-illuminated clouds up to two magnitudes of visual extinction. We combine the column densities of PDR tracers reported in this paper with those of easily photodissociated species, such as HNCO, to derive the fraction of material in the well-shielded core relative to the UV-pervaded envelopes. Chemical models, which include grain formation and photodissociation of HNCO, support the scenario of a photo-dominated chemistry as an explanation to the abundances of the

  3. Probing a Starburst Galaxy's Superwind

    NASA Astrophysics Data System (ADS)

    Stocke, John

    The Cosmic Origins Spectrograph Science Team for IGM studies proposes to observe the bright QSO/starburst galaxy pair, SBS1108+560/M108 for the following purposes: 1. To measure the FUV brightness of the QSO to determine whether an HST/COS observation is viable and to set its exposure times. 2. To determine the locations of the brighter star forming regions in the disk of M108 to compare wth high resolution HI 21cm, H alpha and soft X-ray continuum maps which show supershells, line-emitting loops and extra-planar clumps of hot gas. 3. To use the relative extinctions of near-side and far-side star forming regions to determine the orientation of M108 in space. This determination is required in order to correctly interpret the kinematics of any QSO absorption line system(s) found in our COS spectrum of SBS1108+560. M108 (NGC3556) is a moderate starburst from the IRAS-selected sample of Lehnert & Heckman, moderately inclined on the sky (75 deg.) and very nearby (14 Mpc). The proximity of SBS1108+560 to M108 (25 kpc) and its location quite close to the minor-axis of M108 make this pairing quite unusual (one of only 3 to be observed by COS) and an important opportunity for understanding the nature and dynamics of starburst superwinds. An important question we hope to answer with this set of GALEX and HST data is whether starburst winds from massive spiral galaxies actually escape the gaalxy's gravitational potential and so enrich the IGM with metals."

  4. 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.

  5. 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.

  6. CO Line Emission from Compact Nuclear Starburst Disks around Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Armour, J. N.; Ballantyne, D. R.

    2012-06-01

    There is substantial evidence for a connection between star formation in the nuclear region of a galaxy and growth of the central supermassive black hole. Furthermore, starburst activity in the region around an active galactic nucleus (AGN) may provide the obscuration required by the unified model of AGNs. Molecular line emission is one of the best observational avenues to detect and characterize dense, star-forming gas in galactic nuclei over a range of redshift. This paper presents predictions for the carbon monoxide (CO) line features from models of nuclear starburst disks around AGNs. These small-scale (lsim 100 pc), dense and hot starbursts have CO luminosities similar to scaled-down ultra-luminous infrared galaxies and quasar host galaxies. Nuclear starburst disks that exhibit a pc-scale starburst and could potentially act as the obscuring torus show more efficient CO excitation and higher brightness temperature ratios than those without such a compact starburst. In addition, the compact starburst models predict strong absorption when J Upper >~ 10, a unique observational signature of these objects. These findings allow for the possibility that CO spectral line energy distributions (SLEDs) could be used to determine if starburst disks are responsible for the obscuration in z <~ 1 AGNs. Directly isolating the nuclear CO line emission of such compact regions around AGNs from galactic-scale emission will require high-resolution imaging or selecting AGN host galaxies with weak galactic-scale star formation. Stacking individual CO SLEDs will also be useful in detecting the predicted high-J features.

  7. Structure parameters in molecular tunneling ionization theory

    NASA Astrophysics Data System (ADS)

    Wang, Jun-Ping; Li, Wei; Zhao, Song-Feng

    2014-04-01

    We extracted the accurate structure parameters in molecular tunneling ionization theory (so called MO-ADK theory) for 22 selected linear molecules including some inner orbitals. The molecular wave functions with the correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials numerically constructed using the modified Leeuwen-Baerends (LBα) model.

  8. 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

  9. 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.

  10. Starburst outflows from nearby galaxies

    NASA Technical Reports Server (NTRS)

    Waller, William H.

    1990-01-01

    Starburst outflows from NGC 5461, 1569 and M82 are discussed. The Sc I galaxy, M101, is reknowned for the kpc-size superassociations of star clusters and HII regions that dominate its spiral arms. NGC 5461 is one of the brightest of these superassociations, rivaling the Large Magellanic Cloud in H alpha luminosity. The NGC 5461 superassociation is dominated by a single unresolved HII region of outstanding luminosity (approx. 1000 Orion nebulae). Detailed examination of corresponding continuum images indicates that only the southern plume has any sort of stellar counterpart. The other plumes are clearly diffuse with no underlying hot stars. An image of NGC 1569 is discussed. Besides showing the peculiar arm noted by Zwicky (1971) and the filamentary extensions to the North and South (as noted by Hodge 1974), this image also reveals two arc-like features of diffuse ionized gas to the South. Both arcs are concentric with the bright center of the galaxy - where the super star clusters, A and B are located. The inner arc (Arc 1) appears to follow the same curve as the SW arm thus suggesting that the two features represent limb-brightened fragments of vast superbubble that was blown out by a central starburst sometime in the past. As the classic starburst galaxy, M82 displays all the luminous hallmarks of intense high-mass star formation and outflow activity. The diffuse H alpha and x ray emitting gas along the minor axis provides especially good evidence for a bipolar outflow of hot gas which is shock heating the swept-up interstellar medium (ISM) to temperatures of approx. 10(exp 4) K. An image shows the H alpha emission within the disk and along the minor axis. Another image shows the same field in the light of near-infrared. Both figures are based on charge coupled device images taken with the McGraw-Hill 1.3 m telescope (Waller 1989). The longer wavelength emission clearly shows a more extended morphology along the major axis. The morphological discrepancy is most

  11. 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.

  12. 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.

  13. Densitometry and Thermometry of Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Mangum, J. G.; Darling, J.; Menten, K. M.; Henkel, C.; Aalto, S.; Spaans, M.; van der Werf, P.; Ginsburg, A.; Fomalont, E.; Cotton, B.; Kent, B.

    2016-05-01

    With a goal toward deriving the physical conditions in external galaxies, we have conducted a survey and subsequent high spatial resolution imaging of formaldehyde (H2CO) and ammonia (NH3) emission and absorption in a sample of starburst galaxies. In this article we present the results from a subset of this survey which focuses on high spatial resolution measurements of volume density- and kinetic temperature-sensitive transitions of the H2CO molecule. The volume density structure toward the nuclear region of NGC 253 has been derived from θ ≃ 4 arcsec NRAO Very Large Array (VLA) measurements of the 110 - 111 and 211 - 212 K-doublet transitions of H2CO. The kinetic temperature structure toward NGC 253 and NGC 4945 has been derived from θ ≃ 0.5 - 1.0 arcsec measurements of the H2CO 3K-1K+1 - 2K-1K+1 (near 218 GHz) and 5K-1K+1 - 4K-1K+1 (near 365 GHz) transitions acquired using the Atacama Large Millimeter/submillimeter Array (ALMA). These measurements have allowed us to characterize the dense gas and kinetic temperature structure within these star forming galaxies, which is a first step toward associating dense star-forming gas and the heating processes at work within galaxies.

  14. Structures in Molecular Clouds: Modeling

    SciTech Connect

    Kane, J O; Mizuta, A; Pound, M W; Remington, B A; Ryutov, D D

    2006-04-20

    We attempt to predict the observed morphology, column density and velocity gradient of Pillar II of the Eagle Nebula, using Rayleigh Taylor (RT) models in which growth is seeded by an initial perturbation in density or in shape of the illuminated surface, and cometary models in which structure is arises from a initially spherical cloud with a dense core. Attempting to mitigate suppression of RT growth by recombination, we use a large cylindrical model volume containing the illuminating source and the self-consistently evolving ablated outflow and the photon flux field, and use initial clouds with finite lateral extent. An RT model shows no growth, while a cometary model appears to be more successful at reproducing observations.

  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. 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.

  17. 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 -}.

  18. 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

  19. From Starburst to Quiescence: Testing Active Galactic Nucleus feedback in Rapidly Quenching Post-starburst Galaxies

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    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 ⊙) = 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 (gsim 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 phase.

  20. PROPERTIES OF NEARBY STARBURST GALAXIES BASED ON THEIR DIFFUSE GAMMA-RAY EMISSION

    SciTech Connect

    Paglione, Timothy A. D.; Abrahams, Ryan D.

    2012-08-20

    The physical relationship between the far-infrared and radio fluxes of star-forming galaxies has yet to be definitively determined. The favored interpretation, the 'calorimeter model', requires that supernova generated cosmic-ray (CR) electrons cool rapidly via synchrotron radiation. However, this cooling should steepen their radio spectra beyond what is observed, and so enhanced ionization losses at low energies from high gas densities are also required. Further, evaluating the minimum energy magnetic field strength with the traditional scaling of the synchrotron flux may underestimate the true value in massive starbursts if their magnetic energy density is comparable to the hydrostatic pressure of their disks. Gamma-ray spectra of starburst galaxies, combined with radio data, provide a less ambiguous estimate of these physical properties in starburst nuclei. While the radio flux is most sensitive to the magnetic field, the GeV gamma-ray spectrum normalization depends primarily on gas density. To this end, spectra above 100 MeV were constructed for two nearby starburst galaxies, NGC 253 and M82, using Fermi data. Their nuclear radio and far-infrared spectra from the literature are compared to new models of the steady-state CR distributions expected from starburst galaxies. Models with high magnetic fields, favoring galaxy calorimetry, are overall better fits to the observations. These solutions also imply relatively high densities and CR ionization rates, consistent with molecular cloud studies.

  1. 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.

  2. 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.

  3. Search for AN Intermediate Mass Black Hole in the Starburst Galaxy NGC2146

    NASA Astrophysics Data System (ADS)

    Matsumoto, Hironori

    2001-09-01

    We discovered an Intermediate Mass Black Hole (IMBH) of 10(3) - 10(6) M_⊙ in the starburst galaxy M82 with Chandra HRC. Our follow-up ground-based observations found a near-infrared star cluster in the vicinity of the IMBH as well as an Expanding Molecular Super Bubble (EMSB) which surrounds the IMBH and has a kinematic energy of 10(55) erg. Based on these results, we propose a scenario that an IMBH is produced by starburst activity and it grows to become a Super Massive Black Hole (SMBH). We believe this scenario can explain the formation of SMBHs in other galaxies universally. We propose a CXO monitoring observation of another starburst galaxy NGC2146 to examine our scenario.

  4. How We Teach Molecular Structure to Freshmen.

    ERIC Educational Resources Information Center

    Hurst, Michael O.

    2002-01-01

    Currently molecular structure is taught in general chemistry using three theories, this being based more on historical development rather than logical pedagogy. Electronegativity is taught with a confusing mixture of definitions that do not correspond to modern practice. Valence bond theory and VSEPR are used together in a way that often confuses…

  5. 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)

  6. Molecular Structure of Human-Liver Glycogen

    PubMed Central

    Deng, Bin; Sullivan, Mitchell A.; Chen, Cheng; Li, Jialun; Powell, Prudence O.; Hu, Zhenxia; Gilbert, Robert G.

    2016-01-01

    Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets. PMID:26934359

  7. 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

  8. 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.

  9. Star formation and dynamics in starburst nuclei

    NASA Technical Reports Server (NTRS)

    Norman, Colin A.

    1987-01-01

    A simple model is presented for gas inflow through a disk galaxy driven by interacting galaxies through the action of a non-axisymmetric disturbance acting on the disk whose gas is modelled as an ensemble of gas clouds. Cloud collisions, as well as being a vital process in forcing gas inflow to the center of the disk, are also assumed to generate massive stars. This ever increasing rate of gas flow toward the center of the galaxy and the associated rapid increase in cloud collisions lead to a centrally concentrated starburst. Starbursts have important consequences for the immediate environment of galaxies. Mildly collimated outflows can be driven by a combination of multiple supernovae and OB star winds. Jets associated with activity in the galactic nucleus can interact strongly with a starburst environment.

  10. Starbursts in Low Luminosity Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    González Delgado, Rosa M.; Cid Fernandes, Roberto

    2005-05-01

    Low Luminosity Active Galactic Nuclei (LLAGN), which comprise low-ionization nuclear emission-line regions (LINERs) and transition-type objects (TOs), represent the most common type of nuclear activity. Here, we search for spectroscopic signatures of starbursts and post-starbursts in LLAGN, and investigate their relationship to the ionization mechanism in LLAGN. The method used is based on the stellar population synthesis of the circumnuclear optical continuum of these galaxies. We have found that intermediate-age populations (108-109 yr) are very common in weak-[O I] LLAGN, but that very young stars (≤107 yr) contribute very little to the central optical continuum of these objects. However, ˜ 1 Gyr ago these nuclei harboured starbursts of size ˜ 100 pc and masses 107-108 M⊙. Meanwhile, most of the strong-[O I] LLAGN have predominantly old stellar populations.

  11. 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.

  12. Students' understanding of molecular structure representations

    NASA Astrophysics Data System (ADS)

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

    2003-10-01

    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 Visualisation Test' was developed and applied. The research indicates that students' appreciation of three-dimensional molecular structures differs according to the kind of representation used. The best results were achieved with the use of concrete, and pseudo-concrete types of representations (e.g. three-dimensional models, their photographs, computer-generated models). However, the use of more abstract types (e.g. schematic representations, stereochemical formula) was less effective. A correlation between students' results on the Chemical Visualisation Test and their educational level, spatial visualisation, and spatial relations skills was shown statistically, but no statistically significant gender differences were observed.

  13. 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.

  14. 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.

  15. 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

  16. 8B structure in Fermionic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Henninger, K. R.; Neff, T.; Feldmeier, H.

    2015-04-01

    The structure of the light exotic nucleus 8B is investigated in the Fermionic Molecular Dynamics (FMD) model. The decay of 8B is responsible for almost the entire high- energy solar-neutrino flux, making structure calculations of 8B important for determining the solar core temperature. 8B is a proton halo candidate thought to exhibit clustering. FMD uses a wave-packet basis and is well-suited for modelling clustering and halos. For a multiconfiguration treatment we construct the many-body Hilbert space from antisymmetrised angular-momentum projected 8-particle states. First results show formation of a proton halo.

  17. Star-formation in the central kpc of the starburst/LINER galaxy NGC 1614

    NASA Astrophysics Data System (ADS)

    Olsson, E.; Aalto, S.; Thomasson, M.; Beswick, R.

    2010-04-01

    Aims: The aim is to investigate the star-formation and LINER (low ionization nuclear emission line region) activity within the central kiloparsec of the galaxy NGC 1614. In this paper the radio continuum morphology, which provides a tracer of both nuclear and star-formation activity, and the distribution and dynamics of the cold molecular and atomic gas feeding this activity, are studied. In particular, the nature of an R ≈ 300 pc nuclear ring of star-formation and its relationship to the LINER activity in NGC 1614 is addressed. Methods: A high angular resolution, multi-wavelength study of the LINER galaxy NGC 1614 has been performed. Deep observations of the CO 1-0 spectral line were performed using the Owens Valley Radio Observatory (OVRO). These data have been complemented by extensive multi-frequency radio continuum and Hi absorption observations using the Very Large Array (VLA) and Multi-Element Radio Linked Interferometer Network (MERLIN). Results: Toward the center of NGC 1614, we have detected a ring of radio continuum emission with a radius of 300 pc. This ring is coincident with previous radio and Paα observations. The dynamical mass of the ring based on Hi absorption is 3.1 × 109 M⊙. The peak of the integrated CO 1-0 emission is shifted by 1” to the north-west of the ring center. An upper limit to the molecular gas mass in the ring region is ~1.7 × 109 M⊙. Inside the ring, there is a north to south elongated 1.4 GHz radio continuum feature, with a nuclear peak. This peak is also seen in the 5 GHz radio continuum and in the CO. Conclusions: We suggest that the R = 300 pc star forming ring represents the radius of a dynamical resonance - as an alternative to the scenario that the starburst is propagating outwards from the center into a molecular ring. The ring-like appearance is probably part of a spiral structure. Substantial amounts of molecular gas have passed the radius of the ring and reached the nuclear region. The nuclear peak seen in 5

  18. Observations of CO J=3-2 in the Outflow of the Starburst Galaxy M82

    NASA Astrophysics Data System (ADS)

    Seaquist, E. R.; Clark, Jason

    2001-05-01

    Observations are presented of the distribution of 12CO J=3-2 emission in the starburst galaxy M82 covering a region 3''×3'' (2.8×2.8 kpc). This area includes the halo region involved in the superwind outflow. More limited coverage is presented for 13CO J=3-2 and C18O J=3-2. The mass of molecular gas in the halo is about 5×108 Msolar, with a dynamical timescale of the order of 107 yr. The results show the region of the outflow at higher CO excitation than previous published observations. Comparison with recently made observations of 12CO J=2-1 shows that the CO gas becomes progressively de-excited at larger distances from the starburst disk, and the isotopic ratio 13CO/12CO J=3-2 also becomes smaller outside the starburst disk. These effects are interpreted as differences in excitation and optical depth between the starburst region and the outflow and outer disk. A comparison between the 12CO J=3-2 emission with a published 850 μm continuum map shows that CO makes a significant contribution to the continuum in this band and that the fractional contribution is greatest near +/-30" from the nucleus approximately along the major axis. The progressively slower rotation of the halo gas with distance above and below the disk, coupled with consideration of the conservation of angular momentum, is analyzed to reveal the pattern of the outflow. The flow appears to diverge more strongly below the disk, with a cone angle of about 90°, which compares to about 40° above the disk. The mass and energetics of the halo molecular gas suggest the possibility that the molecular material and dust in the halo will not escape from M82 but are instead being recycled through the halo after injection as supershells by one or more transient starburst events.

  19. Observations of the CO J=6-5 transition in starburst galaxies

    NASA Technical Reports Server (NTRS)

    Harris, A. I.; Hills, R. E.; Stutzki, J.; Graf, U. U.; Russell, A. P. G.; Tacconi, L. J.; Genzel, R.

    1993-01-01

    Over the past several years, short-submillimeter observations of carbon monoxide's (CO) mid-J rotational levels have revealed the presence of a large amount of excited molecular gas in luminous giant molecular clouds in our Galaxy. Submillimeter lines are specific probes of excited material: collisional excitation of the level energy of 116 K above ground, and 6-5 transition's critical density is approximately 10(exp 6) cm(exp -3) in optically thin gas. Radiative trapping effects reduce the excitation requirements to some extent, but detection of the CO J=6-5 line is nearly indisputable proof of the existence of gas that is both warm and dense. The excitation conditions also imply that cool (T less than 20 K) molecular clouds within the beam neither emit nor absorb in the short-submillimeter lines; in our Galaxy, clouds with active massive star formation emit the strongest short-submillimeter CO rotational lines. We used these properties to explore the distribution of excited molecular material and physical conditions within the star formation regions of several classical starburst nuclei: NGC253, M82, and IC342. We have used the 6-5 transition as a thermometer of warm molecular gas in starburst nuclei, unambiguously finding that the nuclear molecular gas in starburst galaxies is substantially warmer than in typical disk clouds.

  20. Evolutionary paths in starbursting transition dwarf galaxies

    NASA Astrophysics Data System (ADS)

    Dellenbusch, Kate Erika

    2008-10-01

    In this thesis we present an observational optical study of a subgroup of dwarf galaxies which have characteristics of a possible evolutionary transition between actively star-forming systems and inactive dwarf galaxies. The goal of this thesis is to assess the transition nature of these systems and gain insight into their evolutionary histories. Data for the investigation consist primarily of broad-band and narrow-band Ha images taken with the WIYN 0.9m telescope. We find that these galaxies contain central starbursts embedded in older, smooth, elliptical outer stellar envelopes. They also have small HI contents and apparently lack sufficient amounts of ISM to sustain high star formation rates over a significant cosmic timescale; gas exhaustion timescales are < 1 Gyr. We also find these objects have surprisingly high HII region oxygen abundances with values near solar. This suggests the starburst came from internal gas that was previously enriched and that a significant fraction of the synthesized metals are retained. Additionally, these systems are located in loose groups and are not currently interacting with any nearby galaxies. Thus their origins are not immediately clear. We explore possible evolutionary histories for such starburst "transition" dwarf galaxies based on this puzzling set of characteristics and results from moderately deep optical imaging. We consider mechanisms where the starbursts are tied either to interactions with other galaxies or to the state of the interstellar medium.

  1. Explorations of molecular structure-property relationships.

    PubMed

    Seybold, P G

    1999-01-01

    The problem of the relationship between the structure of a molecule and its physical, chemical, and biological properties is one of the most fundamental in chemistry. Three molecular structure-property studies are discussed as illustrations of different approaches to this problem. In the first study the carcinogenic activities of polycyclic aromatic hydrocarbons and their derivatives are examined. Molecular orbital calculations of the presumptive activation steps and species for these compounds (based on the "bay region" theory of activation) are seen to yield a surprisingly good guide to the observed carcinogenic activities. Both activation and deactivation steps are considered. The second study reviews structure-property work on the tissue solubilities of halogenated hydrocarbons. Relatively simple structural descriptors give a good account of the solubilities of these compounds in blood, muscle, fat, and liver tissue. With the aid of principal components analysis it is shown that there are two dominant dimensions to this problem, which can be interpreted in terms of solubilities of the compounds in lipid and saline environments. The final study, which examines the boiling points of aliphatic alcohols, illustrates the value of using more than one descriptor set. The (perhaps surprising) conclusion is that a theoretical model can sometimes be more accurate than the data upon which it is based. Moreover, two models are better than one. PMID:10491848

  2. Filamentary structure in the Orion molecular cloud

    NASA Astrophysics Data System (ADS)

    Bally, John; Langer, William D.; Stark, Antony A.; Wilson, Robert W.

    1987-01-01

    A large-scale (C-13)O map (containing 33,000 spectra on a 1-arcmin grid) is presented for the giant molecular cloud located in the southern part of Ori which contains the Ori Nebula, NGC 1977, and the L1641 dark cloud complex. The overall structure of the cloud is filamentary, with individual features having a length up to 40 times their width. The northern portion of the cloud is compressed, dynamically relaxed, and supports massive star formation. In contrast, the southern part of the Ori A cloud is diffuse, exhibits chaotic spatial and velocity structure, and supports only intermediate- to low-mass star formation. This morphology may be the consequence of the formation and evolution of the Ori OB I association centered north of the molecular cloud. The entire cloud, in addition to the 5000-solar-mass filament containing both OMC-1 and OMC-2, exhibits a north-south velocity gradient. Implications of the observed cloud morphology for theories of molecular cloud evolution are discussed.

  3. Filamentary structure in the Orion molecular cloud

    SciTech Connect

    Bally, J.; Stark, A.A.; Wilson, R.W.; Langer, W.D.

    1987-01-01

    A large-scale (C-13)O map (containing 33,000 spectra on a 1-arcmin grid) is presented for the giant molecular cloud located in the southern part of Ori which contains the Ori Nebula, NGC 1977, and the L1641 dark cloud complex. The overall structure of the cloud is filamentary, with individual features having a length up to 40 times their width. The northern portion of the cloud is compressed, dynamically relaxed, and supports massive star formation. In contrast, the southern part of the Ori A cloud is diffuse, exhibits chaotic spatial and velocity structure, and supports only intermediate- to low-mass star formation. This morphology may be the consequence of the formation and evolution of the Ori OB I association centered north of the molecular cloud. The entire cloud, in addition to the 5000-solar-mass filament containing both OMC-1 and OMC-2, exhibits a north-south velocity gradient. Implications of the observed cloud morphology for theories of molecular cloud evolution are discussed. 14 references.

  4. The Molecular Structure of cis-FONO

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Rice, Julia E.; Langhoff, Stephen R. (Technical Monitor)

    1994-01-01

    The molecular structure of cis-FONO has been determined with the CCSD(T) correlation method using an spdf quality basis set. In agreement with previous coupled-cluster calculations but in disagreement with density functional theory, cis-FONO is found to exhibit normal bond distances. The quadratic and cubic force fields of cis-FONO have also been determined in order to evaluate the effect of vibrational averaging on the molecular geometry. Vibrational averaging is found to increase bond distances, as expected, but it does not affect the qualitative nature of the bonding. The CCSD(T)/spdf harmonic frequencies of cis-FONO support our previous assertion that a band observed at 1200 /cm is a combination band (upsilon(sub 3) + upsilon(sub 4)), and not a fundamental.

  5. The Nature of Starbursts. I. The Star Formation Histories of Eighteen Nearby Starburst Dwarf Galaxies

    NASA Astrophysics Data System (ADS)

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

    2010-09-01

    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 Hα emission usually correlates with the CMD-based SFR during the last 4-10 Myr. However, in four cases, the Hα 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 Hα 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. Based on observations made with the NASA/ESA Hubble Space Telescope

  6. Galactic Center Shells and a Recurrent Starburst Model

    NASA Astrophysics Data System (ADS)

    Sofue, Yoshiaki

    2003-04-01

    By applying filtering techniques to remove straight filaments in the 20-cm VLA radio image of the Galactic Center Arc region, we have shown that numerous concentric radio shells of radii 5 to 20pc are surrounding the Pistol and Sickle region, which we call Galactic Center Shells (GCS).Each shell has thermal energy of the order of1049-50erg.Several CO-line shells are associated, whose kinetic energies are of the order of 1049-50erg. Summing up the energies of recognized GCSs, the total energy amounts to ˜ 1051erg.The GCSs show an excellent correlation with the FIR shells observed at 16-26μm with the MSX.We propose a model in which GCSs were produced by recurrent and/or intermittent starbursts in the Pistol area during the last million years.The most recent burst occurred some 105 years ago, producing an inner round-shaped shell (GCS I);earlier ones a million years ago produced outer shells (GCS II and III), which a re more deformed by interactions with the surrounding ISM and Sgr A halo.We argue that recurrent starbursts had also occurred in the past, which produced larger scale hyper-shell structures as well.A burst some million years ago produced the Galactic Center Lobe, and a much stronger one 15 million years ago produced the North Polar Spur.

  7. 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.

  8. Algorithmic dimensionality reduction for molecular structure analysis

    PubMed Central

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

    2008-01-01

    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. PMID:18715062

  9. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases. PMID:26089747

  10. Structural disorder in molecular framework materials.

    PubMed

    Cairns, Andrew B; Goodwin, Andrew L

    2013-06-21

    It is increasingly apparent that many important classes of molecular framework material exhibit a variety of interesting and useful types of structural disorder. This tutorial review summarises a number of recent efforts to understand better both the complex microscopic nature of this disorder and also how it might be implicated in useful functionalities of these materials. We draw on a number of topical examples including topologically-disordered zeolitic imidazolate frameworks (ZIFs), porous aromatic frameworks (PAFs), the phenomena of temperature-, pressure- and desorption-induced amorphisation, partial interpenetration, ferroelectric transition-metal formates, negative thermal expansion in cyanide frameworks, and the mechanics and processing of layered frameworks. We outline the various uses of pair distribution function (PDF) analysis, dielectric spectroscopy, peak-shape analysis of powder diffraction data and single-crystal diffuse scattering measurements as means of characterising disorder in these systems, and we suggest a number of opportunities for future research in the field. PMID:23471316

  11. 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.

  12. Plant sex chromosomes: molecular structure and function.

    PubMed

    Jamilena, M; Mariotti, B; Manzano, S

    2008-01-01

    Recent molecular and genomic studies carried out in a number of model dioecious plant species, including Asparagus officinalis, Carica papaya, Silene latifolia, Rumex acetosa and Marchantia polymorpha, have shed light on the molecular structure of both homomorphic and heteromorphic sex chromosomes, and also on the gene functions they have maintained since their evolution from a pair of autosomes. The molecular structure of sex chromosomes in species from different plant families represents the evolutionary pathway followed by sex chromosomes during their evolution. The degree of Y chromosome degeneration that accompanies the suppression of recombination between the Xs and Ys differs among species. The primitive Ys of A. officinalis and C. papaya have only diverged from their homomorphic Xs in a short male-specific and non-recombining region (MSY), while the heteromorphic Ys of S. latifolia, R. acetosa and M. polymorpha have diverged from their respective Xs. As in the Y chromosomes of mammals and Drosophila, the accumulation of repetitive DNA, including both transposable elements and satellite DNA, has played an important role in the divergence and size enlargement of plant Ys, and consequently in reducing gene density. Nevertheless, the degeneration process in plants does not appear to have reached the Y-linked genes. Although a low gene density has been found in the sequenced Y chromosome of M. polymorpha, most of its genes are essential and are expressed in the vegetative and reproductive organs in both male and females. Similarly, most of the Y-linked genes that have been isolated and characterized up to now in S. latifolia are housekeeping genes that have X-linked homologues, and are therefore expressed in both males and females. Only one of them seems to be degenerate with respect to its homologous region in the X. Sequence analysis of larger regions in the homomorphic X and Y chromosomes of papaya and asparagus, and also in the heteromorphic sex chromosomes

  13. 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

  14. [Molecular structure of luminal diuretic receptors].

    PubMed

    Gamba, G

    1995-01-01

    Since day to day sodium and water intake is more or less constant, the output by urinary sodium excretion is the key to maintain extracellular fluid volume within physiologic ranges. To achieve this goal, the kidneys ensure that most of the large quantities of filtered sodium are reabsorbed, a function that takes place in the proximal tubule, the loop of Henle and the distal tubule, and then the kidneys adjust the small amount of sodium that is excreted in urine in such a way that sodium balance is maintained. This adjustment occurs in the collecting duct. Three groups of diuretic-sensitive sodium transport mechanisms have been identified in the apical membranes of the distal nephron based on their different sensitivities to diuretics and requirements for chloride and potassium: 1) the sulfamoylbenzoic (or bumetanide)-sensitive Na+:K+:2CI- and Na+:CI- symporters in the thick ascending loop of Henle; 2) the benzothiadiazine (or thiazide)-sensitive Na+:CI- cotransporter in the distal tubule; and 3) the amiloride-sensitive Na+ channel in the collecting tubule. The inhibition of any one of these proteins by diuretics results in increased sodium urinary excretion. Recently, the use of molecular biology techniques, specially the functional expression cloning in Xenopus laevis oocytes, has led to the identification of cDNA's encoding members of the three groups of diuretic-sensitive transport proteins. The present paper reviews the primary structure and some aspects of the relationship between structure and function of these transporters as well as the new protein families emerging from these sequences. It also discusses the future implications of these discoveries on the physiology and pathophysiology of kidney disease and sodium retaining states. PMID:7569367

  15. Filamentary structure in the Orion molecular cloud

    NASA Astrophysics Data System (ADS)

    Bally, J.; Dragovan, M.; Langer, W. D.; Stark, A. A.; Wilson, R. W.

    1986-10-01

    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 portion 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.

  16. Molecular structure of brown-dwarf disks

    NASA Astrophysics Data System (ADS)

    Wiebe, D. S.; Semenov, D. A.; Henning, T.

    2008-11-01

    We describe typical features of the chemical composition of proto-planetary disks around brown dwarfs. We model the chemical evolution in the disks around a low-mass T Tauri star and a cooler brown dwarf over a time span of 1 Myr using a model for the physical structure of an accretion disk with a vertical temperature gradient and an extensive set of gas-phase chemical reactions. We find that the disks of T Tauri stars are, in general, hotter and denser than the disks of lower-luminosity substellar objects. In addition, they have more pronounced vertical temperature gradients. The atmospheres of the disks around low-mass stars are more strongly ionized by UV and X-ray radiation, while less dense brown-dwarf disks have higher fractional ionizations in their midplanes. Nevertheless, in both cases, most molecules are concentrated in the so-called warm molecular layer between the ionized atmosphere and cold midplane, where grains with ice mantles are abundant.

  17. 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.

  18. 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.)

  19. 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.

  20. 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.

  1. Stellar-Nebular Feedback in Galaxian Starbursts: IR Spectral Imaging of HII Regions in M33

    NASA Astrophysics Data System (ADS)

    Waller, William; Boulanger, Francois; Brandl, Bernhard; Garnett, Donald; Gehrz, Robert; Gehrz and other GTO Team Members; Hodge, Paul; Humphreys, Roberta; Lee, Myung Gyoon; Murphy, Eric; Polomski, Elisha; Willner, Steven

    2004-09-01

    We propose a spectrophotometric investigation of starburst activity in the Local Group galaxy, Messier 33. By observing 7 selected giant HII regions that span a decade in metallicity, we will test the generic relationships between the ionizing stellar populations (previously observed with HST), the photo-dissociation regions (PDRs), and their associated dust content. We are especially interested in determining whether the observed variations in the stellar IMFs correlate with variations in the PDRs. We will use the IRS to obtain fully-sampled spectral maps of the 7 selected HII regions at 5.2 ==> 14.5 microns. The resulting datacubes will contain abundant spatial and spectral information on the molecular and dust content in the PDRs. This research program -- in close coordination with complementary GTO programs #5 and #63 -- will provide important benchmarks for interpreting starburst activity on many scales and over many epochs.

  2. 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.

  3. Stellar Rotation Curves of Starbursting Dwarf Galaxies

    NASA Astrophysics Data System (ADS)

    van Zee, Liese; Skillman, Evan D.; Salzer, John J.

    2001-02-01

    A year ago, we successfully completed a pilot project to obtain stellar rotation curves of starbursting dwarf galaxies. These observations provided the first spatially resolved stellar rotation curves of gas-rich dwarf galaxies. We now propose to expand our sample (by a factor of 2) by observing 4 additional dwarf galaxies with the CTIO 4m. The fundamental question to be addressed is whether the gas and stars are kinematically coupled in these small galaxies. These observations will place the first kinematic constraints on evolutionary models for dwarf galaxies.

  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. Near-IR spectral evolution of dusty starburst galaxies

    NASA Astrophysics Data System (ADS)

    Lançon, Ariane; Rocca-Volmerange, Brigitte

    1996-11-01

    We propose a multicomponent analysis of starburst galaxies, based on a model that takes into account the young and evolved stellar components and the gas emission, with their respective extinction, in the frame of a coherent dust distribution pattern. Near-IR signatures are preferentially investigated, in order to penetrate as deep as possible into the dusty starburst cores. We computed the 1.4-2.5 μm spectra of synthetic stellar populations evolving through strong, short timescale bursts of star formation (continuum and lines, R ≃ 500). The evolution model is specifically sensitive to cool stellar populations (AGB and red supergiant stars). It takes advantage of the stellar library of Lançon & Rocca-Volmerange (1992) [A&ASS, 96, 593], observed with the same instrument (FTS/CFHT) as the analysed galaxy sample, so that the instrumental effects are minimised. The main near-IR observable constraints are the molecular signatures of CO and H2O and the slope of the continuum, observed over a range exceptionally broad for spectroscopic data. The H - K colour determined from the spectra measures the intrinsic stellar energy distribution but also differential extinction, which is further constrained by optical emission line ratios. Other observational constraints are the near-IR emission lines (Brγ, He I 2.06 μm, [Fe II] 1.64 μm, H2 2.12 μm) and the far-IR luminosity. The coherence of the results relies on the interpretation in terms of stellar populations from which all observable properties are derived, so that the link between the various wavelength ranges is secured. The luminosity LK is used for the absolute calibration. We apply this approach to the typical spectrum of the core of NGC 1614. Consistent solutions for the starburst characteristics (star-formation rate, IMF, burst age, morphology) are found and the role of each observational constraint in deriving satisfactory models is extensively discussed. The acceptable contamination of the K band light by the

  6. What Do Star Clusters in Nearby Starburst Galaxies Tell Us?

    NASA Astrophysics Data System (ADS)

    Lim, Sungsoon; Lee, M.; Hwang, N.

    2014-01-01

    Nearby starburst galaxies are a good laboratory for the study of starburst processes. M82, one of the most famous starburst galaxies, has been a target for numerous studies of starburst events. Especially, many studies have used star clusters as starburst tracers in M82, but they usually investigated a only small central region. We present a photometric study of star clusters in M82 using wide-field UBVI, YJ, and H band images in the Hubble Space Telescope archive. We find ˜1100 star clusters in 12’x8’ field, and estimate ages and masses of about 630 star clusters using spectral energy distribution fitting method. Young star clusters are located in the disk region, while old star clusters are found in both disk and halo regions. Age distribution of star clusters shows three distinguished populations: young (≦ 5 Myr), intermediate-age (about 500 Myr), and old (≧10 Gyr) star clusters. Several massive young star clusters (≥˜105M⊙) are found in the nuclear region, which are regarded as a result of recent starburst. Interestingly, we also find very massive star clusters (≥˜106M⊙) with intermediate-age in the nuclear region, which indicates another starburst event at about 500 Myr ago. This suggests that there are at least two starburst events: 5 Myr and 500 Myr ago, and that the earlier starburst at about 500 Myr ago may be more violent than the recent one. We also find about 30 star clusters in the halo region of M82. They are probably metal-poor old globular clusters belonging to M82 halo. It suggests that starburst galaxies may also be enshrouded by old stellar populations.

  7. Molecular structure and motion in zero field magnetic resonance

    SciTech Connect

    Jarvie, T.P.

    1989-10-01

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed.

  8. ACA [CI] observations of the starburst galaxy NGC 253

    NASA Astrophysics Data System (ADS)

    Krips, M.; Martín, S.; Sakamoto, K.; Aalto, S.; Bisbas, T. G.; Bolatto, A. D.; Downes, D.; Eckart, A.; Feruglio, Ch.; García-Burillo, S.; Geach, J.; Greve, T. R.; König, S.; Matsushita, S.; Neri, R.; Offner, S.; Peck, A. B.; Viti, S.; Wagg, J.

    2016-07-01

    Context. Carbon monoxide (CO) is widely used as a tracer of the molecular gas in almost all types of environments. However, several shortcomings of CO complicate usaging it as H2 tracer, such as its optical depth effects, the dependence of its abundance on metallicity, or its susceptibility to dissociation in highly irradiated regions. Neutral carbon emission has been proposed to overcome some of these shortcomings and hence to help revealing the limits of CO as a measure of the molecular gas. Aims: We aim to study the general characteristics of the spatially and spectrally resolved carbon line emission in a variety of extragalactic sources and evaluate its potential as complementary H2 tracer to CO. Methods: We used the Atacama Compact Array to map the [CI](3P1-3P0) line emission in the nearby starburst galaxy NGC 253 at unprecedented angular resolution (~3''). This is the first well-resolved interferometric [CI] map of an extragalactic source. Results: We have detected the [CI] line emission at high significance levels along the central disk of NGC 253 and its edges where expanding shells have previously been found in CO. Globally, the distribution of the [CI] line emission strongly resembles that of CO, confirming the results of previous Galactic surveys that [CI] traces the same molecular gas as CO. However, we also identify a significant increase of [CI] line emission with respect to CO in (some of) the outflow or shocked regions of NGC 253, namely the bipolar outflow emerging from the nucleus. A first-order estimate of the [CI] column densities indicates abundances of [CI] that are very similar to the abundance of CO in NGC 253. Interestingly, we find that the [CI] line is marginally optically thick within the disk. Conclusions: The enhancement of the [CI]/CO line ratios (~0.4-0.6) with respect to Galactic values (≤0.1), especially in the shocked regions of NGC 253, clearly indicates that mechanical perturbation such as shocks and the strong radiation

  9. NuSTAR Observations of Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Ptak, Andrew; Hornschemeier, Ann E.; Wik, Daniel R.; Yukita, Mihoko; Lehmer, Bret; Zezas, Andreas; Maccarone, Tom; Venters, Tonia M.; Antoniou, Vallia; Harrison, Fiona; Stern, Daniel; NuSTAR Starburst Team

    2016-01-01

    NuSTAR, the first satellite with hard X-ray focusing optics, opens up the possibility to not only detect starburstn galaxies above 10 keV for the first time but also characterize their hard X-ray properties. Here we present an overview of a NuSTAR program to survey seven normal/starburst galaxies: NGC 253, M82, M83, NGC 3256, NGC 3310, Arp 299, and M31. We also discuss data analysis strategies. All galaxies have been observed coordinated with either Chandra or XMM-Newton or both. The main results of these observations were: we characterized the typical starburst spectrum above 10 keV and showed that the spectrum is soft (photon index ~ 3) above 7 keV and determined that individually detected sources are generally black holes in a "transition" accretion state or neutron star systems accreting near the Eddington rate, and variability on time scales of weeks to months is typically detected. In the case of NGC 253 we decomposed the unresolved hard X-ray emission between background, unresolved binaries and truly diffuse flux and found that the diffuse flux upper limit is marginally above model predictions for inverse-Compton scattering of IR photons by cosmic rays.

  10. 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.

  11. 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.

  12. Green Pea Galaxies: Extreme, Optically-Thin Starbursts?

    NASA Astrophysics Data System (ADS)

    Jaskot, Anne

    2013-10-01

    The high UV luminosities, compact sizes, and enormous ionization parameters of the Green Pea galaxies make them some of the most extreme starburst galaxies known. Most importantly, due to their unusual emission line ratios and high specific star formation rates, the Green Peas are the best candidates for escaping ionizing radiation in the nearby Universe. We propose to study four Green Peas with COS FUV spectra and ACS emission line imaging to constrain the Lyman continuum {LyC} escape fraction and determine the origin of high ionization emission in these galaxies. COS spectra will set strong limits on the LyC optical depth via the residual intensity in the CII 1335 line, while the NV 1240 line will constrain the stellar population's age and ionizing flux. We will also observe the starbursts with ACS ramp filters in [OII], [OIII], HeII, and H-beta to determine whether the nebular emission is consistent with a low LyC optical depth. The [OIII]/[OII] ratio map will reveal the ionization structure of the emitting gas. If the [OIII] emission is found to be more spatially extended than the [OII] in any regions, it will imply that the regions are most likely optically thin. If HeII is found to be spatially offset from the dominant nebular emission, then we infer the presence of shocks. Correcting for this shock contribution to the observed emission is critical to accurately evaluate the LyC optical depth. These observations will either reveal the Green Peas as a class of galaxies having substantial LyC escape fractions or demonstrate that even some of the most extreme galaxies in the nearby Universe are optically thick.

  13. 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.

  14. Unraveling the Molecular Structures of Asphaltenes by Atomic Force Microscopy.

    PubMed

    Schuler, Bruno; Meyer, Gerhard; Peña, Diego; Mullins, Oliver C; Gross, Leo

    2015-08-12

    Petroleum is one of the most precious and complex molecular mixtures existing. Because of its chemical complexity, the solid component of crude oil, the asphaltenes, poses an exceptional challenge for structure analysis, with tremendous economic relevance. Here, we combine atomic-resolution imaging using atomic force microscopy and molecular orbital imaging using scanning tunnelling microscopy to study more than 100 asphaltene molecules. The complexity and range of asphaltene polycyclic aromatic hydrocarbons are established in detail. Identifying molecular structures provides a foundation to understand all aspects of petroleum science from colloidal structure and interfacial interactions to petroleum thermodynamics, enabling a first-principles approach to optimize resource utilization. Particularly, the findings contribute to a long-standing debate about asphaltene molecular architecture. Our technique constitutes a paradigm shift for the analysis of complex molecular mixtures, with possible applications in molecular electronics, organic light emitting diodes, and photovoltaic devices. PMID:26170086

  15. 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.

  16. A Survey of Quantitative Descriptions of Molecular Structure

    PubMed Central

    Guha, Rajarshi; Willighagen, Egon

    2013-01-01

    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. PMID:23110530

  17. Molecular structural studies of human factor VIII.

    PubMed

    McKee, P A; Andersen, J C; Switzer, M E

    1975-01-20

    Neither normal nor hemophilic factor VIII protein enters a 5% sosium dodecyl sulfate gel; on reduction, however, a single 195 000-molecular-weight peptide is observed. Hemophilic and normal factor VIII contain carbohydrate and appear identical in subunit molecular weight, electrical charge, and major antigenic determinants. Thrombin activation and inactivation of factor VIII does not detectably change the subunit molecular weight. Trypsin causes similar activity changes and obviously cleaves the factor VIII subunit. Human plasmin destroys factor VIII procoagulant activity and degrades the factor VIII subunit to 103 000-, 88 000-, and 17 000-molecular-weight peptides. Both normal and hemophilic factor VIII as well as thrombin-inactivated factor VIII support ristocetin-induced platelet aggregation. Purified factor VIII chromatographed on 4% agarose in 1.0 M sodium chloride shows no dissociation of the procoagulant activity from the void volume protein. Gel chromatography on 4% agarose in 0.25 M calcium chloride results in a procoagulant activity peak removed from the void volume protein; both peaks contain protein which does not enter a 5% SDS gel, but on reduction a 195 000-molecular-weight subunit band is observed for each. Both the void volume protein peak and the procoagulant activity peak from the 0.25 M calcium chloride-agarose gel column support ristocetin-induced platelet aggregation. After removal of calcium, a small amount of procoagulant activity is present only in the void volume peak. These data suggest that both the procoagulant and von Willebrand activities are on the same molecule. Thus our previous conclusion remains the same: human factor VIII is a large glycoprotein composed of identical 195 000-molecular-weight subunits jointed by disulfide bonds and is responsible for both antihemophilic and von Willebrand activities in human plasma. PMID:122889

  18. 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 BIMA SONG, SDSS and SAURON. Our analysis illustrates that NGC 1068 is a gravitationally unstable "monster". Its starburst disc is subject to unusually powerful instabilities. Several processes, including AGN/stellar feedback, 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.

  19. Bright Submillimeter Galaxies: Evidence for Maximal Starbursts

    NASA Astrophysics Data System (ADS)

    Aretxaga, I.

    2014-09-01

    AzTEC is a sensitive bolometer camera that, coupled with 10 - 15m-class sub-mm telescopes, has mapped more than 3 sq. deg of the extragalactic sky to depths between 0.7 and 1.1 mJy at 1.1mm, prior to its current installation and operation on the 32m Large Millimeter Telescope (LMT). These extragalactic surveys targeted towards blank-fields and biased high-z environments alike have allowed us to identify a few thousands of submillimeter galaxies, powerful obscured starbursts at high-redshifts (z > 1), some of which have intrinsic Star Formation Rates SFR > 1000 Msun/yr and furthermore are extremely compact (~ 1 kpc). Our results imply that these extraordinary systems are forming stars in a gravitationally bound regime in which gravity prohibits the formation of superwinds, leading to matter accumulation within the galaxy and further generations of star formation.

  20. X-ray emission from starburst galaxies

    NASA Technical Reports Server (NTRS)

    Rephaeli, Yoel; Gruber, Duane; Macdonald, Dan; Persic, Massimo

    1991-01-01

    The results are reported of an investigation of X-ray emission from a sample of 53 IRAS-selected candidate starburst galaxies. Superposed soft and hard X-ray emission from these galaxies in the Einstein-IPC and HEAO-1 A-2 and A-4 energy bands, which span 0.5 to 160 keV, is detected at the 99.6 percent confidence level, after allowing for confusion noise in the HEAO-1 data. Above 15 keV the confidence level is 97 percent. The combined spectrum is flat, with a (photon) power-law index of 1.0 +/- 0.3. The contribution of the population of sources represented by this sample to the 3-50 keV residual cosmic X-ray background is estimated to be at least about 4 percent assuming no evolution. Moderate evolution, for which there is some observational evidence, increases this fractional contribution to about 26 percent.

  1. ROSAT PSPC observations of two starburst galaxies

    NASA Astrophysics Data System (ADS)

    Junkes, N.; Pietsch, W.; Hensler, G.

    1993-12-01

    We present results from ROSAT observations of NGC 1808 and NGC 2903. Exposures of 10 ksec each with the Position-Sensitive Proportional Counter (PSPC) detector show X-ray sources at the central positions of both galaxies which are classified as nuclear starburst galaxies. Both targets, NGC 1808 and NGC 2903 appear slightly extended in X-ray maps in the energy band 0.1-2.4 keV. The X-ray spectrum of NGC 1808 shows almost complete absorption below 0.5 keV, indicating an extremely high hydrogen column density towards that source (NH approx. = 8 x 1021/sq cm resulting from model fits on the PSPC spectrum). In the case of NGC 2903, the number of counts in the ROSAT band is significantly lower than expected from a previous EINSTEIN (HEAO 2) investigation of the source.

  2. Far-infrared activity and starburst galaxies

    NASA Technical Reports Server (NTRS)

    Belfort, P.; Mochkovitch, R.; Dennefeld, M.

    1987-01-01

    After the IRAS discovery of galaxies with large far-infrared to blue luminosity ratio, it has been proposed that an enhanced star formation could be the origin of the far-infrared emission through dust heating. Whether a simple photometric model is able to account for the FIR and optical properties of IRAS galaxies was investigated. The L sub IR/L sub B ratio, (B-V) color and H sub alpha equivalent width of normal spirals are well reproduced with smooth star formation histories. In the case of starburst galaxies, several theoretical diagrams allow us to estimate the burst strength and extinction. L sub IR/L sub B ratio up to 100 can be rather easily reached, whereas extreme values probably require IMF truncated at the low end.

  3. Properties of Dust Extinction in Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Calzetti, D.; Kinney, A. L.; Storchi-Bergmann, T.; Panagia, N.

    1993-05-01

    We have studied the extinction properties of 38 starburst and Blue Compact galaxies covering the metallicity range 8.3<=log (O/H)<=9.2, by analyzing their UV+optical spectra. The UV spectra come from the compilation of IUE spectra by Kinney et al. (Kinney, Bohlin, Calzetti, Panagia, & Wyse, 1993, ApJS, to appear on the May issue). The optical spectra, spanning the wavelength range 3200-7500 Angstroms, have been observed in a IUE-matched aperture. Following standard techniques, we have derived the selective extinction E(B-V) from the Balmer decrement and the metallicity from the [OII] and [OIII] lines. In order to clarify the properties of dust extinction in the UV for starburst galaxies, we have fitted the observed UV fluxes of our galaxies in the wavelength range 1250-2600 Angstroms according to the power law F(lambda )~lambda (beta ) and studied the behaviour of beta as function of the selective extinction E(B-V). We find that these two quantities are correlated and that there is no difference between the loci occupied by the low and high metallicity galaxies in the plane beta -vs-E(B-V). The correlation indicates that a higher metallicity does not change the characteristics of individual grains, but merely increases their number. On this ground, our conclusion is that the shape of the extinction law in the UV does not depend on metallicity, for extinctions E(B-V)>0.2. Although the low metallicity galaxies in our sample follow neither the Large Magellanic Cloud nor the Small Magellanic Cloud extinction laws, the absence in our spectra of prominent 2200 Angstroms dust features illustrates that a simple application of a galactic extinction law may be inadequate to properly correct the UV spectra. Models of clumpy dust layers and of dust mixed with the ionized gas are currently under analysis.

  4. Mapping the HI Neighborhood Around Starburst Dwarf Galaxies NGC 1569, NGC 4214 and NGC 4163

    NASA Astrophysics Data System (ADS)

    Johnson, Megan C.; LITTLE THINGS Team

    2013-01-01

    Dwarf galaxies are believed to be the building blocks of larger galaxies. However, there are some studies that indicate the dwarf galaxies observed in the nearby universe may have formed later, after the most massive galaxies coalesced. Dwarf galaxy formation and evolution is important for our understanding of cosmology. If dwarf galaxies mimic their more massive counterparts, then starburst dwarfs may be present day merger remnants and provide information on the building block hypothesis. The origins of starburst dwarf irregular galaxies of the Magellanic type (dIm) are not well known. The role of interactions and mergers as mechanisms to create these systems has been hypothesized, but not well studied. We present deep HI maps around three starburst dwarf galaxies NGC 1569, NGC 4214 and NGC 4163. The purpose of these maps is to determine if there are tenuous HI structures around these objects that would indicate a recent interaction or merger. We detect HI filamentary structures that may be connected with NGC 1569 thereby indicating a recent interaction with nearby dwarf irregular UGCA 92. However, our map of NGC 4163 and NGC 4214 does not show any tenuous HI at our 5σ sensitivity limit of 1 x 10^18 for a 25 km/s line width.

  5. 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)

  6. Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.

    PubMed

    Beran, Gregory J O

    2016-05-11

    Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. PMID:27008426

  7. FISICA observations of the starburst galaxy, NGC 1569

    NASA Astrophysics Data System (ADS)

    Clark, D. M.; Eikenberry, S. S.; Raines, S. N.; Gruel, N.; Elston, R.; Guzman, R.; Julian, J.; Boreman, G.; Glenn, P. E.; Hull-Allen, C. G.; Hoffman, J.; Rodgers, M.; Thompson, K.; Flint, S.; Comstock, L.; Myrick, B.

    2006-06-01

    Using the Florida Image Slicer for Infrared Cosmology and Astrophysics (FISICA) we obtained observations of the dwarf starburst galaxy NGC 1569. We present our JH band spectra, particularly noting the existence of extended emission in Paschen β and He I.

  8. 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 {}ȯ 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 {}ȯ 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

  9. Adaptive modelling of structured molecular representations for toxicity prediction

    NASA Astrophysics Data System (ADS)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Solaro, Roberto; Tiné, Maria Rosaria

    2012-12-01

    We investigated the possibility of modelling structure-toxicity relationships by direct treatment of the molecular structure (without using descriptors) through an adaptive model able to retain the appropriate structural information. With respect to traditional descriptor-based approaches, this provides a more general and flexible way to tackle prediction problems that is particularly suitable when little or no background knowledge is available. Our method employs a tree-structured molecular representation, which is processed by a recursive neural network (RNN). To explore the realization of RNN modelling in toxicological problems, we employed a data set containing growth impairment concentrations (IGC50) for Tetrahymena pyriformis.

  10. Do Tidal Interactions Trigger Starbursts in Dwarf Galaxies?

    NASA Astrophysics Data System (ADS)

    Martinkus, Charlotte; Cannon, John M.; McQuinn, Kristen B.; Johnson, Megan C.; Skillman, Evan D.; Bailin, Jeremy; Ford, Alyson; Koribalski, Baerbel

    2015-01-01

    Starburst dwarf galaxies are extensively studied systems, though the mechanism that triggers starbursts is poorly understood. Tidal interactions and gas accretion are thought to be potential starburst trigger mechanisms, although internal, secular drivers have not been ruled out. If starbursts are a result of external perturbations, then one would expect to see signatures of interaction in the gaseous disk of the galaxy. To examine this hypothesis, we analyze both archival and newly-obtained deep, wide-field HI maps from the Green Bank Telescope (GBT) of a sample of nineteen well-studied nearby starburst dwarf galaxies to search for such signs of interactions. Our sample is unique in that we have previously derived the star formation histories from Hubble Space Telescope imaging of the resolved stellar populations for all galaxies. In this work we focus on NGC 784 and NGC 672, which both may lie on a filament of dark matter isolated in space. We evaluate methods to determine the presence and properties of low surface-brightness neutral gas in the outer disk regions. This work serves as a prototype for forthcoming analysis of the full sample. With our results we hope to not only establish an effective data analysis procedure, but to also confirm or rule-out tidal interactions as a triggering mechanism of starbursts in this sample of dwarf galaxies.

  11. 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)

  12. Synthesis and molecular structure of gold triarylcorroles.

    PubMed

    Thomas, Kolle E; Alemayehu, Abraham B; Conradie, Jeanet; Beavers, Christine; Ghosh, Abhik

    2011-12-19

    A number of third-row transition-metal corroles have remained elusive as synthetic targets until now, notably osmium, platinum, and gold corroles. Against this backdrop, we present a simple and general synthesis of β-unsubstituted gold(III) triarylcorroles and the first X-ray crystal structure of such a complex. Comparison with analogous copper and silver corrole structures, supplemented by extensive scalar-relativistic, dispersion-corrected density functional theory calculations, suggests that "inherent saddling" may occur for of all coinage metal corroles. The degree of saddling, however, varies considerably among the three metals, decreasing conspicuously along the series Cu > Ag > Au. The structural differences reflect significant differences in metal-corrole bonding, which are also reflected in the electrochemistry and electronic absorption spectra of the complexes. From Cu to Au, the electronic structure changes from noninnocent metal(II)-corrole(•2-) to relatively innocent metal(III)-corrole(3-). PMID:22111600

  13. PHYSICAL PROPERTIES OF THE CIRCUMNUCLEAR STARBURST RING IN THE BARRED GALAXY NGC 1097

    SciTech Connect

    Hsieh, Pei-Ying; Matsushita, Satoki; Ho, Paul T. P.; Wu, Ya-Lin; Liu, Guilin; Oi, Nagisa

    2011-08-01

    We report high-resolution {sup 12}CO(J = 2-1), {sup 13}CO(J = 2-1), and {sup 12}CO(J = 3-2) imaging of the Seyfert 1/starburst ring galaxy NGC 1097 with the Submillimeter Array for the purpose of studying the physical and kinematic properties of the 1 kpc circumnuclear starburst ring. Individual star clusters as detected in the Hubble Space Telescope map of Pa{alpha} line emission have been used to determine the star formation rate (SFR), and are compared with the properties of the molecular gas. The molecular ring has been resolved into individual clumps at the giant molecular cloud association (GMA) scale of 200-300 pc in all three CO lines. The intersection between the dust lanes and the starburst ring, which is associated with the orbit-crowding region, is resolved into two physically/kinematically distinct features in the 1.''5 x 1.''0 (105 x 70 pc) {sup 12}CO(J = 2-1) map. The clumps associated with the dust lanes have broader line widths, higher surface gas densities, and lower SFRs, while the narrow line clumps associated with the starburst ring have opposite characteristics. A Toomre-Q value lower than unity at the radius of the ring suggests that the molecular ring is gravitationally unstable to fragmentation at GMA scale. The line widths and surface density of the gas mass of the clumps show an azimuthal variation related to the large-scale dynamics. The SFR, on the other hand, is not significantly affected by the dynamics, but has a correlation with the intensity ratio of {sup 12}CO (J = 3-2) and {sup 12}CO(J = 2-1), which traces the denser gas associated with star formation. Our resolved CO map, especially in the orbit-crowding region, observationally demonstrates for the first time that the physical/kinematic properties of GMAs are affected by the large-scale bar-potential dynamics in NGC 1097.

  14. Molecular gymnastics: serpin structure, folding and misfolding.

    PubMed

    Whisstock, James C; Bottomley, Stephen P

    2006-12-01

    The native state of serpins represents a long-lived intermediate or metastable structure on the serpin folding pathway. Upon interaction with a protease, the serpin trap is sprung and the molecule continues to fold into a more stable conformation. However, thermodynamic stability can also be achieved through alternative, unproductive folding pathways that result in the formation of inactive conformations. Our increasing understanding of the mechanism of protease inhibition and the dynamics of native serpin structures has begun to reveal how evolution has harnessed the actual process of protein folding (rather than the final folded outcome) to elegantly achieve function. The cost of using metastability for function, however, is an increased propensity for misfolding. PMID:17079131

  15. 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

  16. A High-Resolution Map of 12CO J = 6-5 Emission in the Starburst Galaxy M82

    NASA Astrophysics Data System (ADS)

    Seaquist, E. R.; Lee, S. W.; Moriarty-Schieven, G. H.

    2006-02-01

    We present a map of 12CO J=6-5 emission of the nuclear region of the nearby starburst galaxy M82 at resolution 7" taken with the James Clerk Maxwell Telescope (JCMT). This is the highest resolution map yet available at this transition. A detailed quantitative comparison is made with emission at 12CO J=1-0 at the same resolution, yielding new insights into the excitation of molecular gas in this galaxy. The excitation is found to be highest in the central area of the starburst region where the ratio r61=12CO J=6-5/12CO J=1-0 is as high as 0.5, compared to the mean value over the starburst region of 0.24. The excitation ratio peaks along the inner edge of the molecular ring outlined by atomic and molecular gas at lower excitation, and also in two spurs extending northward from the disk toward the outflow associated with the superwind. Emission with higher than average excitation is also found to be associated with the supershell surrounding the luminous SNR candidate 41.9+58, and possibly on a larger scale in gas whose orbits are strongly influenced by the stellar bar. The higher excitation in M82 is likely to be caused predominantly by local increases in kinetic temperature and/or in the geometric filling factor of a preexisting higher excitation component and less likely to be caused by local increases in gas density.

  17. Modeling Small Stellar Populations Using Starburst99

    NASA Astrophysics Data System (ADS)

    Vazquez, Gerardo Arturo; Leitherer, Claus

    2015-08-01

    Stellar populations synthesis models have proven to be excellent tools to learn about galaxy evolution. However, modeling small stellar populations (lower than 105 M⊙) has been an intriguing and continuous to be a field of intensive research. In this work, we have developed a new approach to form stars from clusters first, where massive stars are formed from fractions of mass of small stellar clusters. This new approximation is based on the empirical power law (mc-2) for the mass function of clusters between 20-1100 M⊙ found in recent years and the maximum stellar mass that can be formed in a cluster. Incorporating this new approach to form clusters has made us upgrade the way we integrate the stellar properties and the way that the isochrone is produced with a new technique. To produce the new models we have used the most recent version of Starburst99 that incorporates the most recent stellar evolution models with rotation. On the verge of solving nearby stellar populations and observing small stellar populations across the universe, this new approach brings a new scope on trying to disentangle the nature of hyper and supermassive stars in small stellar populations. In this work we present this new approach and the results when these models are applied to very energetic stellar populations such as the cluster in NGC 3603. Our most important result is that we have modeled the ionizing power of this cluster and some others by forming enough supermassive stars in a cluster of ~104 M⊙.

  18. Complementary molecular information changes our perception of food web structure

    PubMed Central

    Wirta, Helena K.; Hebert, Paul D. N.; Kaartinen, Riikka; Prosser, Sean W.; Várkonyi, Gergely; Roslin, Tomas

    2014-01-01

    How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host–parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them. PMID:24449902

  19. 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.

  20. 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.

  1. A far-IR view of the starburst-driven superwind in NGC 2146

    SciTech Connect

    Kreckel, K.; Groves, B.; Lyubenova, M.; Schinnerer, E.; Meidt, S.; Armus, L.; Díaz-Santos, T.; Appleton, P.; Croxall, K. V.; Dale, D. A.; Hunt, L. K.; Beirão, P.; Bolatto, A. D.; Calzetti, D.; Donovan Meyer, J.; Draine, B. T.; Hinz, J.; Kennicutt, R. C.; Murphy, E. J.; Smith, J. D. T.; and others

    2014-07-20

    NGC 2146, a nearby luminous infrared galaxy, presents evidence for outflows along the disk minor axis in all gas phases (ionized, neutral atomic, and molecular). We present an analysis of the multi-phase, starburst-driven superwind in the central 5 kpc as traced in spatially resolved spectral line observations, using far-IR Herschel PACS spectroscopy, to probe the effects on the atomic and ionized gas, and optical integral field spectroscopy to examine the ionized gas through diagnostic line ratios. We observe an increased ∼250 km s{sup –1} velocity dispersion in the [O I] 63 μm, [O III] 88 μm, [N II] 122 μm, and [C II] 158 μm fine-structure lines that is spatially coincident with high excitation gas above and below the disk. We model this with a slow ∼200 km s{sup –1} shock and trace the superwind to the edge of our field of view 2.5 kpc above the disk. We present new SOFIA 37 μm observations to explore the warm dust distribution, and detect no clear dust entrainment in the outflow. The stellar kinematics appear decoupled from the regular disk rotation seen in all gas phases, consistent with a recent merger event disrupting the system. We consider the role of the superwind in the evolution of NGC 2146 and speculate on the evolutionary future of the system. Our observations of NGC 2146 in the far-IR allow an unobscured view of the wind, crucial for tracing the superwind to the launching region at the disk center, and provide a local analog for future ALMA observations of outflows in high-redshift systems.

  2. 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.

  3. Comprehensive Molecular Structure of the Eukaryotic Ribosome

    PubMed Central

    Taylor, Derek J.; Devkota, Batsal; Huang, Andrew D.; Topf, Maya; Narayanan, Eswar; Sali, Andrej; Harvey, Stephen C.; Frank, Joachim

    2009-01-01

    Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than bacterial ribosomes, which are implicated in extra-ribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial and novel interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2. PMID:20004163

  4. Filaments, ridges and a mini-starburst - HOBYS' view of high mass star formation with Herschel

    NASA Astrophysics Data System (ADS)

    Hill, T.; Motte, F.; Didelon, P.

    2012-03-01

    With its unprecedented spatial resolution and high sensitivity, Herschel is revolutionising our understanding of high mass star formation and the interstellar medium (ISM). In particular, Herschel is unveiling the filamentary structure and molecular cloud constituents of the ISM where star formation takes place. The Herschel Imaging Survey of OB Young Stellar objects (HOBYS; Motte, Zavagno, Bontemps, see http://www.herschel.fr/cea/hobys/en/index.php) key program targets burgeoning young stellar objects with the aim of characterising them and the environments in which they form. HOBYS has already proven fruitful with many clear examples of high-mass star formation in nearby molecular cloud complexes (e.g. Motte et al., 2010). Through multi-wavelength Herschel observations I will introduce select regions of the HOBYS program, including Vela C, M16 and W48 to start. These data are rich with filamentary structures and a wealth of sources which span a large mass range including, low, intermediate and high-mass objects in the pre-collapse or protostellar phase of formation, many of which will proceed to form stars. The natal filaments themselves come in many shapes and sizes, they can form thick ridge-like structures, be dispersed in low column density regions or cluster in higher density regions. In Vela C, high-mass star formation proceeds preferentially in high column density supercritical filaments, called ridges, which may result from the constructive convergence of flows (Hill et al., 2011). I will present other examples of ridges identified in HOBYS regions. In addition, I will present the latest results on the Eagle Nebula (M16). This region was made iconic by Hubble, but only Herschel can trace the cold, dense early prestellar phases of star formation, and their natal interstellar filaments, in this infamous star-forming complex. The cavity ionised by the nearby OB cluster in M16 serves to heat the Pillars of Creation and the surrounding interstellar filaments

  5. 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.

  6. 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

  7. Connecting the density structure of molecular clouds and star formation.

    NASA Astrophysics Data System (ADS)

    Kainulainen, Jouni

    2015-08-01

    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 in the ISM. This density structure is essentially encapsulated in the probability distribution function of volume densities (rho-PDF), which directly affects the star formation rates predicted by analytic models. Contrasting its fundamental role, the rho-PDF function and its evolution have remained virtually unconstrained by observations. I describe in this contribution our recent progress in attaining observational constraints for the rho-PDFs of molecular clouds. Specifically, I review our first systematic determination of the rho-PDFs in Solar neighborhood molecular clouds. I will also present new evidence of the time evolution of the projected rho-PDFs, i.e., column density PDFs. These results together enable us to build the first observationally constrained link between the evolving density structure of molecular clouds and the star formation within. Finally, I discuss our work to expand the analysis into a Galactic context and to observationally connect the physical processes acting at the scale of molecular clouds with star formation at the scale of galaxies.

  8. Determination of structure parameters in molecular tunnelling ionisation model

    NASA Astrophysics Data System (ADS)

    Wang, Jun-Ping; Zhao, Song-Feng; Zhang, Cai-Rong; Li, Wei; Zhou, Xiao-Xin

    2014-04-01

    We extracted the accurate structure parameters in a molecular tunnelling ionisation model (the so-called MO-ADK model) for 23 selected linear molecules including some inner orbitals. The molecular wave functions with the correct asymptotic behaviour are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials numerically constructed using the modified Leeuwen-Baerends (LBα) model. We show that the orientation-dependent ionisation rate reflects the shape of the ionising orbitals in general. The influences of the Stark shifts of the energy levels on the orientation-dependent ionisation rates of the polar molecules are studied. We also examine the angle-dependent ionisation rates (or probabilities) based on the MO-ADK model by comparing with the molecular strong-field approximation calculations and with recent experimental measurements.

  9. 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.

  10. [Structure and molecular mechanisms of infection and replication of HIV].

    PubMed

    Sato, Hironori; Ode, Hirotaka; Motomura, Kazushi; Yokoyama, Masaru

    2009-01-01

    Studies on molecular structure and mechanisms of replication of a pathogen are important from both scientific and clinical viewpoints. The replication study allows us to identify key molecules to regulate life cycle of the pathogen and to screen rationally anti-pathogen drugs. The structural study helps understand how the key molecules work at atomic levels and to design adequately the drugs. In this article, we review important findings on structural and replication studies of human immunodeficiency virus (HIV). We also summarize the latest methods for the structural study, mainly focusing on computational simulation technology (in silico analysis). Finally, we summarize briefly standard methods to study replication of viruses. PMID:19177750

  11. 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.

  12. 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. PMID:19779150

  13. A spectroscopic analysis of the starburst galaxies NGC 3395 and NGC 3396

    NASA Astrophysics Data System (ADS)

    Plaks, Kenneth

    2003-11-01

    We have obtained ultraviolet and visible wavelength spectra of 31 bright star forming knots in the interacting galaxies NGC 3395 and NGC 3396 using the Space Telescope Imaging Spectrograph (STIS) on the Hubble Space Telescope. The knots are possible super star clusters on the order of ˜100 pc diameter with measured metallicities on the order of 0.5 0.6 Z⊙ . The spectra are consistent with a massive production of hot young stars in a starburst. Ages of the starburst knots were calculated using several diagnostics from the Leitherer et al. Starburst 99 code (SB99) using an Initial Mass Function (IMF) with a power law coefficient α = 2.35 and an upper mass limit of 100 M⊙ . We modeled our star forming knots as instantaneous starbursts with the measured metallicity and we obtained consistent and reasonable estimates of the starburst age. The UV-brightest knots are ˜5 Myr old in both galaxies. We found no age gradient in the galaxies implying the starburst does not propagate across the galaxy but rather occurs simultaneously everywhere. The data are also consistent with the interpretation that the starburst is not only happening more or less simultaneously within each galaxy, it is also occurring simultaneously in both galaxies. If true, the fact that it is occurring simultaneously in both galaxies gives credence to the interaction being the source of the star formation in line with current theory. While our starforming knots were spatially resolved, at high redshift one cannot resolve individual knots and instead has to rely on spatially unresolved spectra. To assess the representativeness of these spectra of the underlying structure, we simulated the spectra one would observe by defining the entire portion of each galaxy observed as an unresolved knot. We found the metallicities for the unresolved knots were very representative of the resolved knots that made them up. We also found that the ages we derived for the unresolved knots were representative of the

  14. 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. PMID:2781279

  15. 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.

  16. Relating Soil Organic Matter Dynamics to its Molecular Structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our understanding of the dynamics of soil organic matter (SOM) must be integrated with a sound knowledge of it biochemical complexity. The molecular structure of SOM was determined in 98% sand soils to eliminate the known protective effects of clay on the amount and turnover rate of the SOM constitu...

  17. Formaldehyde Densitometry of Starburst Galaxies: Density-independent Global Star Formation

    NASA Astrophysics Data System (ADS)

    Mangum, Jeffrey G.; Darling, Jeremy; Henkel, Christian; Menten, Karl M.

    2013-04-01

    Accurate techniques that allow for the derivation of the spatial density in star formation regions are rare. A technique that has found application for the derivation of spatial densities in Galactic star formation regions utilizes the density-sensitive properties of the K-doublet transitions of formaldehyde (H2CO). In this paper, we present an extension of our survey of the formaldehyde 110-111 (λ = 6.2 cm) and 211-212 (λ = 2.1 cm) K-doublet transitions of H2CO in a sample of 56 starburst systems. We have extended the number of galaxies in which both transitions have been detected from 5 to 13. We have improved our spatial density measurements by incorporating kinetic temperatures based upon NH3 measurements of 11 of the galaxies with a total of 14 velocity components in our sample. Our spatial density measurements lie in a relatively narrow range from 104.5 to 105.5 cm-3. This implies that the Schmidt-Kennicutt relation between L IR and M dense (1) is an indication of the dense gas mass reservoir available to form stars and (2) is not directly dependent upon a higher average density driving the star formation process in the most luminous starburst galaxies. We have also used our H2CO measurements to derive two separate measures of the dense gas mass which are generally smaller, in many cases by a factor of 102-103, than those derived using HCN. This disparity suggests that H2CO traces a denser, more compact component of the giant molecular clouds in our starburst galaxy sample. We also report measurements of the rotationally excited λ = 6.3 cm 2Π1/2 J = 1/2 state of OH and the H111α radio recombination line taken concurrently with our H2CO 110-111 measurements.

  18. Class I methanol megamasers: a potential probe of starburst activity and feedback in active galaxies

    NASA Astrophysics Data System (ADS)

    Chen, X.; Ellingsen, S. P.; Zhang, J.-S.; Wang, J.-Z.; Shen, Z.-Q.; Wu, Q.-W.; Wu, Z.-Z.

    2016-06-01

    Previous observations have shown that the distribution of 36.2-GHz class I methanol megamaser (MM) emission in Arp 220 is highly correlated with the diffuse X-rays. On this basis it was suggested that methanol MM may be produced either by the effects of galactic-outflow-driven shocks and/or cosmic rays. Here we report the results of a single-dish survey undertaken with the Greenbank Telescope (GBT) to improve our understanding of the pumping conditions of extragalactic class I methanol masers and their relationship to starburst and feedback processes within the host galaxies, towards a sample which includes 16 galaxies which show both extended soft X-ray emission, and either OH or H2O MM emission. Large baseline ripples in the GBT spectra limited our results to tentative detections towards 11 of the target galaxies. Analysis of these tentative detections shows that there are significant correlations between the methanol intensity and the host-galaxy infrared, radio and OH MM emission, but no correlation with the X-ray and H2O MM emission. Some sources show methanol emission significantly offset from the systemic velocity of the galaxy (by up to 1000 km s-1) and we propose that these are associated with galactic-scale outflows from active galactic nuclei (AGNs) feedback. The combined observational properties suggest that class I methanol MMs are related to significant starburst and molecular outflow activity and hence may provide a potential probe of AGN feedback and starburst processes in the host galaxies.

  19. 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.

  20. 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

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

    NASA Astrophysics Data System (ADS)

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

    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

  2. Consequences of Starbursts for the Interstellar and Intergalactic Medium

    NASA Astrophysics Data System (ADS)

    Breitschwerdt, Dieter; de Avillez, Miguel; Dorfi, Ernst

    Star formation in general, and starbursts in particular, drive the evolution of galaxies. To understand the process of galactic matter cycle quantitatively, it is absolutely necessary to follow the evolution of the components of the interstellar medium, such as gas, magnetic fields, cosmic rays in detail over sufficiently long time scales. Due to the non-linearity of the interactions between the various components, and the turbulent nature of the plasma, high resolution numerical simulations offer the best strategy to further our understanding. The results of our numerical studies can be summarized as follows: (i) Supernova explosions are the most important energy input sources in the ISM and lead to a high level of turbulence in the plasma, coupling structures on all scales, (ii) more than half of the disk mass resides in classically thermally unstable temperature regimes, (iii) turbulent mixing is the dominant energy transport process over a wide range of scales, (iv) proportionality between magnetic field and density is generally weak, except for the densest regions, (v) magnetic fields, even if they are parallel to the galactic disk, cannot prevent outflow into the halo, (vi) the ionization structure of the plasma depends on its thermal history, and is in general not in collisional ionization equilibrium, (vii) the cooling function varies in space and time, (viii) X-rays can be emitted even at plasma temperatures of the order of 104K due to delayed recombination, both in the disk and the halo, (ix) cosmic rays can help driving a galactic wind, (x) cosmic rays can be accelerated to high energies beyond 1015eV (the "knee") in long lived shocks propagating into the galactic halo, because of time-dependent star formation.

  3. Molecular solids of actinide hexacyanoferrate: Structure and bonding

    NASA Astrophysics Data System (ADS)

    Dupouy, G.; Dumas, T.; Fillaux, C.; Guillaumont, D.; Moisy, P.; Den Auwer, C.; Le Naour, C.; Simoni, E.; Fuster, E. G.; Papalardo, R.; Sanchez Marcos, E.; Hennig, C.; Scheinost, A.; Conradson, S. D.; Shuh, D. K.; Tyliszczak, T.

    2010-03-01

    The hexacyanometallate family is well known in transition metal chemistry because the remarkable electronic delocalization along the metal-cyano-metal bond can be tuned in order to design systems that undergo a reversible and controlled change of their physical properties. We have been working for few years on the description of the molecular and electronic structure of materials formed with [Fe(CN)6]n- building blocks and actinide ions (An = Th, U, Np, Pu, Am) and have compared these new materials to those obtained with lanthanide cations at oxidation state +III. In order to evaluate the influence of the actinide coordination polyhedron on the three-dimensional molecular structure, both atomic number and formal oxidation state have been varied : oxidation states +III, +IV. EXAFS at both iron K edge and actinide LIII edge is the dedicated structural probe to obtain structural information on these systems. Data at both edges have been combined to obtain a three-dimensional model. In addition, qualitative electronic information has been gathered with two spectroscopic tools : UV-Near IR spectrophotometry and low energy XANES data that can probe each atom of the structural unit : Fe, C, N and An. Coupling these spectroscopic tools to theoretical calculations will lead in the future to a better description of bonding in these molecular solids. Of primary interest is the actinide cation ability to form ionic — covalent bonding as 5f orbitals are being filled by modification of oxidation state and/or atomic number.

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

    PubMed

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

    2016-02-01

    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. PMID:26649980

  5. 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.

  6. Structure factor and rheology of chain molecules from molecular dynamics

    NASA Astrophysics Data System (ADS)

    Castrejón-González, Omar; Castillo-Tejas, Jorge; Manero, Octavio; Alvarado, Juan F. J.

    2013-05-01

    Equilibrium and non-equilibrium molecular dynamics were performed to determine the relationship between the static structure factor, the molecular conformation, and the rheological properties of chain molecules. A spring-monomer model with Finitely Extensible Nonlinear Elastic and Lennard-Jones force field potentials was used to describe chain molecules. The equations of motion were solved for shear flow with SLLOD equations of motion integrated with Verlet's algorithm. A multiple time scale algorithm extended to non-equilibrium situations was used as the integration method. Concentric circular patterns in the structure factor were obtained, indicating an isotropic Newtonian behavior. Under simple shear flow, some peaks in the structure factor were emerged corresponding to an anisotropic pattern as chains aligned along the flow direction. Pure chain molecules and chain molecules in solution displayed shear-thinning regions. Power-law and Carreau-Yasuda models were used to adjust the generated data. Results are in qualitative agreement with rheological and light scattering experiments.

  7. 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.

  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. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  10. 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

  11. Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods.

    PubMed

    Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua

    2015-01-13

    We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207

  12. 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. PMID:12725967

  13. ANATOMY OF A POST-STARBURST MINOR MERGER: A MULTI-WAVELENGTH WFC3 STUDY OF NGC 4150

    SciTech Connect

    Crockett, R. Mark; Kaviraj, Sugata; Silk, Joseph I.; Whitmore, Bradley C.; Mutchler, Max; Bond, Howard E.; O'Connell, Robert W.; Balick, Bruce; Calzetti, Daniela; Carollo, C. Marcella; Disney, Michael J.; Dopita, Michael A.; Frogel, Jay A.; Hall, Donald N. B.; Holtzman, Jon A.; Kimble, Randy A.; McCarthy, Patrick J.; Paresce, Francesco; Saha, Abhijit; Trauger, John T.

    2011-02-01

    We present a spatially resolved near-UV/optical study, using the Wide Field Camera 3 (WFC3) on board the Hubble Space Telescope, of NGC 4150, a sub-L{sub *}, early-type galaxy (ETG) of around 6 x 10{sup 9} M{sub sun}, which has been observed as part of the WFC3 Early-Release Science Programme. Previous work indicates that this galaxy has a large reservoir of molecular hydrogen gas, exhibits a kinematically decoupled core (a likely indication of recent merging) and strong, central H{beta} absorption (indicative of young stars). While relatively uninspiring in its optical image, the core of NGC 4150 shows ubiquitous near-UV emission and remarkable dusty substructure. Our analysis shows this galaxy to lie in the near-UV green valley, and its pixel-by-pixel photometry exhibits a narrow range of near-UV/optical colors that are similar to those of nearby E+A (post-starburst) galaxies and lie between those of M83 (an actively star-forming spiral) and the local quiescent ETG population. We parameterize the properties of the recent star formation (RSF; age, mass fraction, metallicity, and internal dust content) in the NGC 4150 pixels by comparing the observed near-UV/optical photometry to stellar models. The typical age of the RSF is around 0.9 Gyr, consistent with the similarity of the near-UV colors to post-starburst systems, while the morphological structure of the young component supports the proposed merger scenario. The typical RSF metallicity, representative of the metallicity of the gas fuelling star formation, is {approx}0.3-0.5 Z{sub sun}. Assuming that this galaxy is a merger and that the gas is sourced mainly from the infalling companion, these metallicities plausibly indicate the gas-phase metallicity (GPM) of the accreted satellite. Comparison to the local mass-GPM relation suggests (crudely) that the mass of the accreted system is {approx}3 x 10{sup 8} M{sub sun}, making NGC 4150 a 1:20 minor merger. A summation of the pixel RSF mass fractions indicates that

  14. Anatomy of a Post-starburst Minor Merger: A Multi-wavelength WFC3 Study of NGC 4150

    NASA Astrophysics Data System (ADS)

    Crockett, R. Mark; Kaviraj, Sugata; Silk, Joseph I.; Whitmore, Bradley C.; O'Connell, Robert W.; Mutchler, Max; Balick, Bruce; Bond, Howard E.; Calzetti, Daniela; Carollo, C. Marcella; Disney, Michael J.; Dopita, Michael A.; Frogel, Jay A.; Hall, Donald N. B.; Holtzman, Jon A.; Kimble, Randy A.; McCarthy, Patrick J.; Paresce, Francesco; Saha, Abhijit; Trauger, John T.; Walker, Alistair R.; Windhorst, Rogier A.; Young, Erick T.; Jeong, Hyunjin; Yi, Sukyoung K.

    2011-02-01

    We present a spatially resolved near-UV/optical study, using the Wide Field Camera 3 (WFC3) on board the Hubble Space Telescope, of NGC 4150, a sub-L *, early-type galaxy (ETG) of around 6 × 109 M sun, which has been observed as part of the WFC3 Early-Release Science Programme. Previous work indicates that this galaxy has a large reservoir of molecular hydrogen gas, exhibits a kinematically decoupled core (a likely indication of recent merging) and strong, central Hβ absorption (indicative of young stars). While relatively uninspiring in its optical image, the core of NGC 4150 shows ubiquitous near-UV emission and remarkable dusty substructure. Our analysis shows this galaxy to lie in the near-UV green valley, and its pixel-by-pixel photometry exhibits a narrow range of near-UV/optical colors that are similar to those of nearby E+A (post-starburst) galaxies and lie between those of M83 (an actively star-forming spiral) and the local quiescent ETG population. We parameterize the properties of the recent star formation (RSF; age, mass fraction, metallicity, and internal dust content) in the NGC 4150 pixels by comparing the observed near-UV/optical photometry to stellar models. The typical age of the RSF is around 0.9 Gyr, consistent with the similarity of the near-UV colors to post-starburst systems, while the morphological structure of the young component supports the proposed merger scenario. The typical RSF metallicity, representative of the metallicity of the gas fuelling star formation, is ~0.3-0.5 Z sun. Assuming that this galaxy is a merger and that the gas is sourced mainly from the infalling companion, these metallicities plausibly indicate the gas-phase metallicity (GPM) of the accreted satellite. Comparison to the local mass-GPM relation suggests (crudely) that the mass of the accreted system is ~3 × 108 M sun, making NGC 4150 a 1:20 minor merger. A summation of the pixel RSF mass fractions indicates that the RSF contributes ~2%-3% of the stellar mass

  15. Molecular spectroscopy and molecular structure - Selected communications presented at the 1st International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013)

    NASA Astrophysics Data System (ADS)

    Durig, James R.; Fausto, Rui; Ünsalan, Ozan; Bayarı, Sevgi; Kuş, Nihal; Ildız, Gülce Ö.

    2016-01-01

    The First International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013) took place at the Harbiye Cultural Center & Museum, Istanbul, Turkey, September 15-20, 2013. The main aim of the congress was to encourage the exchange of scientific ideas and collaborations all around the world, introduce new techniques and instruments, and discuss recent developments in the field of molecular spectroscopy. Among the different subjects covered, particular emphasis was given to the relevance of spectroscopy to elucidate details of the molecular structure and the chemical and physical behavior of systems ranging from simple molecules to complex biochemical molecules. Besides experimental spectroscopic approaches, related computational and theoretical methods were also considered. In this volume, selected contributions presented at the congress were put together.

  16. Synthesis, molecular structure, spectroscopic analysis, thermodynamic parameters and molecular modeling studies of (2-methoxyphenyl)oxalate

    NASA Astrophysics Data System (ADS)

    Şahin, Zarife Sibel; Kantar, Günay Kaya; Şaşmaz, Selami; Büyükgüngör, Orhan

    2015-05-01

    The aim of this study is to find out the molecular characteristic and structural parameters that govern the chemical behavior of a new (2-methoxyphenyl)oxalate compound and to compare predictions made from theory with experimental observations. The title compound, (2-methoxyphenyl)oxalate, (I), (C16H14O6), has been synthesized. The compound has been characterized by elemental analysis, IR, 1H NMR, 13C NMR spectroscopies and single crystal X-ray diffraction techniques. Optimized molecular structure, harmonic vibrational frequencies, 1H and 13C NMR chemical shifts have been investigated by B3LYP/6-31G(d,p) method using density functional theory (DFT). The calculated results show that the predicted geometry can well reproduce structural parameters. In addition, global chemical reactivity descriptors, molecular electrostatic potential map (MEP), frontier molecular orbitals (FMOs), Mulliken population method and natural population analysis (NPA) and thermodynamic properties have also been studied. The energetic behavior of title compound has been examined in solvent media using polarizable continuum model (PCM).

  17. A dynamic data structure for flexible molecular maintenance and informatics

    PubMed Central

    Bajaj, Chandrajit; Chowdhury, Rezaul Alam; Rasheed, Muhibur

    2011-01-01

    Motivation: We present the ‘Dynamic Packing Grid’ (DPG), a neighborhood data structure for maintaining and manipulating flexible molecules and assemblies, for efficient computation of binding affinities in drug design or in molecular dynamics calculations. Results: DPG can efficiently maintain the molecular surface using only linear space and supports quasi-constant time insertion, deletion and movement (i.e. updates) of atoms or groups of atoms. DPG also supports constant time neighborhood queries from arbitrary points. Our results for maintenance of molecular surface and polarization energy computations using DPG exhibit marked improvement in time and space requirements. Availability: http://www.cs.utexas.edu/~bajaj/cvc/software/DPG.shtml Contact: bajaj@cs.utexas.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21115440

  18. Ab initio molecular crystal structures, spectra, and phase diagrams.

    PubMed

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  19. Molecular structure in soil humic substances: The new view

    SciTech Connect

    Sutton, Rebecca; Sposito, Garrison

    2005-04-21

    A critical examination of published data obtained primarily from recent nuclear magnetic resonance spectroscopy, X-ray absorption near-edge structure spectroscopy, electrospray ionization-mass spectrometry, and pyrolysis studies reveals an evolving new view of the molecular structure of soil humic substances. According to the new view, humic substances are collections of diverse, relatively low molecular mass components forming dynamic associations stabilized by hydrophobic interactions and hydrogen bonds. These associations are capable of organizing into micellar structures in suitable aqueous environments. Humic components display contrasting molecular motional behavior and may be spatially segregated on a scale of nanometers. Within this new structural context, these components comprise any molecules intimately associated with a humic substance, such that they cannot be separated effectively by chemical or physical methods. Thus biomolecules strongly bound within humic fractions are by definition humic components, a conclusion that necessarily calls into question key biogeochemical pathways traditionally thought to be required for the formation of humic substances. Further research is needed to elucidate the intermolecular interactions that link humic components into supramolecular associations and to establish the pathways by which these associations emerge from the degradation of organic litter.

  20. 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.

  1. The Fermi bubbles as starburst wind termination shocks

    NASA Astrophysics Data System (ADS)

    Lacki, Brian C.

    2014-10-01

    The enhanced star formation in the inner 100 pc of the Galaxy launches a superwind at ˜1600 km s-1 for M82-like parameters. The ram pressure of the wind is very low compared to more powerful starburst winds. I show that halo gas stops the wind a few kpc from the Galactic Centre. I suggest that the termination shock accelerates cosmic rays, and that the resulting inverse Compton γ-rays are visible as the Fermi bubbles. The bubbles are then wind bubbles, which the starburst can inflate within 10 Myr. They can remain in steady state as long as the starburst lasts. The shock may accelerate PeV electrons and EeV protons. The bubbles may be analogues of galactic wind termination shocks in the intergalactic medium. I discuss the advantages and problems of this model. I note that any jets from Sgr A* must burrow through the starburst wind bubble before reaching the halo gas, which could affect the early evolution of such jets.

  2. The Starburst-AGN Connection under the Multiwavelength Limelight

    NASA Astrophysics Data System (ADS)

    Guainazzi, Matteo

    2011-11-01

    Since the discovery of a tight relation between supermassive black hole masses, the bulge luminosity, and the stellar velocity dispersion in the local universe galaxies, mounting experimental evidence has been collected pointing to a connection between nuclear activity and star formation over a wide range of redshifts. Although a growing number of galaxies from different samples exhibit simultaneous starburst and AGN phenomenology, it is still a matter of debate whether this is the smoking gun of a causal relation between them, and, if so, with which trend. Basic issues in modern astrophysics, such as the evolution of galaxies and supermassive black holes, AGN feeding and feedback to the interstellar and intergalactic medium, as well as the role played by the environment on the star formation history are related to this "Starburst-AGN Connection". This Workshop aims at gathering observational and theoretical astronomers so as to answer the following questions: * The "Starburst-AGN Connection": A causal relation? * "Starburst-AGN Connection" at low and high redshift: any evidence for evolution? * Is there a connection between AGN obscuration and star formation? * In which way are the star formation and AGN phenomena affected by the environment? * Do stars contribute to AGN fueling? Multiwavelength observations in the last decade have given a paramount contribution to improve our understanding in this field. The Workshop will build on this panoptic view, and aims at contributing to the scientific case of future ground-based and space large observatories.

  3. Unveil the Nature of Post-Starburst Quasars

    NASA Astrophysics Data System (ADS)

    Shang, Zhaohui; Brotherton, Michael; Cales, Sabrina; Canalizo, Gabriella; Dale, Daniel; Ganguly, Rajib; Hines, Dean

    2006-05-01

    We propose to obtain mid-IR spectra of 16 spectroscopically selected post-starburst quasars in order to fully characterize the properties of this new class. Post-starburst quasars are broad-lined AGN that also posses the spectral signatures of massive, moderate-aged stellar populations (in excess of ten billion solar masses and ages of hundreds of Myrs). This class represents several percent of the quasar population and may explicitly reveal how black hole/bulge correlations arise. We will compare their mid-IR SED and possible PAH features with other classes. The current project, which will also incorporate HST, SDSS, IRTF, KPNO and Keck data, will for the first time determine reliably for a sample of objects the properties of the massive starbursts (ages, masses), their black holes mass, accretion rate, morphologies, environments, and the relationships among these. Beyond just characterizing the properties of these populations, we plan to investigate the hypothesis that post-starburst quasars are an evolutionary phase in the lifetime of most quasars.

  4. 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"

  5. Multi-Wavelength Diagnostics of Starbirth in Starbursts

    NASA Astrophysics Data System (ADS)

    Waller, William

    2005-07-01

    From the Orion Nebula to the Hubble Deep Field, starburst activity can be seen transforming galaxian clouds of gas into populous clusters of stars. The pyrotechnics and chemical enrichment associated with this activity have led to outcomes as ubiquitous as interstellar dust and as exquisite as life on Earth. In this talk, I will focus on the circumstances of star formation in the environmental context of ongoing starburst activity. I begin with the premises that (1) the formation of a single star takes time, (2) the formation of a populous cluster takes even more time, and (3) ``stuff'' happens in the interim. Hubble images of the Orion Nebula and Eagle Nebula show how hot stars can excavate neighboring clouds of gas and photoevaporate the star-forming cores that are exposed. Hubble observations of giant HII regions in M33 reveal a significant variation in the stellar populations, such that the most metal-rich HII regions contain the greatest proportions of the most massive stars. ISO and Spitzer observations of these same HII regions reveal corresponding variations in the nebular response. These multi-wavelength diagnostics of the stellar-nebular feedback in galaxian starbursts suggest a star-forming mechanism which is subject to photo-evaporative ablation -- an erosive process that is mediated by the metal abundance and corresponding amounts of protective dust in the starbursting environment.

  6. 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.

  7. Starburst in the Intragroup Medium of Stephan's Quintet

    NASA Technical Reports Server (NTRS)

    Xu, C.; Tuffs, R.

    1998-01-01

    Based on new ISO mid-infrared observations and ground based H(alpha) and near-infrared observations, we report the detection of a bright starburst in the intragroup medium (IGM) of the famous compact group of galaxies Stephan's Quintet.

  8. Structural and Molecular Modeling Features of P2X Receptors

    PubMed Central

    Alves, Luiz Anastacio; da Silva, João Herminio Martins; Ferreira, Dinarte Neto Moreira; Fidalgo-Neto, Antonio Augusto; Teixeira, Pedro Celso Nogueira; de Souza, Cristina Alves Magalhães; Caffarena, Ernesto Raúl; de Freitas, Mônica Santos

    2014-01-01

    Currently, adenosine 5′-triphosphate (ATP) is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors. PMID:24637936

  9. Application of machine learning to structural molecular biology.

    PubMed

    Sternberg, M J; King, R D; Lewis, R A; Muggleton, S

    1994-06-29

    A technique of machine learning, inductive logic programming implemented in the program GOLEM, has been applied to three problems in structural molecular biology. These problems are: the prediction of protein secondary structure; the identification of rules governing the arrangement of beta-sheets strands in the tertiary folding of proteins; and the modelling of a quantitative structure activity relationship (QSAR) of a series of drugs. For secondary structure prediction and the QSAR, GOLEM yielded predictions comparable with contemporary approaches including neural networks. Rules for beta-strand arrangement are derived and it is planned to contrast their accuracy with those obtained by human inspection. In all three studies GOLEM discovered rules that provided insight into the stereochemistry of the system. We conclude machine learning used together with human intervention will provide a powerful tool to discover patterns in biological sequences and structures. PMID:7800706

  10. Dense gas in nearby galaxies. XIII. CO submillimeter line emission from the starburst galaxy M 82

    NASA Astrophysics Data System (ADS)

    Mao, R. Q.; Henkel, C.; Schulz, A.; Zielinsky, M.; Mauersberger, R.; Störzer, H.; Wilson, T. L.; Gensheimer, P.

    2000-06-01

    12CO J = 1-0, 2-1, 4-3, 7-6, and 13CO 1-0, 2-1, and 3-2 line emission was mapped with angular resolutions of 13'' - 22'' toward the nuclear region of the archetypical starburst galaxy M 82. There are two hotspots on either side of the dynamical center, with the south-western lobe being slightly more prominent. Lobe spacings are not identical for all transitions: For the submillimeter CO lines, the spacing is ~ 15''; for the millimeter lines (CO J = 2-1 and 1-0) the spacing is ~ 26'', indicating the presence of a `low' and a `high' CO excitation component. A Large Velocity Gradient (LVG) excitation analysis of the submillimeter lines leads to inconsistencies, since area and volume filling factors are almost the same, resulting in cloud sizes along the lines-of-sight that match the entire size of the M 82 starburst region. Nevertheless, LVG column densities agree with estimates derived from the dust emission in the far infrared and at submillimeter wavelengths. 22'' beam averaged total column densities are N(CO) ~ 5 1018 and N(H_2) ~ 1023 \\cmsq; the total molecular mass is a few 108 \\solmass. Accounting for high UV fluxes and variations in kinetic temperature and assuming that the observed emission arises from photon dominated regions (PDRs) resolves the problems related to an LVG treatment of the radiative transfer. Spatial densities are as in the LVG case (\

  11. Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

    PubMed Central

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E.

    2014-01-01

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand the structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as means to sample conformational space for a better understanding of the relevance of a given model. From this discussion, the major limitations with modeling, in general, were highlighted. These are the difficult issues in sampling conformational space effectively—the multiple minima or conformational sampling problems—and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These are discussed in detail in this unit. PMID:18428877

  12. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    PubMed

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-01-01

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. PMID:25631536

  13. Prediction of reactive hazards based on molecular structure.

    PubMed

    Saraf, S R; Rogers, W J; Mannan, M S

    2003-03-17

    There is considerable interest in prediction of reactive hazards based on chemical structure. Calorimetric measurements to determine reactivity can be resource consuming, so computational methods to predict reactivity hazards present an attractive option. This paper reviews some of the commonly employed theoretical hazard evaluation techniques, including the oxygen-balance method, ASTM CHETAH, and calculated adiabatic reaction temperature (CART). It also discusses the development of a study table to correlate and predict calorimetric properties of pure compounds. Quantitative structure-property relationships (QSPR) based on quantum mechanical calculations can be employed to correlate calorimetrically measured onset temperatures, T(o), and energies of reaction, -deltaH, with molecular properties. To test the feasibility of this approach, the QSPR technique is used to correlate differential scanning calorimeter (DSC) data, T(o) and -deltaH, with molecular properties for 19 nitro compounds. PMID:12628775

  14. 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. PMID:18158914

  15. Molecular structure by two-dimensional NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Freeman, R.

    Two examples are presented of the use of two-dimensional NMR spectroscopy to solve molecular structure problems. The first is called correlation spectroscopy (COSY) and it allows us to disentangle a complex network of spin-spin couplings. By dispersing the NMR information in two frequency dimensions, it facilitates the analysis of very complex spectra of organic and biochemical molecules, normally too crowded to be tractable. The second application exploits the special properties of multiple-quantum coherence to explore the molecular framework one CC linkage at a time. The natural product panamine is used as a test example; with some supplementary evidence, the structure of this six-ringed heterocyclic molecule is elucidated from the double-quantum filtered two-dimensional spectrum.

  16. Advances in multimodality molecular imaging of bone structure and function

    PubMed Central

    Lambers, Floor M; Kuhn, Gisela; Müller, Ralph

    2012-01-01

    The skeleton is important to the body as a source of minerals and blood cells and provides a structural framework for strength, mobility and the protection of organs. Bone diseases and disorders can have deteriorating effects on the skeleton, but the biological processes underlying anatomical changes in bone diseases occurring in vivo are not well understood, mostly due to the lack of appropriate analysis techniques. Therefore, there is ongoing research in the development of novel in vivo imaging techniques and molecular markers that might help to gain more knowledge of these pathological pathways in animal models and patients. This perspective provides an overview of the latest developments in molecular imaging applied to bone. It emphasizes that multimodality imaging, the combination of multiple imaging techniques encompassing different image modalities, enhances the interpretability of data, and is imperative for the understanding of the biological processes and the associated changes in bone structure and function relationships in vivo. PMID:27127622

  17. 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. PMID:17661440

  18. Toxicological implications of esterases-From molecular structures to functions

    SciTech Connect

    Satoh, Tetsuo . E-mail: satohbri@peach.ifnet.or.jp

    2005-09-01

    This article reports on a keynote lecture at the 10th International Congress of Toxicology sponsored by the International Union of Toxicology and held on July 2004. Current developments in molecular-based studies into the structure and function of cholinesterases, carboxylesterases, and paraoxonases are described. This article covers mechanisms of regulation of gene expression of the various esterases by developmental factors and xenobiotics, as well as the interplay between physiological and chemical regulation of the enzyme activity.

  19. 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.

  20. Optimization techniques in molecular structure and function elucidation.

    PubMed

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems. PMID:20160866

  1. 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

  2. The crystal and molecular structure of triethanol-ammonium nitrate

    NASA Astrophysics Data System (ADS)

    Bracuti, A. J.

    1992-12-01

    The liquid propellant used in the 155-mm regenerative liquid propellant gun is XM46. XM46 is a solution of 60 percent hydroxyl ammonium nitrate (HAN), 20 percent triethanolammonium nitrate (TEAN), and 20 percent water. This material exhibits rather unusual liquid properties that have been attributed to its being a 'molten eutectic' of fused salts rather than a normal aqueous solution of two different nitrate salts. A hydrogen-bonded liquid structure for eutectic LP1946 was proposed previously based on the known structures of neat HAN and water and a best-guess estimate of the TEAN structure. To verify this estimate, the molecular structure of neat TEAN was recently determined. This investigation revealed TEAN has very unusual and interesting bifurcated intermolecular and trifurcated intramolecular hydrogen bonding configurations within the crystal. If these hydrogen bonding configurations are retained in aqueous solution, they could be responsible in some part to the observed unusual liquid properties of liquid propellant XM46.

  3. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  4. 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

  5. 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.

  6. Efficient Transfer of Genetic Material into Mammalian Cells Using Starburst Polyamidoamine Dendrimers

    NASA Astrophysics Data System (ADS)

    Kukowska-Latallo, Jolanta F.; Bielinska, Anna U.; Johnson, Jennifer; Spindler, Ralph; Tomalia, Donald A.; Baker, James R.

    1996-05-01

    Starburst polyamidoamine dendrimers are a new class of synthetic polymers with unique structural and physical characteristics. These polymers were investigated for the ability to bind DNA and enhance DNA transfer and expression in a variety of mammalian cell lines. Twenty different types of polyamidoamine dendrimers were synthesized, and the polymer structure was confirmed using well-defined analytical techniques. The efficiency of plasmid DNA transfection using dendrimers was examined using two reporter gene systems: firefly luciferase and bacterial β -galactosidase. The transfections were performed using various dendrimers, and levels of expression of the reporter protein were determined. Highly efficient transfection of a broad range of eukaryotic cells and cell lines was achieved with minimal cytotoxicity using the DNA/dendrimer complexes. However, the ability to transfect cells was restricted to certain types of dendrimers and in some situations required the presence of additional compounds, such as DEAE-dextran, that appeared to alter the nature of the complex. A few cell lines demonstrated enhanced transfection with the addition of chloroquine, indicating endosomal localization of the complexes. The capability of a dendrimer to transfect cells appeared to depend on the size, shape, and number of primary amino groups on the surface of the polymer. However, the specific dendrimer most efficient in achieving transfection varied between different types of cells. These studies demonstrate that Starburst dendrimers can transfect a wide variety of cell types in vitro and offer an efficient method for producing permanently transfected cell lines.

  7. Triggering and Feedback: The Relation between the H I Gas and the Starburst in the Dwarf Galaxy NGC 1569

    NASA Astrophysics Data System (ADS)

    Mühle, S.; Klein, U.; Wilcots, E. M.; Hüttemeister, S.

    2005-08-01

    As part of our study on the impact of violent star formation on the interstellar medium (ISM) of dwarf galaxies, we report observations of neutral atomic hydrogen (H I) in the starburst dwarf galaxy NGC 1569. High-resolution measurements with the Very Large Array (B, C, and D configuration) are aimed at identifying morphological and kinematical signatures in H I caused by the starburst. Our kinematical data suggest a huge hole in the H I distribution, probably due to the large number of supernovae explosions in the center of the galaxy over the past 20 Myr. Investigating the large-scale H I structure, we confirm the existence of a possible H I companion and a so-called H I bridge east of NGC 1569. Furthermore, we report the detection of additional low-intensity H I halo emission, which leads us to suggest a revised halo structure. On the basis of our new picture, we discuss the origin of the halo gas and possible implications for the evolution of the starburst in NGC 1569.

  8. SYNCHRONIZED FORMATION OF STARBURST AND POST-STARBURST GALAXIES IN MERGING CLUSTERS OF GALAXIES

    SciTech Connect

    Bekki, Kenji; Owers, Matt S.; Couch, Warrick J.

    2010-07-20

    We propose that synchronized triggering of star formation in gas-rich galaxies is possible during major mergers of cluster of galaxies, based on new numerical simulations of the time evolution of the physical properties of the intracluster medium (ICM) during such a merger event. Our numerical simulations show that the external pressure of the ICM, in which cluster member galaxies are embedded, can increase significantly during cluster merging. As such, efficient star formation can be triggered in gas-rich members as a result of the strong compression of their cold gas by the increased pressure. We also suggest that these star-forming galaxies can subsequently be transformed into post-starburst galaxies, with their spatial distribution within the cluster being different than that of the rest of the population. We discuss whether this possible merger-induced enhancement in the number of star-forming and post-star-forming cluster galaxies is consistent with the observed evolution of galaxies in merging clusters.

  9. Filamentary Structure in Orion and Monoceros Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Lahaise, W. H.; Bhavsar, S. P.

    1994-05-01

    The filamentary structure in 13CO radio maps of the Orion A, Orion B and Monoceros R2 molecular clouds was analyzed using the Minimal Spanning Tree. This represents the first time the MST has been applied to an extended region such as maps of molecular clouds. The method of preparing and analyzing the data is presented. Integrated maps over a range of velocities were examined as well as a velocity cube constructed from individual 0.5 km s-1 wide channel maps. The results show that there is overwhelming objective and statistical evidence that the filamentary structure does exist in all three of these regions. Previous techniques to identify filaments were generally visual, and therefore subjective. The major filaments in Orion A show linear features extending throughout the entire length. The structure in the velocity cube clearly shows the continuous velocity gradient. Orion B cloud shows distinct regions with north to south orientations. The velocity cube contains a number of filaments at greatly differing velocities, with little evidence of large scale velocity gradients. Mon R2 cloud exhibits two main filamentary components, one of which is associated with both bright condensed regions. The velocity structure reveals an overall velocity gradient.

  10. 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.

  11. 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

  12. The Nature of Starburst Activity in M82

    NASA Astrophysics Data System (ADS)

    Förster Schreiber, N. M.; Genzel, R.; Lutz, D.; Sternberg, A.

    2003-12-01

    We present new evolutionary synthesis models of M82 based mainly on observations consisting of near-infrared integral field spectroscopy and mid-infrared spectroscopy. The models incorporate stellar evolution, spectral synthesis, and photoionization modeling and are optimized forλ=1-45 μm observations of starburst galaxies. The data allow us to model the starburst regions on scales as small as 25 pc. We investigate the initial mass function (IMF) of the stars and constrain quantitatively the spatial and temporal evolution of starburst activity in M82. We find a typical decay timescale for individual burst sites of a few million years. The data are consistent with the formation of very massive stars (>~50-100 Msolar) and require a flattening of the starburst IMF below a few solar masses, assuming a Salpeter slope dN/dm~m-2.35 at higher masses. Our results are well matched by a scenario in which the global starburst activity in M82 occurred in two successive episodes each lasting a few million years, peaking about 107 yr and 5×106yr ago. The first episode took place throughout the central regions of M82 and was particularly intense at the nucleus, while the second episode occurred predominantly in a circumnuclear ring and along the stellar bar. We interpret this sequence as resulting from the gravitational interaction between M82 and its neighbor M81, and subsequent bar-driven evolution. The short burst duration on all spatial scales indicates strong negative feedback effects of starburst activity, both locally and globally. Simple energetics considerations suggest that the collective mechanical energy released by massive stars was able to rapidly inhibit star formation after the onset of each episode. 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 United Kingdom) and with the participation of ISAS and NASA. The SWS is a joint project of SRON and

  13. 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. PMID:25871768

  14. 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.

  15. 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.

  16. The Filamentary Structure of the Lupus 3 Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Benedettini, Milena

    We present the column density map of the Lupus 3 molecular cloud derived from the Herschel photometric maps. We compared the Herschel continuum maps, tracing the dense and cold dust emission, with the CS (2-1) map observed with the Mopra 22-m antenna, tracing the dense gas. Both the continuum and the CS maps show a well defined filamentary structure, with most of the dense cores being on the filaments. The CS (2-1) line shows a double peak in the central part of the longest filament due to the presence of two distinct gas components along this line of sight. Therefore, what seems a single filament in the Herschel map is actually the overlap of two kinematically distinct filaments. This case clearly shows that kinematical information is essential for the correct interpretation of filaments in molecular clouds.

  17. Molecular structure and pathophysiological roles of the Mitochondrial Calcium Uniporter.

    PubMed

    Mammucari, Cristina; Raffaello, Anna; Vecellio Reane, Denis; Rizzuto, Rosario

    2016-10-01

    Mitochondrial Ca(2+) uptake regulates a wide array of cell functions, from stimulation of aerobic metabolism and ATP production in physiological settings, to induction of cell death in pathological conditions. The molecular identity of the Mitochondrial Calcium Uniporter (MCU), the highly selective channel responsible for Ca(2+) entry through the IMM, has been described less than five years ago. Since then, research has been conducted to clarify the modulation of its activity, which relies on the dynamic interaction with regulatory proteins, and its contribution to the pathophysiology of organs and tissues. Particular attention has been placed on characterizing the role of MCU in cardiac and skeletal muscles. In this review we summarize the molecular structure and regulation of the MCU complex in addition to its pathophysiological role, with particular attention to striated muscle tissues. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou. PMID:26968367

  18. Molecular structures of carotenoids as predicted by MNDO-AM1 molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Hashimoto, Hideki; Yoda, Takeshi; Kobayashi, Takayoshi; Young, Andrew J.

    2002-02-01

    Semi-empirical molecular orbital calculations using AM1 Hamiltonian (MNDO-AM1 method) were performed for a number of biologically important carotenoid molecules, namely all- trans-β-carotene, all- trans-zeaxanthin, and all- trans-violaxanthin (found in higher plants and algae) together with all- trans-canthaxanthin, all- trans-astaxanthin, and all- trans-tunaxanthin in order to predict their stable structures. The molecular structures of all- trans-β-carotene, all- trans-canthaxanthin, and all- trans-astaxanthin predicted based on molecular orbital calculations were compared with those determined by X-ray crystallography. Predicted bond lengths, bond angles, and dihedral angles showed an excellent agreement with those determined experimentally, a fact that validated the present theoretical calculations. Comparison of the bond lengths, bond angles and dihedral angles of the most stable conformer among all the carotenoid molecules showed that the displacements are localized around the substituent groups and hence around the cyclohexene rings. The most stable conformers of all- trans-zeaxanthin and all- trans-violaxanthin gave rise to a torsion angle around the C6-C7 bond to be ±48.7 and -84.8°, respectively. This difference is a key factor in relation to the biological function of these two carotenoids in plants and algae (the xanthophyll cycle). Further analyses by calculating the atomic charges and using enpartment calculations (division of bond energies between component atoms) were performed to ascribe the cause of the different observed torsion angles.

  19. Structural and molecular modeling studies of quinazolinone anticonvulsants.

    PubMed

    Duke, N E; Codding, P W

    1993-08-01

    Studies of derivatives of the anticonvulsant methaqualone led to the discovery that unsaturation in the 2-substituent produced active but less toxic compounds; accordingly, 2-arylethanone derivatives have been developed. The crystal structures of five 2-arylethanone derivatives of methaqualone were determined to probe structure-activity relationships. Although these compounds display different activities, the solid-state and calculated structures are similar: each compound is observed as the neamine tautomer containing an intramolecular hydrogen bond between the ethanone and the amine N atom and the molecular conformations are the same. These studies conclude that recognition of the anticonvulsants arises from specific binding of an ortho substituent on the N(3) phenyl substituent, rather than from binding of a particular conformation or tautomeric form adopted by the compound containing an ortho substituent, and that such recognition is characteristic of a broad range of anticonvulsant drugs. Crystal data: [see text]. PMID:8397980

  20. 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.

  1. The molecular scale structure of water at interfaces

    NASA Astrophysics Data System (ADS)

    Salmeron, Miquel

    2004-03-01

    The molecular scale structure of water at surfaces and interfaces is an unresolved and fundamental topic in many areas of science and technology, and determines its wetting properties. In our studies of this very interesting topic we used scanning probes (STM, AFM), and electron and vibrational spectroscopies. STM studies on Pd(111) reveal that at low temperature (below 130K) water adsorbs as an intact molecule, forming clusters of dimers, trimers, etc. and finally H-bonded hexagonal structures with a V3xV3R30º periodicity. When the temperature is below 100K the O-H bonds in this structure are nearly parallel to the substrate except at the island edges where they point down towards the substrate or up leaving dangling bonds. Above 130K other structures form with molecules having unsaturated H bonds that point outwards from the surface and forming a superstructure of the V3xV3 structure. We have also studied the formation of dangling bonds in other water interfaces, including ice-vapor and on insulating substrates. On the ice surface, a thin layer exists that contains many H-dangling bonds near 0ºC. The thickness of this layer is less than a nanometer below -1ºC. On the basal plane of mica (an alumino silicate) water forms hexagonal structures with no unsaturated H-bonds and with the molecular dipole pointing on average towards the surface. On subsequent layers below 0ºC, the dipolar orientation persist and gives rise to ferroelectric ice. Above 0ºC however water layers above the first have free, unsaturated H-bonds pointing outwards from the surface as in the liquid form. On alkali halide surfaces water adsorbs preferentially at step edges at low humidity solvating the cations first. At higher humidity both cations and anions are solvated and finally, at deliquescence, when the salt dissolves, the anions segregate preferentially at the surface.

  2. Roles in Modulation of Molecular Structures on Metal Surfaces

    NASA Astrophysics Data System (ADS)

    Gao, H.-J.

    2007-03-01

    We studied the adsorption of organic molecules, their growth behavior, and their physical properties on silver and gold surfaces at the single molecule or sub-molecular scale by using low-temperature scanning tunneling microscopes. Combined with low energy electron diffraction and first-principles density functional theory calculations, the key parameters in modulating molecular structures on metals are analyzed. It is found that the alkyl chains of quinacridone derivatives (QA) determine the orientation of molecular overlayers on an Ag(110) substrate. The interaction of QA and the Ag substrate is primarily due to chemical bonding of oxygen to specific positions at the silver substrate, determining the molecular orientation and preferred adsorption site. However, the intermolecular arrangement can be adjusted via the length of attached alkyl chains. We are thus able to fabricate uniform QA films with very well controlled physical properties. Furthermore, by thermal and chemical control, we are able to self-assemble three dimensional molecular nanostructures, e.g. ordered PTCDA structures exclusively on flat Ag(111) facets, or DMe-DCNQI structures exclusively on stepped Ag(221) facets. It is demonstrated that bonding, the key factor for selectivity, occurs via the end-atoms, while the molecule's mid-region arches away from the substrate. Theoretical results, obtained by high-level theory, are consistent with the experimental observations, which have previously been interpreted in terms of bonding through the mid-region. In collaboration with D.X. Shi, S.X. Du, W. Ji, Z.T. Deng, L. Gao, Institute of Physics, and X. Lin, Chinese Academy of Sciences, China; C. Seidel and H. Fuchs, Universit"at M"unster, Germany; W.A. Hofer, The University of Liverpool, Britain; and S. T. Pantelides, Vanderbilt University, USA. [1] D.X. Shi et al., Phys. Rev. Lett. 96, 226101(2006). [2] S.X. Du et al., Phys. Rev. Lett. 96, 226101(2006). [3] L. Gao et al., Phys. Rev. B 73, 075424(2006).

  3. The interface of protein structure, protein biophysics, and molecular evolution

    PubMed Central

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  4. Quantum Theory of Atomic and Molecular Structures and Interactions

    NASA Astrophysics Data System (ADS)

    Makrides, Constantinos

    This dissertation consists of topics in two related areas of research that together provide quantum mechanical descriptions of atomic and molecular interactions and reactions. The first is the ab initio electronic structure calculation that provides the atomic and molecular interaction potential, including the long-range potential. The second is the quantum theory of interactions that uses such potentials to understand scattering, long-range molecules, and reactions. In ab initio electronic structure calculations, we present results of dynamic polarizabilities for a variety of atoms and molecules, and the long-range dispersion coefficients for a number of atom-atom and atom-molecule cases. We also present results of a potential energy surface for the triatomic lithium-ytterbium-lithium system, aimed at understanding the related chemical reactions. In the quantum theory of interactions, we present a multichannel quantum-defect theory (MQDT) for atomic interactions in a magnetic field. This subject, which is complex especially for atoms with hyperfine structure, is essential for the understanding and the realization of control and tuning of atomic interactions by a magnetic field: a key feature that has popularized cold atom physics in its investigations of few-body and many-body quantum systems. Through the example of LiK, we show how MQDT provides a systematic and an efficient understanding of atomic interaction in a magnetic field, especially magnetic Feshbach resonances in nonzero partial waves.

  5. 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.

  6. NGC1266: Compton-thick AGN or Ultra-compact Starburst?

    NASA Astrophysics Data System (ADS)

    Lanz, Lauranne; Alatalo, Katherine A.; Brightman, Murray; Ogle, Patrick M.; Appleton, Philip N.

    2016-01-01

    NGC1266 is a nearby lenticular galaxy hosting a massive molecular outflow driven by its active galactic nucleus (AGN). The turbulence injected into its ISM by the outflow may account for the suppression of its star formation by a factor of 50-150. ALMA and CARMA measurements of dense gas tracers had shown that its nuclear region lies behind a column of N(H2) = 3 x 10^24 cm^-2, and ALMA barely resolved a region of continuum FIR emission contained within 30pc of the nucleus emitting L(IR)>10^10 solar luminosities. With out recent NuSTAR observation of this galaxies, we determine whether the dust is heated by a Compton-thick AGN or an ultra-compact central starburst.

  7. 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

  8. 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

  9. 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.

  10. [Cardiac potassium channels: molecular structure, physiology, pathophysiology and therapeutic implications].

    PubMed

    Mironov, N Iu; Golitsyn, S P

    2013-01-01

    Potassium channels and currents play essential roles in cardiac repolarization. Potassium channel blockade by class III antiarrhythmic drugs prolongs cardiac repolarization and results in termination and prevention of cardiac arrhythmias. Excessive inhomogeneous repolarization prolongation may lead to electrical instability and proarrhythmia (Torsade de Pointes tachycardia). This review focuses on molecular structure, physiology, pathophysiology and therapeutic potential of potassium channels of cardiac conduction system and myocardium providing information on recent findings in pathogenesis of cardiac arrhythmias, including inherited genetic abnormalities, and future perspectives. PMID:24654438

  11. Starbursts and Wispy Drops : Surfactants Spreading on Gel Substrates

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Shomeek; Daniels, Karen; Behringer, Robert

    2005-11-01

    We report a phase diagram for a novel instability seen in drops of nonionic surfactant solution (Triton X-305) spreading on viscoelastic agar gel substrate . This system allows us to examine the effect of varying the effective fluidity/stiffness of aqueous substrates. The morphology is strongly affected by the substrate fluidity, ranging from spreading starbursts of arms on weak gels, to wispy drops on intermediate strength gels, to circular drops on stiff gels. We analyze the dynamics of spreading in the starburst phase, where the arm length grows as t ^3/4 at early times, independent of the gel strength and surfactant concentration. The number of arms is proportional to the surfactant concentration and inversely proportional to the gel strength. Ongoing work is exploring the effects of changing the drop volume.

  12. 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.

  13. Structural Assembly of Molecular Complexes Based on Residual Dipolar Couplings

    PubMed Central

    Berlin, Konstantin; O’Leary, Dianne P.; Fushman, David

    2010-01-01

    We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDC) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein-protein complex by utilizing the RDC’s sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein-protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein-protein complex based solely on experimental RDC data and the prediction of the alignment tensor from three-dimensional structures. Thus, despite the purely angular nature of residual dipolar couplings, they can be converted into intermolecular distance/translational constraints. Additionally we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of the protein complexes. PMID:20550109

  14. 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.

  15. The stellar populations in the earliest dusty starburst galaxies

    NASA Astrophysics Data System (ADS)

    Wardlow, Julie; Conley, Alexander; Perez-Fournon, Ismael; Cooray, Asantha; Riechers, Dominik; Dannerbauer, Helmut; Farrah, Duncan; Omont, Alain

    2014-12-01

    We propose Spitzer IRAC imaging of the two brightest spectroscopically confirmed dusty starburst galaxies at z>4 that do not yet have mid-IR observations. The targeted galaxies are members of a rare class of Herschel sources that provide some of the most stringent constraints on galaxy formation theories. The two targets already have complementary optical and far-IR observations, and the proposed short IRAC data are all that is missing to ~double the number of confirmed z>4 dusty starbursts with well-sampled stellar SEDs. The IRAC data are critical for deriving accurate measurements of physical conditions such as dust extinction and stellar mass to ~30% accuracy (~10x better than otherwise). The proposed data complete the IRAC coverage of the four most luminous confirmed z>4 dusty starburst galaxies, which will be observed with HST in cycle 22. The targets already have CO observations and their [CII] 158 micron emission is being mapped with ALMA in cycle 2; with the addition of the proposed IRAC data we will be able to probe the dust-to-gas and stellar-to-gas mass ratios at the highest redshifts and in the most active galaxies. The IRAC data are also key to determining whether these highest redshift dusty starbursts are markers of overdensities in the early Universe via photometric dropout searches. By probing the details of star-formation in the most extreme sources in the first 1.5 Gyr of the Universe the proposed observations will critically test theories of galaxy formation and evolution.

  16. 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.

  17. 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

  18. Molecular structural order and anomalies in liquid silica.

    PubMed

    Shell, M Scott; Debenedetti, Pablo G; Panagiotopoulos, Athanassios Z

    2002-07-01

    The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends recently reported for water [J. R. Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate densities, the distribution of local orientational order is bimodal. At fixed temperature, order parameter extrema occur upon compression: a maximum in orientational order followed by a minimum in translational order. Unlike water, however, silica's translational order parameter minimum is broad, and there is no range of thermodynamic conditions where both parameters are strictly coupled. Furthermore, the temperature-density regime where both structural order parameters decrease upon isothermal compression (the structurally anomalous regime) does not encompass the region of diffusivity anomalies, as was the case for water. PMID:12241346

  19. Structure-Directed Exciton Dynamics in Templated Molecular Nanorings

    PubMed Central

    2015-01-01

    Conjugated polymers with cyclic structures are interesting because their symmetry leads to unique electronic properties. Recent advances in Vernier templating now allow large shape-persistent fully conjugated porphyrin nanorings to be synthesized, exhibiting unique electronic properties. We examine the impact of different conformations on exciton delocalization and emission depolarization in a range of different porphyrin nanoring topologies with comparable spatial extent. Low photoluminescence anisotropy values are found to occur within the first few hundred femtoseconds after pulsed excitation, suggesting ultrafast delocalization of excitons across the nanoring structures. Molecular dynamics simulations show that further polarization memory loss is caused by out-of-plane distortions associated with twisting and bending of the templated nanoring topologies. PMID:25960822

  20. Surfaces of Microparticles in Colloids: Structure and Molecular Adsorption Kinetics

    NASA Astrophysics Data System (ADS)

    Dai, Hai-Lung

    2002-03-01

    Surfaces of micron and sub-micron size particles in liquid solution are probed by second harmonic generation (SHG) facilitated with femtosecond laser pulses. The particles probed include inorganic objects such as carbon black and color pigments, polymeric species like polystyrene beads, and biological systems such as blood cells and ecoli. In the experiments, dye molecules are first adsorbed onto the particle surface to allow generation of second harmonics upon light irradiation. Competition for adsorption between these surface dye molecules and the molecules of interest in the solution is then monitored by the SHG signal to reveal the molecular adsorption kinetics and surface structure. Specifically, surfactant adsorption on polymer surfaces, the structure of carbon black surface, and protein adsorption on biological surfaces, monitored by this technique, will be discussed.

  1. Molecular structure of uranium carbides: Isomers of UC3

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    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.

  2. 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. PMID:23534639

  3. 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.

  4. 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. PMID:26627128

  5. Molecular studies of the structural ecology of natural occlusal caries.

    PubMed

    Dige, Irene; Grønkjær, Lene; Nyvad, Bente

    2014-01-01

    Microbiological studies of occlusal dental biofilms have hitherto been hampered by inaccessibility to the sampling site and demolition of the original biofilm architecture. This study shows for the first time the spatial distribution of bacterial taxa in vivo at various stages of occlusal caries, applying a molecular methodology involving preparation of embedded hard dental tissue slices for fluorescence in situ hybridization (FISH) and confocal microscopy. Eleven freshly extracted teeth were classified according to their occlusal caries status. The teeth were fixed, embedded, sectioned and decalcified before FISH was performed using oligonucleotide probes for selected abundant species/genera associated with occlusal caries including Streptococcus, Actinomyces, Veillonella, Fusobacterium, Lactobacillus and Bifidobacterium. The sites showed distinct differences in the bacterial composition between different ecological niches in occlusal caries. Biofilm observed along the entrance of fissures showed an inner layer of microorganisms organized in palisades often identified as Actinomyces, covered by a more loosely structured bacterial layer consisting of diverse genera, similar to supragingival biofilm. Biofilm within the fissure proper seemed less metabolically active, as judged by low fluorescence signal intensity and presence of material of non-bacterial origin. Bacterial invasion (often Lactobacillus and Bifidobacterium spp.) into the dentinal tubules was seen only at advanced stages of caries with manifest cavity formation. It is concluded that the molecular methodology represents a valuable supplement to previous methods for the study of microbial ecology in caries by allowing analysis of the structural composition of the undisturbed biofilm in caries lesions in vivo. PMID:24852305

  6. 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. PMID:19414173

  7. Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

    PubMed Central

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

    2013-01-01

    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

  8. 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.

  9. 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'…

  10. Molecular Modeling and Structural Analysis of Arylesterase of Ancylostoma Duodenale

    PubMed Central

    Panda, Subhamay; Panda, Santamay; Kumari, Leena

    2016-01-01

    Parasitic worm infection of humans is one of the most commonly prevalent helminth infection that has imposed great impact on society and public health in the developing world. The two species of hookworm, namely Ancylostoma duodenale and Necator americanus may be primarily responsible for causing parasitic infections in human beings. The highly prevalent areas for Ancylostoma duodenale infections are mainly India, Middle East, Australia, northern Africa and other parts of the world. The serum arylesterases/paraoxonases are family of enzymes that is involved in the hydrolysis of a number of organophosphorus insecticides to the nontoxic products. The participation of the enzymes in the breakdown of a variety of organophosphate substrates that is generally made up of paraoxon and numerous aromatic carboxylic acid esters (e.g., phenyl acetate), and hence combats the toxic effect of organophosphates. The aim of the present investigation is to evaluate the arylesterases of Ancylostoma duodenale giving special importance to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure. By the implementation of comparative modeling approach we propose the first molecular model structure of arylesterases of Ancylostoma duodenale.

  11. Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

    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.

  12. 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.

  13. 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.

  14. Structure of Lambda Hypernuclei with Antisymmetrized Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Isaka, Masahiro

    2014-09-01

    In this talk, we will discuss the structure change caused by a Λ particle and structure of neutron-rich (n-rich) and sd shell Λ hypernuclei based on the antisymmetrized molecular dynamics (AMD). One of the unique and interesting aspects of hypernuclei is structure change caused by a hyperon(s) as an impurity in nuclei. In light Λ hypernuclei, experimental and theoretical studies have revealed a couple of interesting structure changes such as shrinkage of the inter-cluster distance. In n-rich and sd shell Λ hypernuclei, it is expected that the variety of structure and structure changes will appear in the low energy regions, because n-rich and sd shell nuclei have various structures. For example, the n-rich nucleus 11Be has the parity-inverted ground-state 1/2+, which is inconsistent with the ordinary shell model picture. In sd shell nuclei, it has been discussed that various deformations appear in the ground and low-lying states. For example, 24Mg is a candidate of triaxially deformed nuclei with the presence of the low-lying 2nd 2+ state. To reveal the structure of the corresponding Λ hypernuclei, we have extended the AMD model for hypernuclei (HyperAMD) and applied it to n-rich and sd shell Λ hypernuclei. The AMD model can describe various nuclear structures without assumptions on clustering and symmetry of nuclear deformations. Combined with the generator coordinate method (GCM), the HyperAMD model succeeded to describe the low-lying structure of p-sd shell Λ hypernuclei. In this study, we investigate several n-rich and sd shell Λ hypernuclei such as Λ12Be and Λ25Mg. In this talk, we will discuss the changes of the parity-inverted ground state of 11Be by adding a Λ particle. Furthermore, in Λ25Mg, we will discuss a possibility to identify the nuclear (triaxial) deformation of Mg by using Λ as a probe.

  15. FORMALDEHYDE DENSITOMETRY OF STARBURST GALAXIES: DENSITY-INDEPENDENT GLOBAL STAR FORMATION

    SciTech Connect

    Mangum, Jeffrey G.; Darling, Jeremy; Henkel, Christian; Menten, Karl M. E-mail: jdarling@origins.colorado.edu E-mail: kmenten@mpifr-bonn.mpg.de

    2013-04-01

    Accurate techniques that allow for the derivation of the spatial density in star formation regions are rare. A technique that has found application for the derivation of spatial densities in Galactic star formation regions utilizes the density-sensitive properties of the K-doublet transitions of formaldehyde (H{sub 2}CO). In this paper, we present an extension of our survey of the formaldehyde 1{sub 10}-1{sub 11} ({lambda} = 6.2 cm) and 2{sub 11}-2{sub 12} ({lambda} = 2.1 cm) K-doublet transitions of H{sub 2}CO in a sample of 56 starburst systems. We have extended the number of galaxies in which both transitions have been detected from 5 to 13. We have improved our spatial density measurements by incorporating kinetic temperatures based upon NH{sub 3} measurements of 11 of the galaxies with a total of 14 velocity components in our sample. Our spatial density measurements lie in a relatively narrow range from 10{sup 4.5} to 10{sup 5.5} cm{sup -3}. This implies that the Schmidt-Kennicutt relation between L{sub IR} and M{sub dense} (1) is an indication of the dense gas mass reservoir available to form stars and (2) is not directly dependent upon a higher average density driving the star formation process in the most luminous starburst galaxies. We have also used our H{sub 2}CO measurements to derive two separate measures of the dense gas mass which are generally smaller, in many cases by a factor of 10{sup 2}-10{sup 3}, than those derived using HCN. This disparity suggests that H{sub 2}CO traces a denser, more compact component of the giant molecular clouds in our starburst galaxy sample. We also report measurements of the rotationally excited {lambda} = 6.3 cm {sup 2}{Pi}{sub 1/2} J = 1/2 state of OH and the H111{alpha} radio recombination line taken concurrently with our H{sub 2}CO 1{sub 10}-1{sub 11} measurements.

  16. Unveiling the molecular mechanism of brassinosteroids: Insights from structure-based molecular modeling studies.

    PubMed

    Lei, Beilei; Liu, Jiyuan; Yao, Xiaojun

    2015-12-01

    Brassinosteroid (BR) phytohormones play indispensable roles in plant growth and development. Brassinolide (BL) and 24-epibrassinolide (24-epiBL) are the most active ones among the BRs reported thus far. Unfortunately, the extremely low natural content and intricate synthesis process limit their popularization in agricultural production. Earlier reports to discover alternative compounds have resulted in molecules with nearly same scaffold structure and without diversity in chemical space. In the present study, receptors structure based BRs regulation mechanism was analyzed. First, we examined the detailed binding interactions and their dynamic stability between BL and its receptor BRI1 and co-receptor BAK1. Then, the binding modes and binding free energies for 24-epiBL and a series of representative BRs binding with BRI1 and BRI1-BAK1 were carried out by molecular docking, energy minimization and MM-PBSA free energy calculation. The obtained binding structures and energetic results provided vital insights into the structural factors affecting the activity from both receptors and BRs aspects. Subsequently, the obtained knowledge will serve as valuable guidance to build pharmacophore models for rational screening of new scaffold alternative BRs. PMID:26362600

  17. Evolution of M82-like starburst winds revisited: 3D radiative cooling hydrodynamical simulations

    NASA Astrophysics Data System (ADS)

    Melioli, C.; de Gouveia Dal Pino, E. M.; Geraissate, F. G.

    2013-04-01

    In this study we present three-dimensional radiative cooling hydrodynamical simulations of galactic winds generated particularly in M82-like starburst galaxies. We have considered intermittent winds induced by supernova (SN) explosions within super star clusters randomly distributed (in space and time) in the central region of the galaxy (within a radius of R = 150 pc) and were able to reproduce the observed M82 wind conditions with its complex morphological outflow structure. We have found that the environmental conditions in the disc in the nearly recent past are crucial to determine whether the wind will develop a large-scale rich filamentary structure, as in M82 wind, or not. If a sufficiently large number of super stellar clusters are built up in a starburst mainly over a period of a few million years, then the simulations reproduce the multiphase gas observed in M82-like winds, i.e. with filaments of sizes about 20-300 pc, velocities of ˜200-500 km s-1, densities in the range 10-1-10 cm-3, embedded in a hot, low-density gas with a density smaller than 10-2 cm-3 and a velocity of ˜2000 km s-1. Otherwise, a `superbubble-like' wind develops, with very poor or no cold filamentary structures. Also, the numerical evolution of the SN ejecta has allowed us to obtain the abundance distribution over the first ˜3 kpc extension of the wind and we have found that the SN explosions change significantly the metallicity only of the hot, low-density wind component for which we obtained abundances ˜5-10 Z⊙ in fair consistency with the observations. Moreover, we have found that the SN-driven wind transports to outside the disc large amounts of energy, momentum and gas, but the more massive high-density component reaches only intermediate altitudes smaller than 1.5 kpc. Therefore, no significant amounts of gas mass are lost to the intergalactic medium and the mass evolution of the galaxy is not much affected by the starburst events occurring in the nuclear region.

  18. The Structure and Evolution of Self-Gravitating Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Holliman, John Herbert, II

    1995-01-01

    We present a theoretical formalism to evaluate the structure of molecular clouds and to determine precollapse conditions in star-forming regions. Models consist of pressure-bounded, self-gravitating spheres of a single -fluid ideal gas. We treat the case without rotation. The analysis is generalized to consider states in hydrostatic equilibrium maintained by multiple pressure components. Individual pressures vary with density as P_i(r) ~ rho^{gamma {rm p},i}(r), where gamma_{rm p},i is the polytropic index. Evolution depends additionally on whether conduction occurs on a dynamical time scale and on the adiabatic index gammai of each component, which is modified to account for the effects of any thermal coupling to the environment of the cloud. Special attention is given to properly representing the major contributors to dynamical support in molecular clouds: the pressures due to static magnetic fields, Alfven waves, and thermal motions. Straightforward adjustments to the model allow us to treat the intrinsically anisotropic support provided by the static fields. We derive structure equations, as well as perturbation equations for performing a linear stability analysis. The analysis provides insight on the nature of dynamical motions due to collapse from an equilibrium state and estimates the mass of condensed objects that form in such a process. After presenting a set of general results, we describe models of star-forming regions that include the major pressure components. We parameterize the extent of ambipolar diffusion. The analysis contributes to the physical understanding of several key results from observations of these regions. Commonly observed quantities are explicitly cross-referenced with model results. We theoretically determine density and linewidth profiles on scales ranging from that of molecular cloud cores to that of giant molecular clouds (GMCs). The model offers an explanation of the mean pressures in GMCs, which are observed to be high relative

  19. A new parametrizable model of molecular electronic structure

    NASA Astrophysics Data System (ADS)

    Laikov, Dimitri N.

    2011-10-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the parametrization procedure - making a direct link to the correlated wavefunction theory. The model has been trained for 15 elements (H, Li-F, Na-Cl, 720 parameters) on a set of 5581 molecules (including ions, transition states, and weakly bound complexes) whose first- and second-order properties were computed by the coupled-cluster theory as a reference, and a good agreement is seen. The model looks promising for the study of large molecular systems, it is believed to be an important step forward from the traditional semiempirical models towards higher accuracy at nearly as low a computational cost.

  20. A new parametrizable model of molecular electronic structure.

    PubMed

    Laikov, Dimitri N

    2011-10-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the parametrization procedure--making a direct link to the correlated wavefunction theory. The model has been trained for 15 elements (H, Li-F, Na-Cl, 720 parameters) on a set of 5581 molecules (including ions, transition states, and weakly bound complexes) whose first- and second-order properties were computed by the coupled-cluster theory as a reference, and a good agreement is seen. The model looks promising for the study of large molecular systems, it is believed to be an important step forward from the traditional semiempirical models towards higher accuracy at nearly as low a computational cost. PMID:21992295

  1. How does the molecular network structure influence PDMS elastomer wettability?

    NASA Astrophysics Data System (ADS)

    Melillo, Matthew; Genzer, Jan

    Poly(dimethylsiloxane) (PDMS) is one of the most common elastomers, with applications ranging from medical devices to absorbents for water treatment. Fundamental understanding of how liquids spread on the surface of and absorb into PDMS networks is of critical importance for the design and use of another application - microfluidic devices. We have systematically studied the effects of polymer molecular weight, loading of tetra-functional crosslinker, end-group chemical functionality, and the extent of dilution of the curing mixture on the mechanical and surface properties of end-linked PDMS networks. The gel and sol fractions, storage and loss moduli, liquid swelling ratios, and water contact angles have all been shown to vary greatly based on the aforementioned variables. Similar trends were observed for the commercial PDMS material, Sylgard-184. Our results have confirmed theories predicting the relationships between modulus and swelling. Furthermore, we have provided new evidence for the strong influence that substrate modulus and molecular network structure have on the wettability of PDMS elastomers. These findings will aid in the design and implementation of efficient microfluidics and other PDMS-based materials that involve the transport of liquids.

  2. Stochastic Molecular Transport on Microtubule Bundles with Structural Defects

    NASA Astrophysics Data System (ADS)

    Gramlich, M. W.; Tabei, S. M. Ali

    Intracellular transport involves complex coordination of multiple components such as: the cytoskeletal network and molecular motors. Perturbations in this process can amplify over time and space, thereby affecting transport. One little studied component of transport are structural defects in the cytoskeletal network. In this talk we will present a stochastic model of the interaction of the molecular motor, kinesin-1, and a bundled cystoskeletal network of microtubules, and explicitly explore the role of microtubule ends (a type of defect) on long-range transport. We will show how different types of end distributions can ultimately result in the same observed transport behavior for bundles. We compare transport on completely uniform bundles, found in the axon, to completely random bundles, found in dendrites. Because of the un-biased random bundle nature, defects affect transport on dendrite bundles more than on uniform bundles in the axon. Further, defects act as large spatial-scale traps that result in random wait-times which have been assumed in previous models.

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

    PubMed

    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. PMID:23298049

  4. Cluster and Shell Structures in the Fermionic Molecular Dynamics Approach

    NASA Astrophysics Data System (ADS)

    Neff, Thomas; Feldmeier, Hans

    Nuclei in the p- and sd-shell are studied within the Fermionic Molecular Dynamics (FMD) model that uses Gaussian wave packets as single-particle states. Intrinsic many-body basis states are given by Slater determinants which have to be projected on parity, angular momentum and total linear momentum to restore the symmetries of the Hamiltonian. The flexibility of the Gaussian basis allows to economically describe states with shell structures as well as states featuring clustering or halos. The same effective interaction derived from the realistic Argonne V18 interaction in the Unitary Correlation Operator Method (UCOM) framework is used for all nuclei. We discuss the spectrum of 12C with a special emphasis on the structure of the first excited 0+ state, the famous Hoyle state. In the FMD approach the Hoyle state is found to be dominated by dilute α-cluster configurations. Recent measurements of the charge radii of Neon isotopes show an intriguing behaviour. This can be explained in FMD calculations by a structure change from 17Ne and 18Ne which can be essentially considered as an 15O or 16O core plus two protons in s2 or d2 configurations, respectively. For the heavier isotopes we find that the admixture of 3He and 4He cluster configurations in the ground states leads to much larger charge radii than obtained in a mean-field calculation.

  5. Electronic Structure and Molecular Dynamics Calculations for KBH4

    NASA Astrophysics Data System (ADS)

    Papaconstantopoulos, Dimitrios; Shabaev, Andrew; Hoang, Khang; Mehl, Michael; Kioussis, Nicholas

    2012-02-01

    In the search for hydrogen storage materials, alkali borohydrides MBH4 (M=Li, Na, K) are especially interesting because of their light weight and the high number of hydrogen atoms per metal atom. Electronic structure calculations can give insights into the properties of these complex hydrides and provide understanding of the structural properties and of the bonding of hydrogen. We have performed first-principles density-functional theory (DFT) and tight-binding (TB) calculations for KBH4 in both the high temperature (HT) and low temperature (LT) phases to understand its electronic and structural properties. Our DFT calculations were carried out using the VASP code. The results were then used as a database to develop a tight-binding Hamiltonian using the NRL-TB method. This approach allowed for computationally efficient calculations of phonon frequencies and elastic constants using the static module of the NRL-TB, and also using the molecular dynamics module to calculate mean-square displacements and formation energies of hydrogen vacancies.

  6. 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.

  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. PMID:25475529

  8. Molecular-dynamics study of structure II hydrogen clathrates.

    PubMed

    Alavi, Saman; Ripmeester, J A; Klug, D D

    2005-07-01

    Molecular-dynamics simulations are used to study the stability of structure II hydrogen clathrates with different H2 guest occupancies. Simulations are done at pressures of 2.5 kbars and 1.013 bars and for temperatures ranging from 100 to 250 K. For a structure II unit cell with 136 water molecules, H2 guest molecule occupancies of 0-64 are studied with uniform occupancies among each type of cage. The simulations show that at 100 K and 2.5 kbars, the most stable configurations have single occupancy in the small cages and quadruple occupancy in the large cages. The optimum occupancy for the large cages decreases as the temperature is raised. Double occupancy in the small cages increases the energy of the structures and causes tetragonal distortion in the unit cell. The spatial distribution of the hydrogen guest molecules in the cages is determined by studying the guest-water and guest-guest radial distribution functions at various temperatures. PMID:16050759

  9. Structural and molecular interrogation of intact biological systems.

    PubMed

    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

    2013-05-16

    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

  10. 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.

  11. 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.

  12. 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.

  13. Neutral Gas and Low-Redshift Starbursts: From Infall to Ionization

    NASA Astrophysics Data System (ADS)

    Jaskot, Anne; Oey, M. S.; Salzer, J. J.; Van Sistine, A.; Haynes, M. P.

    2014-01-01

    The interplay of gas inflows, star formation, and feedback drives galaxy evolution, and starburst galaxies provide important laboratories for probing these processes at their most extreme. With two samples of low-redshift starburst galaxies, we examine the conversion of neutral gas into stars and the subsequent effects of stellar feedback on the neutral interstellar medium (ISM). The ALFALFA Hα survey represents a complete, volume-limited sample of HI-selected galaxies with 21 cm spectra and Hα and R-band imaging. By contrasting the starburst galaxies with the rest of the gas-rich galaxy population, we investigate the roles of galaxy morphology, HI kinematics, and the atomic gas supply in triggering extreme levels of star formation. Both an elevated HI gas supply and an external disturbance are necessary to drive the starbursts. While neutral gas may fuel a starburst, it may also increase starbursts' optical depths and hinder the transport of ionizing radiation. In contrast to the expectations for high-redshift star-forming galaxies, neutral gas appears to effectively bar the escape of ionizing radiation in most low-redshift starbursts. To evaluate the impact of radiative feedback in extreme starbursts, we analyze optical spectra of the Green Pea galaxies, a low-redshift sample selected by their intense [O III] λ5007 emission and compact sizes. We use nebular photoionization and stellar population models to constrain the Peas' burst ages, ionizing sources, and optical depths and find that the Peas are likely optically thin to Lyman continuum (LyC) radiation. These young starbursts still generate substantial ionizing radiation, while recent supernovae may have carved holes in the ISM that enhance LyC photon escape into the intergalactic medium. While the ALFALFA survey demonstrates the role of external processes in triggering starbursts, the Green Peas show that starbursts' radiation can escape to affect their external environment.

  14. 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.

  15. How does star formation proceed in the circumnuclear starburst ring of NGC 6951?

    NASA Astrophysics Data System (ADS)

    van der Laan, T. P. R.; Schinnerer, E.; Emsellem, E.; Hunt, L. K.; McDermid, R. M.; Liu, G.

    2013-03-01

    Gas inflowing along stellar bars is often stalled at the location of circumnuclear rings, which form an effective reservoir for massive star formation and thus shape the central regions of galaxies. However, how exactly star formation proceeds within these circumnuclear starburst rings is the subject of debate. Two main scenarios for this process have been put forward. In the first, the onset of star formation is regulated by the total amount of gas present in the ring with star forming starting, once a mass threshold has been reached, in "random" positions within the ring like "popcorn". In the second, star formation primarily takes place near the locations where the gas enters the ring. This scenario has been dubbed "pearls-on-a-string". Here we combine new optical IFU data covering the full stellar bar with existing multiwavelength data to study the 580 pc radius circumnuclear starburst ring in detail in the nearby spiral galaxy NGC 6951. Using Hubble Space Telescope (HST) archival data together with SAURON and OASIS IFU data, we derive the ages and stellar masses of star clusters, as well as the total stellar content of the central region. Adding information on the molecular gas distribution, stellar and gaseous dynamics, and extinction, we find that the circumnuclear ring in NGC 6951 is ~1-1.5 Gyr old and has been forming stars for most of that time. We see evidence for preferred sites of star formation within the ring, consistent with the "pearls-on-a-string" scenario, when focusing on the youngest stellar populations. The ring's longevity means that this signature is washed out when older stellar populations are included in the analysis. Tables 4 and 5 are available in electronic form at http://www.aanda.orgOASIS maps and SAURON cube are available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr(130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/551/A81

  16. 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.

  17. The Influence of the Molecular Structure of Cyanine Dye on the Component Composition of Molecular Layers

    NASA Astrophysics Data System (ADS)

    Kaliteevskaya, E. N.; Krutyakova, V. P.; Razumova, T. K.; Starovoitov, A. A.

    2016-03-01

    The formation of the component composition of symmetric cationic cyanine dyes on glass is studied. The absorption spectra of layers of three homologous series of dyes with end heterocyclic groups of different spatial and chemical compositions are measured, and the absorption spectra of monomer components and aggregates are separated. The component compositions of layers of different thicknesses are compared. It is shown that the widening of the absorption spectra of molecular layers against the spectra of ethanol solutions of these compounds is caused mainly by the formation of various monomer stereoisomers and molecular aggregates and their interaction with the substrate surface and the neighborhood. The number of isomer forms and their relative concentrations depend on the layer thickness, the electron donor ability and spatial structure of end groups, and the cation conjugation chain length. The influence of the anion manifests itself only in the concentration ratio of the formed monomers and a small shift of the maxima of their absorption bands. The increase in the number of monomer forms produced in the layer corresponds to the increase in the conjugation chain length. Spatial obstacles created by heterocyclic groups inhibit the formation of definite stereoisomers, which reduces the number of components of the layer.

  18. STUDIES OF RELATIONSHIPS BETWEEN MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY BY PATTERN RECOGNITION METHODS

    EPA Science Inventory

    The attempt to rationalize the connections between the molecular structures of organic compounds and their biological activities comprises the field of structure-activity relations (SAR) studies. Correlations between structure and activity are important for the understanding and ...

  19. The Radio–Gamma Correlation in Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Eichmann, B.; Becker Tjus, J.

    2016-04-01

    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.

  20. Stellar masses for thousands of z>1 resolved, dusty starbursts

    NASA Astrophysics Data System (ADS)

    Casey, Caitlin; Smail, Ian; Chapman, Scott; Hung, Chao-Ling; Manning, Sinclaire; Battye, Richard; Abdalla, Filipe; Birkinshaw, Mark; Hales, Christopher; Myers, Steve; Muxlow, Tom; Jackson, Neal; Bacon, David; Brown, Michael; Browne, Ian; Beswick, Rob; Garrington, Simon; Kay, Scott; Leahy, Paddy; Nichol, Bob; Richards, Anita; Wilkinson, Peter; Sanders, David

    2015-10-01

    Dusty star-forming galaxies, with individual star formation rates >100Msun/yr, formed most of the stars in the Universe at early epochs (z 1-2), yet their physical origins and triggering, whether it be from major mergers or secular disk-bound star-formation, is still unsolved. In assessing the role of major galaxy mergers (amongst dusty galaxies) to cosmic star formation, the measurement of galaxies' stellar masses is critical. Starbursts' stellar masses tell us about their past average star formation rate and whether or not the current high-SFR phase is indeed rare (short-lived) or in line with expectation. Can we definitively measure whether the occurrence of major mergers at a given star-formation rate varies with stellar mass, as predicted? Or are high star formation rates simply always indicative of short-lived bursts? Here we propose deep infrared imaging of a new 1.77deg^2 extragalactic legacy field which has very unique, deep, high-resolution radio interferometric coverage from the e-MERLIN SuperCLASS survey; the dataset's radio continuum mapping will allow a unique morphological measurement of obscured star formation in 5000 starbursts, probing the merger fraction of dusty galaxies (which are too dusty for HST morphology). Critically, Spitzer IRAC 3.6um and 4.5um will allow calculation of galaxies' stellar masses and allow us to directly test if higher mass starbursts are less likely to exhibit clumpy, merging morphologies than their lower mass counterparts (a key corollary to the galaxies `main sequence' framework). In addition, IRAC coverage provides an independent AGN indicator (steep mid-IR powerlaw), will improve the quality of photometric redshifts in the field, and will provide crucial near-IR positional counterparts for future submillimeter coverage.

  1. SN Heating Efficiency of the ISM of Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Melioli, C.; de Gouveia dal Pino, E. M.; D'Ercole, A.; Raga, A.

    2004-06-01

    The interstellar medium heated by supernova explosions (SN) may acquire an expansion velocity larger than the escape velocity and leave the galaxy through a supersonic wind. Galactic winds are effectively observed in many local starburst galaxies (Lehnert & Heckman 1996). The SN ejecta are transported out of the galaxies by such winds which must affect the chemical evolution of the galaxies. The effectiveness of the processes mentioned above depends on the heating efficiency (HE) of the SNs, i.e., the ratio between the kinetic plus internal energy density of the ambient gas and the SN energy density. In a starburst region, several SN explosions occur at a large rate inside a relatively small volume. If the successive generations of SN remnants (SNRs) interact with each other very fast, then a superbubble of high temperature and low density will rapidly develop, before a significant increase of the ambient gas density that could lead to substantial losses of energy by radiation. In this case, it is common to assume a value for HE of the order of unity, since most of the available energy of the SNs will be transferred to the ambient gas in the form of kinetic and internal energy, instead of being radiated away. However this assumption fails to reproduce both the chemical and dynamical characteristics of most starburst (SB) galaxies. In order to solve this paradigm, we have constructed a simple semi-analytical model, considering the essential ingredients of a SB environment, i.e., a three-phase medium composed by hot diffuse gas, SNRs and clouds, which is able to qualitatively trace the thermalisation history of the ISM in a SB region and determine the HE evolution (Melioli, de Gouveia Dal Pino, & D'Ercole, A&A, 2003, submitted). Our study has also been accompanied by fully 3-D radiative cooling, hydrodynamical simulations of SNR-SNR and SNR-clouds interactions (see Melioli, de Gouveia Dal Pino, & Raga 2003, in preparation).

  2. Starbursts and Galaxy Evolution: results from COSMOS survey.

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    The search for starbursts galaxies in COSMOS database by a tailored procedure that uses the photometry from SUBARU, results in 220 targets at z<0.5. The typical mass of the starburst is 10^8 and its distribution is similar to that of the quiescent galaxies in the survey at the same redshift range. From the detailed analysis of the galaxies images using the HST, the star forming clumps are characterized. The galaxies are of three different kinds, Snot, Snot and diffuse light and multiple knots. The mass of the knots are typically one order of magnitude below that of the host galaxy and the clumps in multiple knot galaxies are bigger the closer they are to the center. The sSFR however does not change with the particular position of the burst in their host galaxy, which suggests a similar process independently of their location. This result applies also to the galaxies at the largest z range (0.9). Our interpretation is that the star formation is happening at all possible locations on the galaxy discs, possibly from gas accreted from the halo or the IGM, with clumps which grow as they spiral and get to the centermost regions. Our previous work on nearby SF -tadpole galaxies of similar mass reported metallicity drops coinciding with the location of the burst what we have interpreted as SF driven by cold flows. Our results in COSMOS would be consistent with a similar interpretation and a scenario in which medium mass disks are growing by gas accretion that show up as scattered starbursts knots.

  3. The Radio-Gamma Correlation in Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Eichmann, B.; Becker Tjus, J.

    2016-04-01

    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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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. PMID:18459791

  9. 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.

  10. Nuclear structure and reactions in the fermionic molecular dynamics approach

    NASA Astrophysics Data System (ADS)

    Neff, T.; Feldmeier, H.

    2008-05-01

    The Fermionic Molecular Dynamics (FMD) model uses Gaussian wave packets as single-particle states. Intrinsic many-body basis states are constructed as Slater determinants which have to be projected on parity, angular momentum and total linear momentum to restore the symmetries of the Hamiltonian. The flexibility of the Gaussian basis allows to economically describe states with shell structures as well as states featuring clustering or halos. We use an effective interaction that is derived from the realistic Argonne V18 interaction by means of the Unitary Correlation Operator Method (UCOM). A phenomenological momentum-dependent two-body correction simulates contributions from missing three-body forces and three-body correlations. We discuss 12C with a special emphasis on the structure of the excited 0+ and 2+ states. We analyze the degree of α-clustering and confirm, taking inelastic electron scattering data into account, the conjecture that the Hoyle state has to be understood as a loosely bound system of alpha particles. We will also present first results on the application of FMD for the calculation of scattering phase shifts in 3He — 4He.

  11. Molecular Structure and Mobility in Ultrasonically Treated Unfilled Polybutadiene Rubber

    NASA Astrophysics Data System (ADS)

    von Meerwall, E.; Oh, J.-S.; Wagler, T.; Rinaldi, P.; Isayev, A. I.

    2003-10-01

    Ultrasound can change the molecular structure of rubbery polymers in several ways at once, including network formation (crosslinking) and degradation (devulcanization). We have used wide-line proton and spectroscopic 13C transverse NMR relaxation, and the proton pulsed-gradient spin echo method, to examine sonicated unfilled polybutadiene gum rubber. Results correlate well with ultrasound amplitude. The proton T2 relaxation at 70.5 deg. C exhibits three discrete components, due to entangled sol and network; unentangled (light) sol plus dangling chain ends; and oligomer remnants. The 25 deg. C carbon T2 values show no effects of sonication. The diffusivity spectrum of the light sol displays a wide rate distribution, including a fast component from oligomers. Ultrasound exposure increases all diffusion rates, and substantially lowers the relative contribution of the two fastest proton T2 decay components with only small decreases in relaxation times. Ultrasound treatment results in significant isomerization; the cis/trans ratio decreases sharply for samples subjected to the highest amplitudes. The structural implications of these findings will be discussed.

  12. Molecular structure-adsorption study on current textile dyes.

    PubMed

    Örücü, E; Tugcu, G; Saçan, M T

    2014-01-01

    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models. PMID:25529487

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

    PubMed

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

    2015-10-28

    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 ≤ 10,000 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. 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. PMID:26520533

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

    DOE PAGESBeta

    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 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Molecular modeling of nucleic Acid structure: setup and analysis.

    PubMed

    Galindo-Murillo, Rodrigo; Bergonzo, Christina; Cheatham, Thomas E

    2014-01-01

    The last in a set of units by the same authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. The unit describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories. PMID:25606980

  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. Correlation between Post-LASIK Starburst Symptom and Ocular Wavefront Aberrations

    NASA Astrophysics Data System (ADS)

    Liu, Yong-Ji; Mu, Guo-Guang; Wang, Zhao-Qi; Wang-Yan

    2006-06-01

    Monochromatic aberrations in post laser in-situ keratomileusis (LASIK) eyes are measured. The data are categorized into reference group and starburst group according to the visual symptoms. Statistic analysis has been made to find the correlation between the ocular wavefront aberrations and the starburst symptom. The rms aberrations of the 3rd and 4th orders for the starburst group are significantly larger than those for the reference group. The starburst symptom shows a strong correlation with vertical coma, total coma, spherical aberrations. For 3-mm pupil size and 5.8-mm pupil size, the modulation transfer function (MTF) of the starburst group are lower than those of the reference group, but their visual acuities are close. MTF and PSF analyses are made for two groups, and the results are consistent with the statistical analysis, which means the difference between the two groups is mainly due to the third- and fourth-order Zernike aberrations.

  2. CONSTRAINTS ON THE PRESENCE OF WATER MEGAMASER EMISSION IN z {approx} 2.5 ULTRALUMINOUS INFRARED STARBURST GALAXIES

    SciTech Connect

    Wagg, Jeff; Momjian, Emmanuel

    2009-09-15

    We present Expanded Very Large Array (EVLA) and Arecibo observations of two lensed submillimeter galaxies at z {approx} 2.5, in order to search for redshifted 22.235 GHz water megamaser emission. Both SMM J14011+0252 and SMM J16359+6612 have multi-wavelength characteristics consistent with ongoing starburst activity, as well as CO line emission indicating the presence of warm molecular gas. Our observations do not reveal any evidence for H{sub 2}O megamaser emission in either target, while the lensing allows us to obtain deep limits to the H{sub 2}O line luminosities, L{sub H{sub 2}}{sub O}<7470 L{sub odot} (3{sigma}) in the case of SMM J14011+0252, and L{sub H{sub 2}}{sub O}<1893 L{sub odot} for SMM J16359+6612, assuming line widths of 80 km s{sup -1}. Our search for, and subsequent nondetection of, H{sub 2}O megamaser emission in two strongly lensed starburst galaxies rich in gas and dust suggests that such megamaser emission is not likely to be common within the unlensed population of high-redshift starburst galaxies. We use the recent detection of strong H{sub 2}O megamaser emission in the lensed quasar, MG J0414+0534 at z = 2.64 to make predictions for future EVLA C-band surveys of H{sub 2}O megamaser emission in submillimeter galaxies hosting active galactic nuclei.

  3. Dusty Starbursts within a z=3 Large Scale Structure

    NASA Astrophysics Data System (ADS)

    Umehata, H.; Kohno, K.; Tamura, Y.; Iono, D.; Nakanishi, K.; Hatsukade, B.; Ikarashi, S.; Izumi, T.; Matsuda, Y.; Ivison, R.; Yun, M.; Wilson, G.; Hughes, D.

    2015-12-01

    We present the results of an ALMA survey of submillimeter galaxies (SMGs) in the SSA22 field. Totally 45 sources discovered by the AzTEC/ASTE survey were observed at 1.1mm to find 64 ALMA -identified SMGs with S/N≥4.5. This is the largest SMG survey in Band 6 in ALMA Cycle1. Previous panoramic Lyman-alpha emitter (LAE) surveys have unveiled that SSA22 is not a general field but a highly biased field at z=3.1. We find large excess in the number counts and surface number density compared to the ALESS survey in ECDFS, which suggests SMGs are preferentially formed in the dense environment at z˜3.

  4. Structural molecular biology: Recent results from neutron diffraction

    NASA Astrophysics Data System (ADS)

    Timmins, Peter A.

    1995-02-01

    Neutron diffraction is of importance in structural biology at several different levels of resolution. In most cases the unique possibility arising from deuterium labelling or contrast variation is of fundamental importance in providing information complementary to that which can be obtained from X-ray diffraction. At high resolution, neutron crystallography of proteins allows the location of hydrogen atoms in the molecule or of the hydration water, both of which may be central to biological activity. A major difficulty in this field has been the poor signal-to-noise ratio of the data arising not only from relatively low beam intensities and small crystals but, most importantly from the incoherent background due to hydrogen atoms in the sample. Modern methods of molecular biology now offer ways of producing fully deuterated proteins by cloning in bacteria grown on fully deuterated media. At a slightly lower resolution, there are a number of systems which may be ordered in one or two dimensions. This is the case in the purple membrane where neutron diffraction with deuterium labelling has complemented high resolution electron diffraction. Finally there is a class of very large macromolecular systems which can be crystallised and have been studied by X-ray diffraction but in which part of the structure is locally disordered and usually has insufficient contrast to be seen with X-rays. In this case the use of H 2O/D 2O contrast variation allows these components to be located. Examples of this are the nucleic acid in virus structures and detergent bound to membrane proteins.

  5. Human haptoglobin structure and function--a molecular modelling study.

    PubMed

    Polticelli, F; Bocedi, A; Minervini, G; Ascenzi, P

    2008-11-01

    Hemoglobin is the most prominent protein in blood, transporting O(2) and facilitating reactive oxygen and nitrogen species detoxification. Hemoglobin metabolism leads to the release of extra-erythrocytic hemoglobin, with potentially severe consequences for health. Extra-erythrocytic hemoglobin is complexed to haptoglobin for clearance by tissue macrophages. The human gene for haptoglobin consists of three structural alleles: Hp1F, Hp1S and Hp2. The products of the Hp1F and Hp1S alleles differ by only one amino acid, whereas the Hp2 allele is the result of a fusion of the Hp1F and Hp1S alleles, is present only in humans and gives rise to a longer alpha-chain. Haptoglobin consists of a dimer of alphabeta-chains covalently linked by a disulphide bond between the Cys15 residue of each alpha-chain. However, the presence of the Hp1 and Hp2 alleles in humans gives rise to HPT1-1 dimers (covalently linked by Cys15 residues), HPT1-2 hetero-oligomers and HPT2-2 oligomers. In fact, the HPT2 variant displays two free Cys residues (Cys15 and Cys74) whose participation in intermolecular disulphide bonds gives rise to higher-order covalent multimers. Here, the complete modelling of both haptoglobin variants, together with their basic quaternary structure arrangements (i.e. HPT1 dimer and HPT2 trimer), is reported. The structural details of the models, which represent the first complete view of the molecular details of human haptoglobin variants, are discussed in relation to the known haptoglobin function(s). PMID:18959750

  6. The NGC 1614 interacting galaxy. Molecular gas feeding a "ring of fire"

    NASA Astrophysics Data System (ADS)

    König, S.; Aalto, S.; Muller, S.; Beswick, R. J.; Gallagher, J. S.

    2013-05-01

    Minor mergers frequently occur between giant and gas-rich low-mass galaxies and can provide significant amounts of interstellar matter to refuel star formation and power active galactic nuclei (AGN) in the giant systems. Major starbursts and/or AGN result when fresh gas is transported and compressed in the central regions of the giant galaxy. This is the situation in the starburst minor merger NGC 1614, whose molecular medium we explore at half-arcsecond angular resolution through our observations of 12CO (2-1) emission using the Submillimeter Array (SMA). We compare our 12CO (2-1) maps with optical and Paα, Hubble Space Telescope and high angular resolution radio continuum images to study the relationships between dense molecular gas and the NGC 1614 starburst region. The most intense 12CO emission occurs in a partial ring with ~230 pc radius around the center of NGC 1614, with an extension to the northwest into the dust lane that contains diffuse molecular gas. We resolve ten giant molecular associations (GMAs) in the ring, which has an integrated molecular mass of ~8 × 108 M⊙. Our interferometric observations filter out a large part of the 12CO (1-0) emission mapped at shorter spacings, indicating that most of the molecular gas is diffuse and that GMAs only exist near and within the circumnuclear ring. The molecular ring is uneven with most of the mass on the western side, which also contains GMAs extending into a pronounced tidal dust lane. The spatial and kinematic patterns in our data suggest that the northwest extension of the ring is a cosmic umbilical cord that is feeding molecular gas associated with the dust lane and tidal debris into the nuclear ring, which contains the bulk of the starburst activity. The astrophysical process for producing a ring structure for the final resting place of accreted gas in NGC 1614 is not fully understood, but the presence of numerous GMAs suggests an orbit-crowding or resonance phenomenon. There is some evidence that

  7. Biological, molecular, and structural analysis of a cytopathic variant from a molecularly cloned simian immunodeficiency virus.

    PubMed Central

    LaBranche, C C; Sauter, M M; Haggarty, B S; Vance, P J; Romano, J; Hart, T K; Bugelski, P J; Hoxie, J A

    1994-01-01

    Some isolates of simian immunodeficiency virus (SIV) have been shown to infect Sup-T1 cells with slow kinetics and in the absence of cytopathic effects, including cell fusion or CD4 down-modulation (J. A. Hoxie, B. S. Haggarty, S. Bonser, J. Rackowski, H. Shan, and P. Kanki, J. Virol. 62:2557-2568, 1988). In the present study, we describe the isolation and characterization of a SIVmac variant, derived from the BK28 infectious molecular clone, that became highly cytopathic for Sup-T1 cells. This variant, termed CP-MAC, exhibited a number of differences from BK28, including (i) an altered tropism which largely restricted its host range to Sup-T1 cells, (ii) the ability to induce cell fusion and CD4 down-modulation, and (iii) a highly stable interaction of its external (SU) and transmembrane (TM) envelope glycoproteins. In addition, a marked increase in the level of surface envelope glycoproteins was observed both on CP-MAC-infected cells and on virions. The CP-MAC env gene was PCR amplified from infected cells, and sequence analysis identified five amino acid changes in SU and six in TM compared with BK28. The introduction of these changes into BK28 was shown to fully reconstitute the biological and morphological properties of CP-MAC. The limited number of mutations in CP-MAC should enable the molecular determinants to be more precisely defined and help to identify the underlying mechanisms responsible for the striking biological and structural alterations exhibited by this virus. Images PMID:8057433

  8. 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.

  9. Molecular dynamics simulation study on the molecular structures of the amylin fibril models.

    PubMed

    Xu, Weixin; Su, Haibin; Zhang, John Z H; Mu, Yuguang

    2012-12-01

    The structural characterization of amyloid fibers is one of the most investigated areas in structural biology. Recently, protofibril models for amylin, i.e., the 37-residue human islet amyloid polypeptide or hIAPP were suggested by two groups based on NMR (Biochemistry 2007, 46, 13505-13522) and X-ray (Protein Sci. 2008, 17, 1467-1474) techniques. However, there are significant differences in the two models which maybe originate from the polymorphic nature of amylin fibrils. To obtain further insights into the packing and stability features of the different models, we performed a series of molecular dynamics simulations on them. Our analysis showed that even pairs of β-sheets composed of a limited number of β-strands are stable in the 100-ns simulations, which suggests that steric zipper interactions at a β-sheet-β-sheet interface strongly contribute to the stability of these amyloid aggregates. For both models, outer strands are more flexible, which might coincide with the dynamical requirement that outer strands act as growing sites facilitating conformational changes of new incoming chains. Moreover, simulation results showed that the X-ray models are structurally more compact than the NMR models and have more intimate patterns, which lead to more rigid amyloid models. As a result, the X-ray models are energetically more stable than the NMR models. Further modeling analyses verify the most likely amylin fibril model among both NMR and X-ray models. Upon further study of the force-induced dissociation of a single chain from the protofibrils, the binding energy and the mechanical stability of the fibril models are revealed. On these bases, it is possible to reconcile the crystallographic and the NMR data on the basic amylin fiber unit. PMID:23145779

  10. The Driving Mechanism of Starbursts in Galaxy Mergers

    NASA Astrophysics Data System (ADS)

    Teyssier, Romain; Chapon, Damien; Bournaud, Frédéric

    2010-09-01

    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 × 104 M 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 ~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 103 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.

  11. 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.

  12. Mid-infrared Spectral Properties of Post-starburst Quasars

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

    We present Spitzer InfraRed Spectrograph low-resolution spectra of 16 spectroscopically selected post-starburst quasars (PSQs) at z ~ 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 μm 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. Excess Submillimeter Emission in the Starburst Galaxy NGC 3310?

    NASA Astrophysics Data System (ADS)

    Zhu, M.; Papadopoulos, P. P.; Xilouris, M.; Kuno, N.; Lisenfeld, U.

    2011-10-01

    We present a new observational study of the gas and dust properties in the starburst galaxy NGC 3310, whose bulk interstellar medium (ISM) resides in environments that mark (and bracket) the excitation extremes of the ISM conditions found in infrared luminous galaxies (Zhu et al. 2009). One of our major findings is that the dust emission spectrum in NGC 3310 shows a pronounced submillimeter “excess”. We tried to fit this excess by a cold dust component but very low temperatures were required (Tc ˜ 5-11 K) with a correspondingly low gas-to-dust mass ratio of 5-43. We furthermore show that it is not possible to maintain the large quantities of dust required at these low temperatures in this starburst galaxy. Instead, we conclude that the dust properties need to be different from Galactic dust in order to fit the submillimeter “excess”. We show that the dust spectral energy distribution can be fitted by an enhanced abundance of very small grains and discuss different alternatives.

  14. 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.

  15. Are bars essential for starbursts in non-interacting galaxies

    NASA Technical Reports Server (NTRS)

    Pompea, Stephen M.; Rieke, G. H.

    1990-01-01

    Analyzed here are the 1.6 and 2.2 micron images of a sample of galaxies that are classified as unbarred by the Revised Shapley-Ames Catalog. These galaxies have characteristic properties of nuclear starbursts and are examined through near infrared imaging in a search for hidden bars. Researchers selected a sample of 36 galaxies from the Revised Shapley-Ames Catalog that have far infrared luminosities greater than 10(exp 10) solar luminosity and hot Infrared Astronomy Satellite (IRAS) colors between 60 and 100 microns, indicative of nuclear starbursts, but are not classified as Seyfert 1 or 2. Their determination of the presence of a bar relies primarily on an analysis of the 2 micron image using the Galaxy Surface Photometry (GASP) package (Cawson, 1983). The GASP analysis programs determine the galaxy surface brightness and ellipticity profiles as well as the position angle and the center coordinates of the ellipses. To test the way that GASP will characterize the surface brightness of barred galaxies, two galaxies with known bars, NGC 1068 and NGC 2523, were imaged with the 2 micron camera and analyzed with GASP. Fifteen of the sample that are not clearly barred from optical data and are isolated were imaged at 1.6 and 2.2 microns; 9 of these do not appear to have bars. Strong bars therefore do not appear to be an absolute requirement for high infrared luminosity in isolated galaxies.

  16. Starbursts and dusty tori in distant 3CR radio galaxies

    NASA Astrophysics Data System (ADS)

    Podigachoski, Pece; Rocca-Volmerange, Brigitte; Barthel, Peter; Drouart, Guillaume; Fioc, Michel

    2016-08-01

    We present a study of the complete ultraviolet to submillimetre spectral energy distributions (SEDs) of twelve 3CR radio galaxy hosts in the redshift range 1.0 < z < 2.5, which were all detected in the far-infrared by the Herschel Space Observatory. The study employs the new spectro-chemical evolutionary code PÉGASE.3, in combination with recently published clumpy AGN torus models. We uncover the properties of the massive host galaxy stellar populations, the AGN torus luminosities, and the properties of the recent starbursts, which had earlier been inferred in these objects from their infrared SEDs. The PÉGASE.3 fitting yields very luminous (up to 1013 L⊙) young stellar populations with ages of several hundred million years in hosts with masses exceeding 1011 M⊙. Dust masses are seen to increase with redshift, and a surprising correlation - or better upper envelope behaviour - is found between the AGN torus luminosity and the starburst luminosity, as revealed by their associated dust components. The latter consistently exceeds the former by a constant factor, over a range of one order of magnitude in both quantities.

  17. A statistical study of properties of Seyfert and starburst galaxies

    NASA Technical Reports Server (NTRS)

    Dahari, Oved; De Robertis, Michael M.

    1988-01-01

    Spectral and morphological data for 282 Seyfert and emission-line galaxies spanning radio to X-ray wavelengths are compiled. The data include a large number of optical emission-line measurements which have not been reported previously. These data are intended to provide a convenient summary of the relevant properties of these galaxies, as well as a data base to search for correlations among the various parameters in order to obtain a better understanding of the active galaxy phenomenon. The paper presents the data and analyzes the distributions of various properties of Seyfert 1 and Seyfert 2 galaxies and starburst galaxies. It is found that Seyferts 2s have a higher 60 micron/forbidden O III 5007 A flux ratio than Seyfert 1s. This result, combined with the fact that Seyfert 2s are more heavily reddened, indicate that they have a higher dust content. It is also found that starburst nuclei are comparable to Seyfert 2s in far-infrared and 20 cm luminosities, although their optical spectra are markedly different.

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

    PubMed

    Karle, J M; Karle, I L

    1989-07-01

    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

  19. Molecular structure of the Menkes disease gene (ATP7A)

    SciTech Connect

    Dierick, H.A.; Glover, T.W.; Ambrosini, L.

    1995-08-10

    We report a detailed molecular analysis of the genomic structure of the Menkes disease gene (MNK; ATP7A). There are 23 exons in ATP7A covering a genomic region of approximately 140 kb. The size of the individual coding exons varies between 77 and 726 bp, and introns vary in size between 196 bp and approximately 60 kb. All of the splice sites obey the consensus GT-AG rule except the splice donor of intron 9, which is GC instead of GT. The exon following this rare splice donor variant is alternatively spliced. A PGAM pseudogene and two highly polymorphic CA repeats map to introns within the gene. The structure is very similar to that of the closely related Wilson disease gene (WND; ATP7B). From exon 5 (exon 3 in ATP7B) to the end, all of the splice sites occur at exactly the same nucleotide positions as in the WND gene, except for the boundary between exons 17 and 18 (exons 15 and 16 in ATP7B) and a single codon difference at the boundary between exons 4 and 5 of the MNK gene (exons 2 and 3 in ATP7B). In contrast to the WND gene, in which the first four of six metal binding domains are contained in 1 exon, metal binding domains 1 to 4 are divided over 3 exons. The striking similarity of the MNK and WND genes at the genomic level is consistent with their relatively recent divergence from a common ancestral gene. 39 refs., 4 figs., 1 tab.

  20. 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

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

    PubMed

    de Steenhuijsen Piters, Wouter A A; Bogaert, Debby

    2016-01-01

    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

  2. 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

  3. Mineral-Biochar Composites: Molecular Structure and Porosity.

    PubMed

    Rawal, Aditya; Joseph, Stephen D; Hook, James M; Chia, Chee H; Munroe, Paul R; Donne, Scott; Lin, Yun; Phelan, David; Mitchell, David R G; Pace, Ben; Horvat, Joseph; Webber, J Beau W

    2016-07-19

    Dramatic changes in molecular structure, degradation pathway, and porosity of biochar are observed at pyrolysis temperatures ranging from 250 to 550 °C when bamboo biomass is pretreated by iron-sulfate-clay slurries (iron-clay biochar), as compared to untreated bamboo biochar. Electron microscopy analysis of the biochar reveals the infusion of mineral species into the pores of the biochar and the formation of mineral nanostructures. Quantitative (13)C nuclear magnetic resonance (NMR) spectroscopy shows that the presence of the iron clay prevents degradation of the cellulosic fraction at pyrolysis temperatures of 250 °C, whereas at higher temperatures (350-550 °C), the clay promotes biomass degradation, resulting in an increase in both the concentrations of condensed aromatic, acidic, and phenolic carbon species. The porosity of the biochar, as measured by NMR cryoporosimetry, is altered by the iron-clay pretreatment. In the presence of the clay, at lower pyrolysis temperatures, the biochar develops a higher pore volume, while at higher temperature, the presence of clay causes a reduction in the biochar pore volume. The most dramatic reduction in pore volume is observed in the kaolinite-infiltrated biochar at 550 °C, which is attributed to the blocking of the mesopores (2-50 nm pore) by the nonporous metakaolinite formed from kaolinite. PMID:27284608

  4. 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.

  5. Molecular structure, spectral constants, and fermi resonances in chlorine nitrate

    NASA Astrophysics Data System (ADS)

    Petkie, Douglas T.; Butler, Rebecca A. H.; Helminger, Paul; De Lucia, Frank C.

    2004-06-01

    Chlorine nitrate has two low-lying vibrational modes that lead to a series of Fermi resonances in the 9 υ97 υ7 family of levels that include the 9 2⇔7 1 and 9 3⇔7 19 1 dyads and the 9 4⇔9 27 1⇔7 2 and 9 5⇔9 37 1⇔9 17 2 triads. These states, along with the ground and 9 1 vibrational states, have been previously analyzed with millimeter and submillimeter wave spectroscopy and provide a substantial body of data for the investigation of these resonances and their impact on calculated spectroscopic constants and structural parameters. Due to fitting indeterminacies, these previous analyses did not include the main Fermi resonance interaction term. Consequently, the fitted rotational constants are linear combinations of the unmixed rotational constants of the basis vibrational states. In this paper, we have calculated the contributions of the Fermi resonances to the observed rotational constants in a model that determines the vibrational-rotational constants, the Fermi term and the mixing between interacting vibrational states, the cubic potential constant ( φ997) that connects interacting levels through a Fermi resonance, and the inertial defects. These results agree with predictions from ab initio and harmonic force field calculations and provide further experimental information for the determination of the fundamental molecular properties of chlorine nitrate.

  6. Molecular structure from a single NMR sequence (fast-PANACEA)

    NASA Astrophysics Data System (ADS)

    Kupče, Ēriks; Freeman, Ray

    2010-09-01

    The PANACEA experiment combines three standard NMR pulse sequences (INADEQUATE, HSQC and HMBC) into a single entity, and is designed for spectrometers with two or more receivers operating in parallel. For small molecules it offers a direct route to molecular structure. Often the INADEQUATE feature is the rate-determining step, being limited by the low natural abundance of directly coupled 13C sbnd 13C pairs. This new version, fast-PANACEA, speeds up this measurement by two alternative schemes. In the first, the individual 13C sites are excited by selective radiofrequency pulses acting on double-quantum coherence, and encoded according to the rows of a Hadamard matrix. The columns of this matrix are used to decode the experimental data into separate F 2 spectra. This reduction in the number of required scans secures a faster result than the conventional stepwise exploration of the evolution dimension where the Nyquist condition and the resolution requirements must both be satisfied. The second scheme makes use of multiple aliasing in the evolution dimension. Significant speed improvements are achieved by either technique, illustrated by measurements made on samples of menthol and cholesterol. A new stabilization scheme (i-lock) is introduced. This is a software program that corrects the final NMR frequencies based on the observed frequency of a strong X-spin signal. It replaces the conventional deuterium lock, permitting measurements on neat liquids such as peanut oil and silicone oil, and offering advantages where deuterated solvents are undesirable.

  7. Molecular Evolution and Structural Features of IRAK Family Members

    PubMed Central

    Gosu, Vijayakumar; Basith, Shaherin; Durai, Prasannavenkatesh; Choi, Sangdun

    2012-01-01

    The interleukin-1 receptor-associated kinase (IRAK) family comprises critical signaling mediators of the TLR/IL-1R signaling pathways. IRAKs are Ser/Thr kinases. There are 4 members in the vertebrate genome (IRAK1, IRAK2, IRAKM, and IRAK4) and an IRAK homolog, Pelle, in insects. IRAK family members are highly conserved in vertebrates, but the evolutionary relationship between IRAKs in vertebrates and insects is not clear. To investigate the evolutionary history and functional divergence of IRAK members, we performed extensive bioinformatics analysis. The phylogenetic relationship between IRAK sequences suggests that gene duplication events occurred in the evolutionary lineage, leading to early vertebrates. A comparative phylogenetic analysis with insect homologs of IRAKs suggests that the Tube protein is a homolog of IRAK4, unlike the anticipated protein, Pelle. Furthermore, the analysis supports that an IRAK4-like kinase is an ancestral protein in the metazoan lineage of the IRAK family. Through functional analysis, several potentially diverged sites were identified in the common death domain and kinase domain. These sites have been constrained during evolution by strong purifying selection, suggesting their functional importance within IRAKs. In summary, our study highlighted the molecular evolution of the IRAK family, predicted the amino acids that contributed to functional divergence, and identified structural variations among the IRAK paralogs that may provide a starting point for further experimental investigations. PMID:23166766

  8. 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.

  9. Free ion yields in liquids: Molecular structure and track effects

    SciTech Connect

    Holroyd, R.

    1992-05-01

    The signal generated in a liquid-filled ionization chamber is proporational to the ions that escape, the free ion yield or, G{sub fi}. Recent results show how molecular structure, rate of energy loss (dE/dx) and pressure affect G{sub fi} and give further insight into the ionization process in liquids. As a consequence of the passage of high energy charged particles through a liquid, molecules are ionized and excited. The electrons have kinetic energy initially which allow them to travel some distance away from their geminate cations. The electrons may lose energy to vibrational modes but a significant fraction of the separation occurs while the electrons have subvibrational (near thermal) energy. When the electron finally thermalizes it is within the coulombic field of its parent cation and the two ions constitute a geminate pair. The free ion yield is determined by the fraction of geminate pairs which separate to form free ions as against those that recombine to form excited states.

  10. Free ion yields in liquids: Molecular structure and track effects

    SciTech Connect

    Holroyd, R.

    1992-01-01

    The signal generated in a liquid-filled ionization chamber is proporational to the ions that escape, the free ion yield or, G{sub fi}. Recent results show how molecular structure, rate of energy loss (dE/dx) and pressure affect G{sub fi} and give further insight into the ionization process in liquids. As a consequence of the passage of high energy charged particles through a liquid, molecules are ionized and excited. The electrons have kinetic energy initially which allow them to travel some distance away from their geminate cations. The electrons may lose energy to vibrational modes but a significant fraction of the separation occurs while the electrons have subvibrational (near thermal) energy. When the electron finally thermalizes it is within the coulombic field of its parent cation and the two ions constitute a geminate pair. The free ion yield is determined by the fraction of geminate pairs which separate to form free ions as against those that recombine to form excited states.

  11. 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. PMID:26927616

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure.

    PubMed

    Zou, Wei; Sissons, Mike; Warren, Frederick J; Gidley, Michael J; Gilbert, Robert G

    2016-11-01

    The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh)<100nm; this protein(s) was susceptible to proteolysis. Thus the compact structure of pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh>100nm. PMID:27516291

  18. Undergraduate chemistry students' conceptions of atomic structure, molecular structure and chemical bonding

    NASA Astrophysics Data System (ADS)

    Campbell, Erin Roberts

    The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from

  19. ESTIMATION OF GAS-LIQUID CHROMATOGRAPHIC RETENTION TIMES FROM MOLECULAR STRUCTURE

    EPA Science Inventory

    A new type of computer program called SPARC (SPARC Performs Automated Reasoning in Chemistry) was developed to predict chemical reactivity parameters and physical properties of organic molecules from their molecular structures based on fundamental chemical structure theory. PARC'...

  20. 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

  1. 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.

  2. Near-infrared integral-field spectroscopy of violent starburst environments

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard

    2006-01-01

    Near-infrared (NIR) integral-field spectroscopy (IFS) of violent starburst environments at high spatial (and spectral) resolution has the potential to revolutionise our ideas regarding the local interactions between the newly formed massive stars and the interstellar medium (ISM) of their host galaxies. To illustrate this point, I present NIR IFS analysis of the central starburst region of NGC 1140, obtained with CIRPASS on Gemini-South. While strong [FeII] emission is found throughout the galaxy, higher-order Brackett emission is predominantly associated with the northern starburst region. Based on the spatial distributions of the [FeII] versus Brackett line emission, I conclude that a galaxy-wide starburst was induced several ×107 yr ago, with more recent starburst activity concentrated around the northern starburst region. I look forward and discuss the exciting prospects that IFS at higher spatial (and spectral) resolution will allow us trace (i) the massive outflows ("superwinds") expected to originate in the dense, young massive star clusters commonly found in intense starburst environments, and (ii) their impact on the galaxy's ISM.

  3. The Intrinsic Properties of the Stellar Clusters in the M82 Starburst Complex: Propagating Star Formation?

    NASA Astrophysics Data System (ADS)

    Satyapal, S.; Watson, Dan M.; Pipher, J. L.; Forrest, W. J.; Greenhouse, M. A.; Smith, H. A.; Fischer, J.; Woodward, Charles E.

    1997-07-01

    Near-Infrared spectroscopy combined with high spatial resolution imaging have been used in this work to probe the central 500 pc of M82. Imaging observations in the 2.36 μm CO band head are added to our previously published near-infrared hydrogen recombination line imaging, near-infrared broadband imaging, and 3.29 μm dust feature imaging observations, in order to study the nature of the starburst stellar population. A starburst model is constructed and compared with the observations of the stellar clusters in the starburst complex. Our analysis implies that the typical age for the starburst clusters is 107 yr. In addition, our high spatial resolution observations indicate that there is an age dispersion within the starburst complex that is correlated with projected distance from the center of the galaxy. The inferred age dispersion is 6 × 106 yr. If the starburst in M82 is propagating outward from the center, this age dispersion corresponds to a velocity of propagation, originating in the center, of ~50 km s-1. Our quantitative analysis also reveals that a Salpeter initial mass function, extending from 0.1 to 100 M⊙, can fit the observed properties of M82 without using up more than 30% of the total dynamical mass in the starburst.

  4. SALT/RSS Longslit Spectroscopy of the NGC 1140 Starburst

    NASA Astrophysics Data System (ADS)

    Burgh, Eric B.; Gallagher, J. S., III; Nordsieck, K. H.; Percival, J. W.; Smith, M. P.; O'Donoghue, D.; Buckley, D. A.; Loaring, N. S.

    2006-06-01

    We present a long-slit spectrum of the amorphous starbursting dwarf galaxy NGC 1140 taken by the Robert Stobie Spectrograph of the Southern African Large Telescope during its commissioning phase in November 2005. A 1.2 arcsecond wide longslit oriented along the major axis in conjunction with a volume phase holographic grating were used to produce a 800 Angstrom wide spectrum, centered on H-alpha, with a resolving power of 5500. Twelve minutes of data were obtained. Emission features from H-alpha, [NII], [SII] and HeI were observed. The peak of the emission features is observed to be 2 arcseconds north of the stellar continuum, consistent with HST imaging of the galaxy, and a bright knot of gas with a velocity offset of 100 km/s is detected about 18 arcseconds south of the continuum peak. The emission lines are well-resolved with FWHM 80-100 km/s in the inner galaxy, typical of intensely star-forming regions, while FWHM 100-140 km/s are seen in the outer galaxy, suggesting a possible galactic wind. The complex velocity field is consistent with the merger model for NGC 1140. The intensity ratio of the [SII] doublet, 6717/6731 is 1.3, indicating a low electron density, and thus modest thermal pressure despite the galaxy's starburst status. The H-alpha/[SII] ratio, which is an indicator of the presence of shocks,varies along the slit with a maximum of 8 at the peak of the gaseous emission and dropping to nearly 2 at the edges of the galaxy, with a value of 3 for the offset knot of gas. Thus shocks could play a role in the outer galaxy, while the knot is more likely a star forming region. We interpret our results in the context of a starburst induced by the merger of two low mass galaxies, as previously discussed by Hunter et al. (1994, ApJS, 91, 79).

  5. Molecular-Level Understanding of Structural Changes of Organic Crystals Induced by Macroscopic Mechanical Stimulation.

    PubMed

    Seki, Tomohiro; Ito, Hajime

    2016-03-18

    Structural changes to molecular crystals upon mechanical stimulation have attracted attention for sensing, recording, and microactuation. Comprehensive structure information is required to understand relationships between the mechanical force applied, the crystal structure, and the bulk property changes in order to develop general design concepts for mechanoresponsive compounds. Unfortunately, mechanical stimulation of organic crystals typically deteriorates their integrity, preventing detailed structure analyses by single-crystal X-ray diffraction (XRD) methods. However, in the past three years, several interesting studies have been reported in which molecular crystals retain their integrity even after a mechanically induced crystalline structure change. These materials have allowed us to investigate how macroscopic mechanical forces affect the microscopic structures of molecular crystals by single-crystal XRD analyses. This Minireview summarizes current knowledge of mechanically induced structure changes in molecular crystals, which will facilitate research in this field. PMID:26748640

  6. Furosemide's one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics.

    PubMed

    Widdifield, Cory M; Robson, Harry; Hodgkinson, Paul

    2016-05-10

    The potential of NMR crystallography to verify molecular crystal structures deposited in structural databases is evaluated, with two structures of the pharmaceutical furosemide serving as examples. While the structures differ in the placement of one H atom, using this approach, we verify one of the structures in the Cambridge Structural Database using quantitative tools, while establishing that the other structure does not meet the verification criteria. PMID:27115483

  7. Molecular aggregation of rhodamine dyes in dispersions of layered silicates: influence of dye molecular structure and silicate properties.

    PubMed

    Bujdák, Juraj; Iyi, Nobuo

    2006-02-01

    The molecular aggregation of six rhodamine dyes (rhodamine 560, B, 3B, 19, 6G, 123) in layered silicate (saponite and fluorohectorite) dispersions was investigated by using visible (vis) spectroscopy. The dye molecular aggregation was influenced by the properties of both the silicates and the dyes themselves. The layer charge of the silicates enhanced the molecular aggregation of the hydrophilic, cationic dyes. The presence of a carboxyl acid group in the dye molecules inhibited adsorption of the dyes on the surface of fluorohectorite, a silicate with a high charge density. A lower or no adsorption could be observed by vis spectroscopy. Strong association of the dyes to the silicate surface led to remarkable changes in the dye spectra, mainly due to the molecular aggregation. Dye assemblies initially formed after mixing the dye solutions with silicate dispersions were unstable. Decomposition of the dye molecular assemblies, and the formation of new species or molecular aggregate rearrangements, were studied on the bases of time-difference spectra. The reaction pathways were specific, not only for the dyes, depending upon their molecular structure and properties, but also on the silicate substrates. PMID:16471802

  8. Starbursts and wispy drops in surfactants spreading on gels

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Shomeek; Daniels, Karen E.; Behringer, Robert P.

    2004-11-01

    We report a phase diagram for a novel instability seen in drops of nonionic surfactant solution (Triton X-305) spreading on a viscoelastic agar gel substrate. This system allows us to examine the effect of varying the fluidity of an aqueous substrates. The instabilities of the surfactant drop are strongly influenced by the substrate fluidity. For the lowest agar concentration (below the gelation point), the drop breaks into approximately 10 thin spreading arms in a starburst formation. For substrates just below the gelation transition, the central drop remains but is decorated with thin, branching wisps. Above the gelation transition, the surfactant drops are circular as for a solid substrate. The phenomenon is only weakly dependent on the surfactant concentration, which has been varied over three orders of magnitude and across the critical micellar concentration. This work has been supported under NSF Grant DMR-0244498.

  9. Mechanical Feedback: From Stellar Wind Bubbles to Starbursts (Invited Talk)

    NASA Astrophysics Data System (ADS)

    Oey, M. S.; Clarke, C. J.; Massey, P.

    The current understanding of mechanical feedback is reviewed by evaluating the standard, adiabatic model for shell formation and evolution. This model is relevant to phenomena ranging from individual stellar-wind bubbles to galactic superwinds, forming the basis for our understanding of the multiphase ISM, IGM, and galactic evolutionary processes. Although significant discrepancies between the model and observation have been identified, to date there are none that require a fundamental revision. A variety of evidence, ranging over three orders of magnitude in spatial scale, is broadly consistent with the standard model. This includes kinematics of individual objects, observations of hot gas, the size distribution of HI shells, and outflow rates from starburst galaxies. However, some of the most pressing issues relating to shell evolution are still outstanding and obstruct efforts to resolve key questions like the fate of the hot gas.

  10. Brackett alpha and gamma Observations of Starburst and Seyfert Galaxies

    NASA Astrophysics Data System (ADS)

    Kawara, Kimiaki; Nishida, Minoru; Phillips, M. M.

    1989-02-01

    Br (Brackett) α and γ line fluxes of starburst and Seyfert galaxies are presented. The Bra line has been detected in seven of 12 galaxies. These data are combined with published Brackett line fluxes of M82 and NGC 253 to examine the relation between the extinction, A_v_, derived from the Brα/Brγ ratio and the optical depth, τ(10), of the silicate absorption at 10 microns. Generally speaking, a line of slope A_v_/τ(10) = 14 fits the data well, which is the same relation as found in the Milky Way. In the type 2 Seyferts NGC 1068 and NGC 5506, the observed Brα/Brγ ratios may not be simply explained by case B recombination with heavy extinction. The extinction values derived from Brα/Brγ are compared with those determined from optical and X-ray observations, and the implications are discussed.

  11. Filamentary Structure of the Orion A Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Suri, S.; Schilke, P.; Sánchez-Monge, Á.

    2016-05-01

    Interstellar filaments pervade molecular clouds on all scales providing a bridge between the gas with relatively low densities and the dense clumps. In this work, we characterize various physical properties of filaments in the Orion A molecular cloud using preliminary datasets from the CARMA Orion project. We use an automated filament finding algorithm, DisPerSE, on 3D datacubes, and custom characterization algorithms.

  12. Westerlund 1: monolithic formation of a starburst cluster

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    Westerlund 1 is in all likelihood the most massive young cluster in the Milky Way, with a mass on the order of 105 Msol. We have been observing its massive star population for ten years, measuring radial velocity changes for a substantial fraction of its OB stars and evolved supergiants. The properties of the evolved population are entirely consisting with a single burst of star formation, in excellent agreement with the results of studies based on the lower-mass population.Here we will present two new studies of the cluster: 1) A direct measurement of its average radial velocity and velocity dispersion based on individual measurements for several dozen stars with constant radial velocity and 2) A search for massive stars in its immediate neighbourhood using multi-object spectroscopy.The results of these two studies show that Westerlund 1 is decidedly subvirial and has a systemic radial velocity significantly different from that of nearby gas, which was assumed to provide a dynamical distance by previous authors. Moreover, the dynamical distance is inconsistent with the properties of the high-mass stellar population. In addition, we find that the cluster is completely isolated, with hardly any massive star in its vicinity that could be associated 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.Westerlund 1 is thus the best example we have of a starburst cluster formed monolithically.

  13. 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.

  14. Hubble Space Telescope Imaging of Post-starburst Quasars

    NASA Astrophysics Data System (ADS)

    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.

    2011-11-01

    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 burst ~ 1010 M 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.

  15. 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.

  16. Obscured Starburst Activity in High Redshift Clusters and Groups

    NASA Astrophysics Data System (ADS)

    Kocevski, Dale; Lemaux, B.; Lubin, L.; Gal, R.

    2011-01-01

    Using Spitzer MIPS 24um imaging and extensive Keck spectroscopy we have found evidence for environmentally triggered starburst activity within six clusters and groups at z 0.9. I will show that the density of 24um-detected galaxies in the cluster environment is nearly twice that of the surrounding field at this redshift and that this overdensity scales with the cluster's dynamical state. The 24um-bright members often appear optically unremarkable and exhibit only moderate [OII] line emission due to severe obscuration. Although their spatial distribution suggests they are an infalling population, a close examination of their spectral properties, morphologies and optical colors indicate they are not simply analogs of the field population that have yet to be quenched. Using stacked DEIMOS spectra, we find the 24um-detected cluster and group galaxies exhibit elevated levels of Balmer absorption compared to galaxies undergoing normal, continuous star formation. A similar excess is not observed in field galaxies with equivalent infrared luminosities, indicating a greater fraction of the detected cluster and group members have experienced a burst of star formation in the recent past compared to their counterparts in the field. Our results suggest that gas-rich galaxies at high redshift experience a temporary increase in their star formation activity as they assemble into denser environments. Using HST ACS imaging we find that disturbed morphologies are common among the obscured starburst population and become more prevalent in regions of higher galaxy density. We conclude that mergers are the dominant triggering mechanism responsible for the enhanced star formation found in the group galaxies, while a mix of harassment and mergers are likely driving the activity of the cluster galaxies.

  17. Prototypes for infrared astronomical spectroscopy: A starburst galaxy, a data acquisition system, and a data reduction system

    NASA Astrophysics Data System (ADS)

    Achtermann, Jeffrey Mark

    1994-01-01

    Over the last twenty years advances in detector technology have transformed infrared astronomy from a curiosity into a valuable tool of modern astronomy. This change also required advancements in three key areas: data acquisition systems, data reduction systems, and the astronomical interpretation of infrared observations. A data acquisition system based on digital signal processors (DSPs) and capable of accommodating the high throughput of infrared arrays was constructed. By using off-the-shelf components, system design was simplified, construction time and cost were reduced, and reliability was increased. The use of DSPs shifts much of the functionality and development work from hardware to software. The acquisition software is a distributed system running on two Sun SPARCstations and two DSP cards containing Motorola DSP56001s. The data acquisition software takes advantage of the object-oriented features of C++ to modularize the software system. The modularity of this system allows it to be easily adapted to other telescopes and/or arrays. A general astronomical reduction system was created. The system allows the easily manipulation of three dimensional arrays in mathematical expressions, can automatically process data taken in the common infrared observing modes, and provides a uniquely flexible plotting interface which allows data to be viewed as spectra, contour plots, color images, or as a 'movie'. Observations of (Ne-II)(12.8 micro-m), (Ar-III)(8.99 micro-m), (S-IV)(10.51 micro-m), and Hydrogen Bra (4.06 micro-m) were used to probe the excitation and kinematics within the starburst nucleus of M82. The temperature of the stars ionizing the starburst region is approximately 33,000 K, cooler than most Galactic H-II regions. This may be the result of either in initial mass function that does not produce high mass stars or the termination of the starburst 4 x 106 years ago. Within the starburst region, the ionized gas is distributed in a nuclear ring and two

  18. 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.

  19. Insights from the Molecular Dynamics Simulation of Cellobiohydrolase Cel6A Molecular Structural Model from Aspergillus fumigatus NITDGPKA3.

    PubMed

    Dodda, Subba Reddy; Sarkar, Nibedita; Aikat, Kaustav; Krishnaraj, Navanietha R; Bhattacharjee, Sanchari; Bagchi, Angshuman; Mukhopadhyay, Sudit S

    2016-01-01

    Global demand for bioethanol is increasing tremendously as it could help to replace the conventional fossil fuel and at the same time supporting the bioremediation of huge volume of cellulosic wastes generated from different sources. Ideal genetic engineering approaches are essential to improve the efficacy of the bioethanol production processes for real time applications. A locally isolated fungal strain Aspergillus fumigatus NITDGPKA3 was used in our laboratory for the hydrolysis of lignocellulose with good cellulolytic activity when compared with other contemporary fungal strains. An attempt is made to sequence the cellobiohydrolases (CBHs) of A. fumigatus NITDGPKA3, model its structure to predict its catalytic activity towards improving the protein by genetic engineering approaches. Herein, the structure of the sequenced Cellobiohydrolases (CBHs) of A. fumigatus NITDGPKA3, modelled by homology modelling and its validation is reported. Further the catalytic activity of the modelled CBH enzyme was assessed by molecular docking analysis. Phylogenetic analysis showed that CBH from A. fumigatus NITDGPKA3 belongs to the Glycohydro 6 (Cel6A) super family. Molecular modeling and molecular dynamics simulation suggest the structural and functional mechanism of the enzyme. The structures of both the cellulose binding (CBD) and catalytic domain (CD) have been compared with most widely studied CBH of Trichoderma reesei. The molecular docking with cellulose suggests that Gln 248, Pro 287, Val236, Asn284, and Ala288 are the main amino acids involved in the hydrolysis of the β, 1-4, glycosidic bonds of cellulose. PMID:27109185

  20. DYNAMICAL STRUCTURE OF THE MOLECULAR INTERSTELLAR MEDIUM IN AN EXTREMELY BRIGHT, MULTIPLY LENSED z {approx_equal} 3 SUBMILLIMETER GALAXY DISCOVERED WITH HERSCHEL

    SciTech Connect

    Riechers, Dominik A.; Cooray, A.; Carpenter, J. M.; Bock, J.; Omont, A.; Neri, R.; Cox, P.; Harris, A. I.; Baker, A. J.; Frayer, D. T.; Auld, R.; Aussel, H.; Chanial, P.; Blundell, R.; Brisbin, D.; Burgarella, D.; Chapman, S. C.; Clements, D. L.

    2011-05-20

    We report the detection of CO(J = 5 {yields} 4), CO(J = 3 {yields} 2), and CO(J = 1 {yields} 0) emission in the strongly lensed, Herschel/SPIRE-selected submillimeter galaxy (SMG) HERMES J105751.1+573027 at z = 2.9574 {+-} 0.0001, using the Plateau de Bure Interferometer, the Combined Array for Research in Millimeter-wave Astronomy, and the Green Bank Telescope. The observations spatially resolve the molecular gas into four lensed images with a maximum separation of {approx}9'' and reveal the internal gas dynamics in this system. We derive lensing-corrected CO line luminosities of L'{sub CO(1-0)} = (4.17 {+-} 0.41), L'{sub CO(3-2)} = (3.96 {+-} 0.20), and L'{sub CO(5-4)} = (3.45 {+-} 0.20) x 10{sup 10} ({mu}{sub L}/10.9){sup -1} K km s{sup -1} pc{sup 2}, corresponding to luminosity ratios of r{sub 31} = 0.95 {+-} 0.10, r{sub 53} = 0.87 {+-} 0.06, and r{sub 51} = 0.83 {+-} 0.09. This suggests a total molecular gas mass of M{sub gas} = 3.3x10{sup 10} ({alpha}{sub CO}/0.8) ({mu}{sub L}/10.9){sup -1} M{sub sun}. The gas mass, gas mass fraction, gas depletion timescale, star formation efficiency, and specific star formation rate are typical for an SMG. The velocity structure of the gas reservoir suggests that the brightest two lensed images are dynamically resolved projections of the same dust-obscured region in the galaxy that are kinematically offset from the unresolved fainter images. The resolved kinematics appear consistent with the complex velocity structure observed in major, 'wet' (i.e., gas-rich) mergers. Major mergers are commonly observed in SMGs and are likely to be responsible for fueling their intense starbursts at high gas consumption rates. This study demonstrates the level of detail to which galaxies in the early universe can be studied by utilizing the increase in effective spatial resolution and sensitivity provided by gravitational lensing.

  1. 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.

  2. INSTANTANEOUS STARBURST OF THE MASSIVE CLUSTERS WESTERLUND 1 AND NGC 3603 YC

    SciTech Connect

    Kudryavtseva, Natalia; Brandner, Wolfgang; Gennaro, Mario; Rochau, Boyke; Henning, Thomas; Stolte, Andrea; Andersen, Morten; Da Rio, Nicola; Tognelli, Emanuele; Hogg, David; Clark, Simon; Waters, Rens

    2012-05-10

    We present a new method to determine the age spread of resolved stellar populations in a starburst cluster. The method relies on a two-step process. In the first step, kinematic members of the cluster are identified based on multi-epoch astrometric monitoring. In the second step, a Bayesian analysis is carried out, comparing the observed photometric sequence of cluster members with sets of theoretical isochrones. When applying this methodology to optical and near-infrared high angular resolution Hubble Space Telescope (HST) and adaptive optics observations of the {approx}5 Myr old starburst cluster Westerlund 1 and {approx}2 Myr old starburst cluster NGC 3603 YC, we derive upper limits for the age spreads of 0.4 and 0.1 Myr, respectively. The results strongly suggest that star formation in these starburst clusters happened almost instantaneously.

  3. Hi Gas Cycles and Lyman Continuum Optical Depth in Low-Redshift Starbursts

    NASA Astrophysics Data System (ADS)

    Jaskot, Anne Elizabeth

    Neutral gas both fuels star formation and determines the propagation of ionizing photons. In this work, we reveal the interactions between H I, star formation, and radiative feedback in two samples of low-redshift starbursts. Using the ALFALFA-Halpha sample, we present the first comparison of starbursts and non-starbursts within a statistically uniform, H I-selected sample. The moderate H I gas fractions of the starbursts relative to non-starbursts indicate efficient HI to H2 conversion and show that the H I supply is largely unaffected by ionizing radiation. Mergers may trigger the more massive starbursts, while the absence of obvious kinematical disturbances in dwarf starbursts may indicate periodic starburst activity, triggered by cycles of gas expulsion and re-accretion. While the ALFALFA-Halpha galaxies demonstrate that starbursts may maintain large H I reservoirs, the more powerful starbursts in the Green Pea (GP) galaxies illustrate the effects of extreme radiative feedback on neutral gas. To investigate whether the enormous [O III]/[O II] ratios in the most extreme GPs indicate LyC escape, we use photoionization modeling to constrain their ionizing sources and optical depths. Radiation from Wolf-Rayet stars or unusually hot O stars reproduces the observed [O III]/[O II] ratios, but no clear signatures of these stars are present. The GP spectra do suggest the presence of shocks, however, and accounting for shock emission necessitates a low optical depth. We therefore suggest that the GPs may be a new class of low-redshift LyC Emitters (LCEs), and we evaluate this scenario using Hubble Space Telescope COS spectra of four GPs. With these spectra, we develop a simple physical picture of the neutral gas optical depth and geometry that explains the previously enigmatic link between Lyalpha, Si II, and Si II* lines observed in high-redshift Lyalpha Emitters. Two GPs are likely optically thin along the line of sight, and their strong, narrow Lyalpha emission, weak

  4. 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

  5. The heating of dust in starburst galaxies: The contribution of the nonionizing radiation

    NASA Technical Reports Server (NTRS)

    Calzetti, D.; Bohlin, R. C.; Kinney, Anne L.; Storchi-Bergmann, T.; Heckman, Timothy M.

    1995-01-01

    The IUE UV and optical spectra and the far-infrared (FIR) IRAS flux densities of a sample of starburst and blue compact galaxies are used to investigate the relationship between dust obscuration and dust emission. The amount of dust obscuration at UV wavelengths correlates with the FIR-to-blue ratio; and an analysis of the correlation indicates that not only the ionizing but also the nonionizing radiation contribute to the FIR emission. The amount of UV and optical energy lost to dust obscuration accounts for most of the cool dust FIUR emission and for about 70% of the warm dust FIR emission. The remaining 30% of the warm dust FIR flux is probably due to dust emission from regions of star formation which are embedded in opaque giant molecular clouds and do not contribute to the integrated UV and optical spectrum. The use of the FIR emission as an indicator of high-mass star formation rate in star-forming galaxies can be problematic, since the contribution to the FIR flux from cool dust emission heated by relatively old stars is nonnegligible.

  6. 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.

  7. Algorithm for Finding Similar Shapes in Large Molecular Structures Libraries

    Energy Science and Technology Software Center (ESTSC)

    1994-10-19

    The SHAPES software consists of methods and algorithms for representing and rapidly comparing molecular shapes. Molecular shapes algorithms are a class of algorithm derived and applied for recognizing when two three-dimensional shapes share common features. They proceed from the notion that the shapes to be compared are regions in three-dimensional space. The algorithms allow recognition of when localized subregions from two or more different shapes could never be superimposed by any rigid-body motion. Rigid-body motionsmore » are arbitrary combinations of translations and rotations.« less

  8. 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

  9. Electronic structure and conformation of polymers from cluster molecular orbital and molecular mechanics calculations: Polyimide

    SciTech Connect

    Kafafi, S.A. ); LaFemina, J.P. ); Nauss, J.L. )

    1990-11-21

    Full geometry optimizations using molecular mechanics and the quantum chemical AM1 method have been carried out to determine the minimum energy conformation of pyromellitic dianhydride-oxydianiline polyimide (PMDA-ODA PI). The phenyl-imide twist angle for this compound was determined to be {approximately}30. These computations also provided a quantitative determination of the energy gap (7 eV), electron affinity ({minus}2 eV), and ionization potential (8.97 eV). Computations on the PMDA-ODA PI radical anion provided an estimate of the hopping barrier for an electron to hop from one chain to another (3.2 eV), the mechanism believed responsible for photoconduction. Moreover, the use of qualitative molecular orbital theory (QMOT) arguments provided an interpretation of these results in a simple molecular orbital framework.

  10. Molecular and structural preservation of dehydrated bio-tissue for THz spectroscopy

    NASA Astrophysics Data System (ADS)

    Png, Gretel M.; Choi, Jin Wook; Guest, Ian; Ng, Brian W.-H.; Mickan, Samuel P.; Abbott, Derek; Zhang, Xi-Cheng

    2007-12-01

    Terahertz transmission through freshly excised biological tissue is limited by the tissue's high water content. Tissue fixation methods that remove water, such as fixation in Formalin, destroy the structural information of proteins hence are not suitable for THz applications. Dehydration is one possible method for revealing the tissue's underlying molecular structure and components. In this study, we measured the THz responses over time of dehydrating fresh, necrotic and lyophilized rat tissue. Our results show that as expected, THz absorption increases dramatically with drying and tissue freshness can be maintained through lyophilization. Dehydrated biological tissue with retained molecular structure can be useful for future laser-based THz wave molecular analysis.

  11. The rest-frame optical morphology of starburst galaxies at 1 < z < 3.5

    NASA Astrophysics Data System (ADS)

    Lee, Bomee; Giavalisco, Mauro; Candels, Goods-Hershcel

    2015-01-01

    Using CANDELS combined with GOODS-Herschel in the GOODS-North and South field, we investigate the rest-frame optical morphologies of starburst galaxies at 1 We compare morphologies of MS and SB galaxies using non-parametric (Sersic Index) and parametric measures as well as the visual identification. FIR luminous starburst galaxies are usually interpreted as major wet mergers. We find that the average morphologies of SB galaxies are disky and generally have much more diffuse optical light profile than massive compact early-type galaxies (ETGs), challenging gas-rich merging as the primary dissipative mechanism to assemble very compact, massive galaxies. We find that the sizes of the SB galaxies are clearly larger than those of the MS galaxies on average. NIR to MIR colors of starburst galaxies show no evidence of highly dust-obscured compact component, which could eventually emerge as the massive compact core. Very compact SB galaxies are rather rare, and hence even from a statistical standpoint, our morphological analysis of starburst galaxies does not support the popular mechanism that powerful starburst in a highly dissipative wet merger of gas-rich disks, and subsequent quenching, is the key driver behind the formation of the massive, compact early-type galaxies observed at z~2. The light distribution of the bulk of stars in starburst galaxies is simply not compact enough to eventually evolve into the massive ultra compact ETGs at high redshift universe.

  12. 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.

  13. The Starburst Cluster Westerlund 1 and its Galactic Siblings -- Observation Confronts Theory

    NASA Astrophysics Data System (ADS)

    Brandner, W.

    2008-05-01

    Because of their large number of stars spread over the entire stellar mass spectrum, starburst clusters are highly suitable to benchmark and calibrate star-formation models and theories. Among the handful of Galactic starburst clusters, Westerlund 1 with its estimated 150 O-stars, W-R stars, supergiants and hypergiants is the most massive young cluster identified to date in the Milky Way. While previous studies of Westerlund 1 focused largely on optical and X-ray observations of its evolved massive stellar population, we have analyzed near-infrared data, resulting in the first in-depth study of the ``lower-mass'' main sequence and pre-main sequence cluster population, i.e., of stars in the mass range 0.4 to 30 solar masses. The derived properties of the cluster population allow us to test theoretical evolutionary tracks. By comparison of Westerlund 1's half-mass radius with younger starburst clusters like NGC 3603 YC and Arches, and somewhat older massive clusters like RSGC1 and RSGC2, we find evidence for a rapid dissolution of Galactic starburst clusters, which has interesting implications for the long-term survival of starburst clusters, and the question to which extent Galactic starburst clusters might mimic proto-globular clusters.

  14. Structure of classical trajectories in multidimensional bound molecular systems

    SciTech Connect

    Ashton, C.J.; Muckerman, J.T.

    1983-07-21

    A computational method is described which enables visualization of the coordinate space envelopes of classical trajectories in multidimensional bound molecular systems. The method is exemplified by application to a realistic three-dimensional model of the vibrating water molecule, and its utility in the application of semiclassical quantization techniques is emphasized. 8 figures.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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. PMID:26648584

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

    PubMed

    de la Llave, Ezequiel; 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. PMID:26567676

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    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.

  4. A linear correlation between H2 v = 1-0 S(1) and forbidden O I 6300 emission in Seyfert and starburst galaxies

    SciTech Connect

    Mouri, H.; Taniguchi, Y.; Kawara, K.; Nishida, M. Kiso Observatory, Mitake National Astronomical Observatory of Japan, Mitaka Kyoto Univ. )

    1989-11-01

    A good linear correlation is found between the H2 v = 1-0 S(1)/Br-gamma and the forbidden O I 6300/H-alpha emission-line ratios on a sample of 28 galaxies containing an AGN or a starburst nucleus (SBN). In the SBNs, the observed relation between the line ratios concerned matches the relation for SNRs. Thus the dominant excitation mechanism of molecular hydrogen is shock heating. In the AGNs, X-ray heating is the dominant mechanism because the model of Lepp and McCray (1983) reasonably explains the observed correlation. 48 refs.

  5. 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...

  6. 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...

  7. COMPUTER-ASSISTED STUDIES OF MOLECULAR STRUCTURE-BIOLOGICAL ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Computer-assisted methods can be used to investigate the relationships between the molecular structures of compounds and their biological activity. A number of approaches have been reported in the literature, including correlations of activity with substituent constants, conforma...

  8. 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...

  9. Fueling nuclear activity in disk galaxies: Starbursts and monsters

    NASA Astrophysics Data System (ADS)

    Heller, Clayton H.; Shlosman, Isaac

    1994-03-01

    We study the evolution of the gas distribution in a globally unstable galactic disk with a particular emphasis on the gasdynamics in the central kiloparsec and the fueling activity there. The two-component self-gravitating disk is embedded in a responsive halo of comparable mass. The gas and stars are evolved using a three-dimensional hybrid smoothed particle hydrodynamics/N-body code and the gravitational interactions are calculated using a hierarchical TREE algorithm. A massive 'star formation' is introduced when the gas becomes Jeans unstable and locally exceeds the critical density of approximately 100 solar mass pc-3. The newly formed OB stars deposit energy in the gas by means of radiation-driven winds and supernovae. This energy is partially thermalized (efficiency of a few percent); the rest is radiated away. Models without star formation are evolved for a comparison. The effect of a massive object at the disk center is studied by placing a 'seed' black hole (BH) of 5 x 107 solar mass with an accretion radius of 20 pc. The tendency of the system to form a massive object 'spontaneously' is tested in models without the BH. We find that for models without star formation the bar- or dynamical friction-driven inflows lead to (1) domination of the central kpc by a few massive clouds that evolve into a single object probably via a cloud binary system, with and without a 'seed' BH, (2) accretion onto the BH which has a sporadic character, and (3) formation of remnant disks around the BH with a radius of 60-80 pc which result from the capture and digestion of clouds. For models with star formation, we find that (1) the enrgy input into the gas induces angular momentum loss and inflow rates by a factor less than 3, (2) the star formation is concentrated mainly at the apocenters of the gaseous circulation in the stellar bar and in the nuclear region, (3) the nuclear starburst phase appears to be very luminous approximately 1045-1046 erg/s and episodic with a typical

  10. Recent Star-formation in Post-Starburst Quasars

    NASA Astrophysics Data System (ADS)

    Townsend, Shonda; Ganguly, R.; Strom, A.; Cales, S.; Brotherton, M. S.

    2011-01-01

    Post-Starburst Quasars (PSQ, alternatively Q+As) show simultaneously the spectrum of a massive A-type stellar population and a quasar. The prototype PSQ, UNJ1025-0040, shows a UV excess over the quasar spectrum, indicating more recent star-formation (Brotherton et al 2002). To gauge the frequency and distribution of these younger stellar populations in PSQs, we have collected GALEX (GR45) and 2MASS photometry for 409 objects. The objects are catalog 609 spectroscopically-selected PSQs from Brotherton et al. (2010) that uses similar criteria as Zabludoff et al. (1996) for post-starburst galaxies (PSG, E+A). For comparison, we have compiled two samples: (1) 16,000 quasars that is matched in redshift (0.01-0.7) and Sloan-u magnitude (16.1-21.2), which is blueward of the Balmer edge and provides the least contamination from the massive stellar population; and (2) 500 PSGs from Goto et al. (2007). 389 (55) PSQs show an NUV (FUV) excess over the expected UV flux if the underlying quasar were ``normal.'’ 126 (460) objects show an NUV (FUV) decrement. The observed NUV to u-band flux ratio of the median PSQ rises from 1 at z=0.01 to 2.5 at z=0.4, while the same for the median QSO remains at 1. The observed FUV to u-band flux ratio of the median QSO rises slightly from 0.6 to 0.8 over the redshift range 0.05-0.2, whereas the median PSQ is nearly a factor of three lower. The disparity between the median PSQ and QSO suggests the presence of young stars that add in NUV light, but not FUV light. To quantify the youth and mass of this putative population, we will present preliminary efforts to model PSQs using two simple stellar populations, an underlying quasar, and dust reddening. We acknowledge funding from GALEX through grant NNX10AC63G.

  11. Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures.

    PubMed

    Cole, Jason C; Groom, Colin R; Korb, Oliver; McCabe, Patrick; Shields, Gregory P

    2016-04-25

    This paper describes a novel way to use the structural information contained in the Cambridge Structural Database (CSD) to drive geometry optimization of organic molecules. We describe how CSD structural information is transformed into objective functions for gradient-based optimization to provide good quality geometries for a large variety of organic molecules. Performance is assessed by minimizing different sets of organic molecules reporting RMSD movements for bond lengths, valence angles, torsion angles, and heavy atom positions. PMID:26977906

  12. 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.

  13. Quantitative structure-activity relationship correlation between molecular structure and the Rayleigh enantiomeric enrichment factor.

    PubMed

    Jammer, S; Rizkov, D; Gelman, F; Lev, O

    2015-08-01

    It was recently demonstrated that under environmentally relevant conditions the Rayleigh equation is valid to describe the enantiomeric enrichment - conversion relationship, yielding a proportional constant called the enantiomeric enrichment factor, εER. In the present study we demonstrate a quantitative structure-activity relationship model (QSAR) that describes well the dependence of εER on molecular structure. The enantiomeric enrichment factor can be predicted by the linear Hansch model, which correlates biological activity with physicochemical properties. Enantioselective hydrolysis of sixteen derivatives of 2-(phenoxy)propionate (PPMs) have been analyzed during enzymatic degradation by lipases from Pseudomonas fluorescens (PFL), Pseudomonas cepacia (PCL), and Candida rugosa (CRL). In all cases the QSAR relationships were significant with R(2) values of 0.90-0.93, and showed high predictive abilities with internal and external validations providing QLOO(2) values of 0.85-0.87 and QExt(2) values of 0.8-0.91. Moreover, it is demonstrated that this model enables differentiation between enzymes with different binding site shapes. The enantioselectivity of PFL and PCL was dictated by electronic properties, whereas the enantioselectivity of CRL was determined by lipophilicity and steric factors. The predictive ability of the QSAR model demonstrated in the present study may serve as a helpful tool in environmental studies, assisting in source tracking of unstudied chiral compounds belonging to a well-studied homologous series. PMID:26153539

  14. Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships.

    PubMed

    Buttingsrud, Bård; Ryeng, Einar; King, Ross D; Alsberg, Bjørn K

    2006-06-01

    The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity. PMID:17054018

  15. 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. PMID:21844601

  16. Structural basis for molecular recognition at serotonin receptors.

    PubMed

    Wang, Chong; Jiang, Yi; Ma, Jinming; Wu, Huixian; Wacker, Daniel; Katritch, Vsevolod; Han, Gye Won; Liu, Wei; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D; Gao, Xiang; Zhou, X Edward; Melcher, Karsten; Zhang, Chenghai; Bai, Fang; Yang, Huaiyu; Yang, Linlin; Jiang, Hualiang; Roth, Bryan L; Cherezov, Vadim; Stevens, Raymond C; Xu, H Eric

    2013-05-01

    Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiology through the 5-HT receptor family. We report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist antimigraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserved in the 5-HT receptor family, clarifying the family-wide agonist activity of 5-HT. Compared with the structure of the 5-HT2B receptor, the 5-HT1B receptor displays a 3 angstrom outward shift at the extracellular end of helix V, resulting in a more open extended pocket that explains subtype selectivity. Together with docking and mutagenesis studies, these structures provide a comprehensive structural basis for understanding receptor-ligand interactions and designing subtype-selective serotonergic drugs. PMID:23519210

  17. 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.

  18. 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

  19. The structural biology of molecular recognition by vancomycin.

    PubMed

    Loll, P J; Axelsen, P H

    2000-01-01

    Vancomycin is the archetype among naturally occurring compounds known as glycopeptide antibiotics. Because it is a vital therapeutic agent used world-wide for the treatment of infections with gram-positive bacteria, emerging bacterial resistance to vancomycin is a major public health threat. Recent investigations into the mechanisms of action of glycopeptide antibiotics are driven by a need to understand their detailed mechanism of action so that new agents can be developed to overcome resistance. These investigations have revealed that glycopeptide antibiotics exhibit a rich array of complex cooperative phenomena when they bind target ligands, making them valuable model systems for the study of molecular recognition. PMID:10940250

  20. Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics

    PubMed Central

    Parker, David; Bryant, Zev; Delp, Scott L.

    2010-01-01

    Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org. PMID:20428469

  1. 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

    2016-03-01

    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. PMID:26876376

  2. Structure and Molecular Evolution of CDGSH Iron-Sulfur Domains

    PubMed Central

    Lai, Shaomei; Ye, Keqiong

    2011-01-01

    The recently discovered CDGSH iron-sulfur domains (CISDs) are classified into seven major types with a wide distribution throughout the three domains of life. The type 1 protein mitoNEET has been shown to fold into a dimer with the signature CDGSH motif binding to a [2Fe-2S] cluster. However, the structures of all other types of CISDs were unknown. Here we report the crystal structures of type 3, 4, and 6 CISDs determined at 1.5 Å, 1.8 Å and 1.15 Å resolution, respectively. The type 3 and 4 CISD each contain one CDGSH motif and adopt a dimeric structure. Although similar to each other, the two structures have permutated topologies, and both are distinct from the type 1 structure. The type 6 CISD contains tandem CDGSH motifs and adopts a monomeric structure with an internal pseudo dyad symmetry. All currently known CISD structures share dual iron-sulfur binding modules and a β-sandwich for either intermolecular or intramolecular dimerization. The iron-sulfur binding module, the β-strand N-terminal to the module and a proline motif are conserved among different type structures, but the dimerization module and the interface and orientation between the two iron-sulfur binding modules are divergent. Sequence analysis further shows resemblance between CISD types 4 and 7 and between 1 and 2. Our findings suggest that all CISDs share common ancestry and diverged into three primary folds with a characteristic phylogenetic distribution: a eukaryote-specific fold adopted by types 1 and 2 proteins, a prokaryote-specific fold adopted by types 3, 4 and 7 proteins, and a tandem-motif fold adopted by types 5 and 6 proteins. Our comprehensive structural, sequential and phylogenetic analysis provides significant insight into the assembly principles and evolutionary relationship of CISDs. PMID:21949752

  3. 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.

  4. 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.

  5. 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.

  6. Mid-infrared diagnostics to distinguish AGNs from starbursts

    NASA Astrophysics Data System (ADS)

    Laurent, O.; Mirabel, I. F.; Charmandaris, V.; Gallais, P.; Madden, S. C.; Sauvage, M.; Vigroux, L.; Cesarsky, C.

    2000-07-01

    We present new mid-infrared (MIR) diagnostics to distinguish emission of active galactic nuclei (AGN) from that originating in starburst regions. Our method uses empirical spectroscopic criteria based on the fact that MIR emission from star forming or active galaxies arises mostly from HII regions, photo-dissociation regions (PDRs) and AGNs. The analysis of the strength of the 6.2 mu m Unidentified Infrared Band (UIB) and the MIR continuum shows that UIBs are very faint or absent in regions harboring the intense and hard radiation fields of AGNs and pure HII regions, where the UIB carriers could be destroyed. The MIR signature of AGNs is the presence of an important continuum in the 3-10 mu m band which originates from very hot dust heated by the intense AGN radiation field. Using these two distinct spectral properties found in our MIR templates, we build diagnostic diagrams which provide quantitative estimates of the AGN, PDR and HII region contribution in a given MIR spectrum. This new MIR classification can be used to reveal the presence of AGNs highly obscured by large columns of dust. Based on observations made with ISO, an ESA project with instruments funded by ESA Member States (especially the PI countries: France, Germany, the Netherlands and the United Kingdom) and with the participation of ISAS and NASA.

  7. The Effects of Dust on the Ultraviolet Spectral Energy Distribution of Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Gordon, K. D.; Witt, A. N.

    1994-05-01

    The effects of dust on the spectral energy distribution (SED) of starburst regions of galaxies was investigated using Monte Carlo techniques to model the transport of radiation in systems where the dust and stars are mixed. In a recent paper, Calzetti, Kinney, & Storchi-Bergmann (ApJ, 10 July 1994) derive an extinction curve from observations of starburst galaxies assuming the dust is in a screen geometry. This gives an extinction curve where the geometrical effects of mixing of the dust and stars are convolved with the extinguishing effects of the dust. The resulting extinction curve is greyer than the Galactic extinction curve and featureless in the ultraviolet, i.e. lacking both the 2200 Angstroms bump and far-UV rise. In an attempt to explain this ``effective'' starburst extinction curve we have modeled the effects of dust on the SED of starbursts. A simple starburst model was used to determine the different populations of stars as a function of the starburst age. The flux at 23 wavelengths, ranging between 1000 Angstroms to 5500 Angstroms, was computed using Monte Carlo techniques assuming the dust and stars were spherically distributed. The dust was assumed to have similar properties as dust in our Galaxy. The distribution of different star types ranged from mostly centrally located for O stars to constant density for A and later stars. In addition, the fraction of stars lying outside the dust ranged from very few for O stars to a majority for A and later stars. Combining the two models, it was found that the SED was strongly dependent on the distribution of the different types of stars relative to the dust, the age of the starburst, and the amount of dust. The ``effective'' UV extinction curve became greyer and featureless as the amount of dust was increased. For example, the 2200 Angstroms bump was almost non-existent for large amounts of dust. This work was supported by NASA LTSA Grant NAGW-3168.

  8. Rangewide molecular structuring in the Utah sucker (Catostomus ardens).

    PubMed

    Mock, K E; Evans, R P; Crawford, M; Cardall, B L; Janecke, S U; Miller, M P

    2006-07-01

    The Utah sucker (Catostomus ardens) is endemic to the Bonneville Basin and the upper Snake River drainage in western North America, and is thought to hybridize with the federally endangered June sucker (Chasmistes liorus mictus) in Utah Lake (Bonneville Basin). Here we describe the discovery of a major subdivision in Utah suckers (4.5% mitochondrial sequence divergence) between the ancient Snake River drainage and the Bonneville Basin. This boundary has not previously been recognized in Utah suckers based on morphologic variation, but has been recently described in two endemic cyprinids in the region. Populations in valleys east of the Wasatch Mountains in Utah clustered with the Snake River populations, suggesting that these valleys may have had an ancient hydrologic connection to the Snake River. We also found evidence of population isolation within the Bonneville Basin, corresponding to two Pleistocene sub-basins of the ancient Lake Bonneville. In contrast, we found no molecular evidence for deep divergence between Utah suckers and June suckers in Utah Lake or for a history of hybridization between divergent lineages in that population, although we recognize that demographic events may have obscured this signal. These findings suggest that the morphological differences between Utah and June suckers in Utah Lake may be the result of strong, and relatively recent, ecological selection. In summary, morphological and molecular characters seem to vary along different axes in different portions of the range of this taxon, providing an interesting system for studying the contributions of neutral and adaptive variation to species diversity. PMID:16780436

  9. Structural hierarchy in molecular films of two class II hydrophobins.

    PubMed

    Paananen, Arja; Vuorimaa, Elina; Torkkeli, Mika; Penttilä, Merja; Kauranen, Martti; Ikkala, Olli; Lemmetyinen, Helge; Serimaa, Ritva; Linder, Markus B

    2003-05-13

    Hydrophobins are highly surface-active proteins that are specific to filamentous fungi. They function as coatings on various fungal structures, enable aerial growth of hyphae, and facilitate attachment to surfaces. Little is known about their structures and structure-function relationships. In this work we show highly organized surface layers of hydrophobins, representing the most detailed structural study of hydrophobin films so far. Langmuir-Blodgett films of class II hydrophobins HFBI and HFBII from Trichoderma reesei were prepared and analyzed by atomic force microscopy. The films showed highly ordered two-dimensional crystalline structures. By combining our recent results on small-angle X-ray scattering of hydrophobin solutions, we found that the unit cells in the films have dimensions similar to those of tetrameric aggregates found in solutions. Further analysis leads to a model in which the building blocks of the two-dimensional crystals are shape-persistent supramolecules consisting of four hydrophobin molecules. The results also indicate functional and structural differences between HFBI and HFBII that help to explain differences in their properties. The possibility that the highly organized surface assemblies of hydrophobins could allow a route for manufacturing functional surfaces is suggested. PMID:12731866

  10. 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.

  11. 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.

  12. 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.

  13. Dust Structure and Composition Within Molecular Clouds and Cores

    NASA Astrophysics Data System (ADS)

    Chapman, Nicholas L.; Mundy, L. G.

    2007-12-01

    We observed three molecular clouds and four isolated cores in both the JHK and Spitzer wavelengths. Our goal was to use these deep infrared data to map changes in the extinction law and the dust properties throughout our observed regions. The clouds we observed were Ophiuchus, Perseus, and Serpens and the cores were L204C-2, L1152, L1155C-2, and L1228. From 3.6-8 microns, we found that regions with column densities Ak < 0.5 in our clouds have an extinction law similar to the one observed in the diffuse ISM. At higher extinctions, there is evidence for grain growth because the extinction law flattens compared to that of the diffuse ISM and becomes more consistent with the extinction law predicted by the Weingartner & Draine (2001) Rv = 5.5 dust model. This model utilizes dust grains up to 10 times larger than those in the diffuse ISM. We observed this same extinction law in the cores, even for column densities Ak 1-2 in some of our clouds and cores, we see evidence at 5.8 microns for water ice forming on the dust grains. Two of our cores have molecular outflows which appear to be destroying large dust grains resulting in an extinction law similar to that found in the diffuse ISM. In both our clouds and cores, the extinction law at 24 microns is almost always 2-3 times higher than the value predicted by current dust models, consistent with the results found by Flaherty et al. (2007). Overall, there are relatively few stars with high S/N detections at 24 microns. More observations are needed to understand the nature of the extinction law at this wavelength. Support for this work was provided by NASA through JPL contracts 1224608, 1230782, 1230779, 1264793, and 1264492.

  14. The density structure of the L1157 molecular outflow

    NASA Astrophysics Data System (ADS)

    Gómez-Ruiz, A. I.; Codella, C.; Lefloch, B.; Benedettini, M.; Busquet, G.; Ceccarelli, C.; Nisini, B.; Podio, L.; Viti, S.

    2015-02-01

    We present a multiline CS survey towards the brightest bow-shock B1 in the prototypical chemically active protostellar outflow L1157. We made use of (sub-)mm data obtained in the framework of the Chemical HErschel Surveys of Star forming regions and Astrochemical Surveys at IRAM (ASAI) key science programs. We detected 12C32S, 12C34S, 13C32S, and 12C33S emissions, for a total of 18 transitions, with Eu up to ˜180 K. The unprecedented sensitivity of the survey allows us to carefully analyse the line profiles, revealing high-velocity emission, up to 20 km s-1 with respect to the systemic. The profiles can be well fitted by a combination of two exponential laws that are remarkably similar to what previously found using CO. These components have been related to the cavity walls produced by the ˜2000 yr B1 shock and the older (˜4000 yr) B2 shock, respectively. The combination of low- and high-excitation CS emission was used to properly sample the different physical components expected in a shocked region. Our CS observations show that this molecule is highlighting the dense, nH2 = 1-5 × 105 cm-3, cavity walls produced by the episodic outflow in L1157. In addition, the highest excitation (Eu ≥ 130 K) CS lines provide us with the signature of denser (1-5 × 106 cm-3) gas, associated with a molecular reformation zone of a dissociative J-type shock, which is expected to arise where the precessing jet impacting the molecular cavities. The CS fractional abundance increases up to ˜10-7 in all the kinematical components. This value is consistent with what previously found for prototypical protostars and it is in agreement with the prediction of the abundances obtained via the chemical code Astrochem.

  15. A UNIVERSAL, LOCAL STAR FORMATION LAW IN GALACTIC CLOUDS, NEARBY GALAXIES, HIGH-REDSHIFT DISKS, AND STARBURSTS

    SciTech Connect

    Krumholz, Mark R.; Dekel, Avishai; McKee, Christopher F. E-mail: dekel@phys.huji.ac.il

    2012-01-20

    Star formation laws are rules that relate the rate of star formation in a particular region, either an entire galaxy or some portion of it, to the properties of the gas, or other galactic properties, in that region. While observations of Local Group galaxies show a very simple, local star formation law in which the star formation rate per unit area in each patch of a galaxy scales linearly with the molecular gas surface density in that patch, recent observations of both Milky Way molecular clouds and high-redshift galaxies apparently show a more complicated relationship in which regions of equal molecular gas surface density can form stars at quite different rates. These data have been interpreted as implying either that different star formation laws may apply in different circumstances, that the star formation law is sensitive to large-scale galaxy properties rather than local properties, or that there are high-density thresholds for star formation. Here we collate observations of the relationship between gas and star formation rate from resolved observations of Milky Way molecular clouds, from kpc-scale observations of Local Group galaxies, and from unresolved observations of both disk and starburst galaxies in the local universe and at high redshift. We show that all of these data are in fact consistent with a simple, local, volumetric star formation law. The apparent variations stem from the fact that the observed objects have a wide variety of three-dimensional size scales and degrees of internal clumping, so even at fixed gas column density the regions being observed can have wildly varying volume densities. We provide a simple theoretical framework to remove this projection effect, and we use it to show that all the data, from small solar neighborhood clouds with masses {approx}10{sup 3} M{sub Sun} to submillimeter galaxies with masses {approx}10{sup 11} M{sub Sun }, fall on a single star formation law in which the star formation rate is simply {approx}1% of

  16. Outflow of hot and cold molecular gas from the obscured secondary nucleus of NGC 3256: closing in on feedback physics

    NASA Astrophysics Data System (ADS)

    Emonts, B. H. C.; Piqueras-López, J.; Colina, L.; Arribas, S.; Villar-Martín, M.; Pereira-Santaella, M.; Garcia-Burillo, S.; Alonso-Herrero, A.

    2014-12-01

    The nuclei of merging galaxies are often deeply buried in dense layers of gas and dust. In these regions, gas outflows driven by starburst and active galactic nuclear activity are believed to play a crucial role in the evolution of these galaxies. However, to fully understand this process it is essential to resolve the morphology and kinematics of such outflows. Using near-infrared integral-field spectroscopy obtained with SINFONI on the Very Large Telescope, we detect a kpc-scale structure of high-velocity molecular hydrogen (H2) gas associated with the deeply buried secondary nucleus of the infrared-luminous merger-galaxy NGC 3256. We show that this structure is most likely the hot component of a molecular outflow, which was recently also detected in the cold molecular gas through CO emission. This outflow, with a total molecular gas mass of MH2 ~ 2 × 107M⊙, is among the first to be spatially resolved in both the hot molecular H2 gas with VLT/SINFONI and the cold molecular CO emitting gas with ALMA. The hot and cold components share a similar morphology and kinematics, with a hot-to-cold molecular gas mass ratio of ~ 6 × 10-5. The high (~100 pc) resolution at which we map the geometry and velocity structure of the hot outflow reveals a biconical morphology with opening angle ~40° and gas spread across a FWZI ~ 1200 km s-1. Because this collimated outflow is oriented close to the plane of the sky, the molecular gas may reach maximum intrinsic outflow velocities of ~1800 km s-1, with an average mass outflow rate of at least Ṁoutfl ~ 20 M⊙ yr-1. By modeling the line-ratios of various near-infrared H2 transitions, we show that the H2-emitting gas in the outflow is heated through shocks or X-rays to a temperature of T ~ 1900 ± 300 K. The energy needed to drive the collimated outflow is most likely provided by a hidden Compton-thick AGN or by the nuclear starburst. We show that the global kinematics of the molecular outflow that we detect in NGC 3256 mimic

  17. Fluorescence characteristics of size-fractionated dissolved organic matter: implications for a molecular assembly based structure?

    PubMed

    Romera-Castillo, Cristina; Chen, Meilian; Yamashita, Youhei; Jaffé, Rudolf

    2014-05-15

    Surface freshwater samples from Everglades National Park, Florida, were used to investigate the size distributions of natural dissolved organic matter (DOM) and associated fluorescence characteristics along the molecular weight continuum. Samples were fractionated using size exclusion chromatography (SEC) and characterized by spectroscopic means, in particular Excitation-Emission Matrix fluorescence modeled with parallel factor analysis (EEM-PARAFAC). Most of the eight components obtained from PARAFAC modeling were broadly distributed across the DOM molecular weight range, and the optical properties of the eight size fractions for all samples studied were quite consistent among each other. Humic-like components presented a similar distribution in all the samples, with enrichment in the middle molecular weight range. Some variability in the relative distribution of the different humic-like components was observed among the different size fractions and among samples. The protein like fluorescence, although also generally present in all fractions, was more variable but generally enriched in the highest and lowest molecular weight fractions. These observations are in agreement with the hypothesis of a supramolecular structure for DOM, and suggest that DOM fluorescence characteristics may be controlled by molecular assemblies with similar optical properties, distributed along the molecular weight continuum. This study highlights the importance of studying the molecular structure of DOM on a molecular size distribution perspective, which may have important implications in understanding the environmental dynamics such materials. PMID:24602859

  18. Molecular structure, spectroscopic assignments and other quantum chemical calculations of anticancer drugs - A review.

    PubMed

    Ghasemi, A S; Deilam, M; Sharifi-Rad, J; Ashrafi, F; Hoseini-Alfatemi, S M

    2015-01-01

    In many texts, both theoretical and experimental studies on molecular structure and spectroscopic assignments of anticancer medicines have been reported. Molecular geometry parameters have been experimentally obtained by x-ray structure determination method and optimized using computational chemistry method like density functional theory. In this review, we consider calculations based on density function theory at B3LYP/6-31G (d,p) and B3LYP/6-311++G (d,p) levels of theory. Based on optimized geometric parameters of the molecules, molecular structures (length of bonds, bond angles and torsion angles) and vibrational assignments have been obtained. Molecular stability and bond strength have been investigated by applying natural bond orbital (NBO) analysis. Other molecular properties such as mulliken population analysis, thermodynamic properties and polarizabitities of these drugs have been reported. Calculated energies of HOMO and LUMO show that charge transfer occurs in the molecular. Information about the size, shape, charge density distribution and site of molecular chemical reactivity has been obtained by mapping electron density isosurface of electrostatic and compared with experiment data. PMID:26638891

  19. 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.

  20. Molecular structures of unbound and transcribing RNA polymerase III

    PubMed Central

    Hoffmann, Niklas A.; Jakobi, Arjen J.; Moreno-Morcillo, Maria; Glatt, Sebastian; Kosinski, Jan; Hagen, Wim J. H.; Sachse, Carsten; Müller, Christoph W.

    2015-01-01

    Transcription of genes encoding small structured RNAs such as tRNAs, spliceosomal U6 snRNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet structurally least characterized eukaryotic RNA polymerase. The cryo-EM structures of the S. cerevisiae Pol III elongating complex at 3.9 Å resolution and the apo Pol III enzyme in two different conformations at 4.6 and 4.7 Å resolution, respectively, allow for the first time to build a 17-subunit atomic model of Pol III. The reconstructions reveal the precise orientation of the C82/C34/C31 heterotrimer in close proximity to the stalk. The C53/C37 heterodimer positions residues involved in transcription termination close to the non-template DNA strand. In the apo Pol III structures, the stalk adopts different orientations coupled with closed and open conformations of the clamp. Our results provide novel insights into Pol III-specific transcription and the adaptation of Pol III towards its small transcriptional targets. PMID:26605533

  1. 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.

  2. 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. PMID:23399176

  3. 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. PMID:26752623

  4. Using Three-Dimensional Models to Teach Molecular Structures in High School Chemistry.

    ERIC Educational Resources Information Center

    Copolo, Cynthia F.; Hounshell, Paul B.

    1995-01-01

    Compares the effects of using two- and three-dimensional model representations of molecular structures on student learning of organic chemical structures. Reports that students using both three-dimensional computer models and ball-and-stick models scored higher on the three-dimensional retention test of isomeric identification but lower on a…

  5. 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…

  6. 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…

  7. 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. PMID:27524659

  8. Using molecular structure for reliable predicting enthalpy of melting of nitroaromatic energetic compounds.

    PubMed

    Semnani, Abolfazl; Keshavarz, Mohammad Hossein

    2010-06-15

    In this work, a reliable simple method has been introduced for predicting enthalpy of melting of nitroaromatic energetic compounds through their molecular structures. This method can be used for a wide range of nitroaromatics including halogenated nitroaromatic compounds. The contribution of hydrogen bonding and polar groups as well as structural parameters can be used to improve the predicted values on the basis of the number of carbon, nitrogen and oxygen atoms. The predicted results show that this method gives reliable prediction of standard enthalpy of melting with respect to the best available methods for different nitroaromatic compounds including high explosives with complex molecular structures. PMID:20117881

  9. 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

  10. Bias-dependent molecular-level structure of electrical double layer in ionic liquid on graphite

    SciTech Connect

    Black, Jennifer M; Walters, Deron; Labuda, Aleksander; Feng, Guang; Hillesheim, Patrick C; Dai, Sheng; Cummings, Peter T; Kalinin, Sergei V; Proksch, Roger; Balke, Nina

    2013-01-01

    Bias-dependent structure of electrochemical double layers at liquid-solid interfaces underpin a multitude of phenomena in virtually all areas of scientific enquiry ranging from energy storage and conversion systems, biology, to geophysics and geochemistry. Here we report the bias-evolution of the electric double layer structure of an ionic liquid on highly ordered pyrolytic graphite as a model system for carbon-based electrodes for electrochemical supercapacitors measured by atomic force microscopy. Matching the observed structures to molecular dynamics simulations allows us to resolve steric effects due to cation and anion layers. We observe reconfiguration under applied bias and the orientational transitions in the Stern layer. The synergy between molecular dynamics simulation and experiment provides a comprehensive picture of structural phenomena and long- and short range interactions. This insight will improve understanding of the mechanism of charge storage in electrochemical capacitors on a molecular level which can be used to enhance their electrochemical performance.

  11. Aqueous solubility of polychlorinated biphenyls related to molecular structure

    SciTech Connect

    Opperhulzen, A.; Gobas, F.A.P.C.; Van der Steen, J.M.D.; Hutzinger, O.

    1988-06-01

    Aqueous solubilities of polychlorinated biphenyls show a linear relationship between logarithms of aqueous activity coefficients and total surface areas (TSA) or total molecular volumes (TMV). The aqueous activity coefficients were calculated from experimental solubility data and values taken from the literature. The correlations improved substantially if a differential heat capacity between supercooled liquid and solid chemical (..delta..C/sub p/) equal to the entropy of fusion (..delta..S/sub f/), instead of ..delta..C/sub p/ = O, was assumed. In addition, it was found that dissolution of 2,2',4,4'-tetra- and 2,2',4,4'5,5'-hexachlorobiphenyl was accompanied by positive enthalpy and entropy changes, the entropy being dominant at room temperature. For the former compound, it was shown that the entropy of fusion is approximately to J K/sup -1/ mol/sup -1/, which is in agreement with the Walden rule. For 2,2',4,4',5,5'-hexachlorobiphenyl, it was shown that a Hildebrand plot provides a constant slope. This supported the assumption that differential heat capacity (..delta..C/sub p/) equals the entropy of fusion.

  12. Computational Electronic Structure of Photoinduced Spin Transitions in Molecular Photoswithches

    NASA Astrophysics Data System (ADS)

    Chachiyo, Teepanis

    2005-03-01

    Minimum Energy Crossing Points (MECPs) are the energy barriers associated with radiationless spin-crossover. Understanding the mechanisms of such spin-forbidden processes is of great fundamental and practical interest. Methods of locating MECPs have been developed by several authors with, in general, a poor convergence behavior which increases the computational cost. We present a new method based on spin density functional theory (SDFT) that exhibits fast logarithmic convergence and is suitable for large molecular systems. Spin photo-switchable compounds are becoming a growing area of research since, in principle, it is possible to exploit their spin degrees of freedom to store bits of information. For instance, the photoswitch [Fe(ptz)6](BF4)2;(ptz=1-propyltetrazole) has a singlet (S=0) ground state and, upon optical excitation, becomes trapped in a quintet state (S=2) as long as T < 50K. We applied our MECP methodology to study its geometrical and spin dynamics during spin crossover. Our results are useful for elucidating the geometric rearrangements and microscopic mechanisms that control the lifetime and the critical temperature of the meta-stable high spin (quintet) state. For example, the MECP-SDFT calculations showed that the transition from singlet ground state to a triplet ``intermediate'' state is accompanied by an unusually large 0.3å bond length elongation of the iron axial ligands.

  13. 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.

  14. DNA damage tolerance by recombination: Molecular pathways and DNA structures.

    PubMed

    Branzei, Dana; Szakal, Barnabas

    2016-08-01

    Replication perturbations activate DNA damage tolerance (DDT) pathways, which are crucial to promote replication completion and to prevent fork breakage, a leading cause of genome instability. One mode of DDT uses translesion synthesis polymerases, which however can also introduce mutations. The other DDT mode involves recombination-mediated mechanisms, which are generally accurate. DDT occurs prevalently postreplicatively, but in certain situations homologous recombination is needed to restart forks. Fork reversal can function to stabilize stalled forks, but may also promote error-prone outcome when used for fork restart. Recent years have witnessed important advances in our understanding of the mechanisms and DNA structures that mediate recombination-mediated damage-bypass and highlighted principles that regulate DDT pathway choice locally and temporally. In this review we summarize the current knowledge and paradoxes on recombination-mediated DDT pathways and their workings, discuss how the intermediate DNA structures may influence genome integrity, and outline key open questions for future research. PMID:27236213

  15. Crystal and molecular structure of perindopril erbumine salt

    NASA Astrophysics Data System (ADS)

    Remko, M.; Bojarska, J.; Ježko, P.; Sieroń, L.; Olczak, A.; Maniukiewicz, W.

    2011-06-01

    The crystal structure of perindopril (2S,3aS,7aS)-1-[(2S)-2-[[(2S)-1-ethoxy-1-oxopentan-2-yl]amino]propanoyl]-2,3,3a,4,5,6,7,7a-octahydroindole-2-carboxylic acid) erbumine salt C 23H 43N 3O 5, angiotensin-converting enzyme inhibitor, was determined from single-crystal X-ray diffraction data. The compound crystallizes in the triclinic, non-centrosymetric space group P1, with unit cell dimensions a = 6.575(3), b = 12.165(5), c = 16.988(8) Å and α = 97.153(4), β = 94.417(4), γ = 90.349(4)°, Z = 2. The structure was refined by full matrix least squares methods to R = 0.037. In the solid state ionized molecules of perindopril and erbumine are linked together forming a complex via O⋯HN + hydrogen bonds between the positively charged amino groups of the erbuminium cations and oxygen atoms of the perindopril carboxylate groups. Intermolecular N sbnd H⋯O and C sbnd H⋯O contacts seem to be effective in the stabilization of the structure, resulting in the formation of a three-dimensional network. The gas-phase structure of perindopril-erbumine complex was optimized by the HF/6-31G(d) and Becke3LYP/6-31G(d) methods. The conformational behavior of this salt in water was examined using the CPCM and Onsager models. In both the gas phase and water solution the perindopril erbumine will exist in prevailing triclinic form.

  16. 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.

  17. 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. PMID:26826800

  18. Microwave Spectrum of the SD+3 Ion: Molecular Structure.

    PubMed

    Araki; Ozeki; Saito

    1998-11-01

    The J = 1-0 to 4-3 spectral lines of SD+3 were measured in the 152-610 GHz region using a source-modulated microwave spectrometer. The SD+3 ion was generated in a free space absorption cell by a hollow-cathode discharge in a gas mixture of D2S and D2. The rotational constant B0 and the centrifugal distortion constants DJ and DJK were determined from the measured frequencies. A vibration-rotation analysis was carried out and the rz structures of SH+3 and SD+3 were derived from their zero point averaged rotational constants, expressed as SH+3: rz = 1.36512(22) Å and thetaz = 94.098(26) degrees, and SD+3: rz = 1.36086(16) Å and thetaz = 94.1211(195) degrees, where the difference between thetaz(HSH) and thetaz(DSD) was assumed to be the same as that between thetaz(HPH) of PH3 and thetaz(DPD) of PD3. From the shift between the rz structures of SH+3 and SD+3, the re structure of SH+3 was estimated to be re = 1.35001(113) Å, thetae = 94.181(135) degrees. Copyright 1998 Academic Press. PMID:9770407

  19. Structural design and molecular evolution of a cytokine receptor superfamily.

    PubMed Central

    Bazan, J F

    1990-01-01

    A family of cytokine receptors comprising molecules specific for a diverse group of hematopoietic factors and growth hormones has been principally defined by a striking homology of binding domains. This work proposes that the approximately 200-residue binding segment of the canonical cytokine receptor is composed of two discrete folding domains that share a significant sequence and structural resemblance. Analogous motifs are found in tandem approximately 100-amino acid domains in the extracellular segments of a receptor family formed by the interferon-alpha/beta and -gamma receptors and tissue factor, a membrane tether for a coagulation protease. Domains from the receptor supergroup reveal clear evolutionary links to fibronectin type III structures, approximately 90-amino acid modules that are typically found in cell surface molecules with adhesive functions. Predictive structural analysis of the shared receptor and fibronectin domains locates seven beta-strands in conserved regions of the chain; these strands are modeled to fold into antiparallel beta-sandwiches with a topology that is similar to immunoglobulin constant domains. These findings have strong implications for understanding the evolutionary emergence of an important class of regulatory molecules from primitive adhesive modules. In addition, the resulting double-barrel design of the receptors and the spatial clustering of conserved residues suggest a likely binding site for cytokine ligands. Images PMID:2169613

  20. 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

  1. 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.

  2. 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

    2016-05-01

    We present a detailed study of the neutral and ionised 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 ionised 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.

  3. Aspects of the interstellar medium in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Fanelli, Michael N.

    1990-07-01

    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.

  4. Redshift detection of the most distant lensed starbursts

    NASA Astrophysics Data System (ADS)

    Dunne, Loretta; van der Werf, Paul; Massardi, Marcella; White, Glenn; Serjeant, Stephen; Michalowski, Michal; Thompson, Mark; Birkinshaw, Mark; Andreani, Paola; Stevens, Jamie; Omont, Alain; Smith, Matthew; Ivison, Rob; Thomson, Alasdair; Eales, Steve; Ibar, Edo; Benford, Dominic; Dannerbauer, Helmut; Leeuw, Lerothodi; Temi, Pasquale; Negrello, Mattia; Clements, Dave; Bussmann, Shane; Maddox, Steve; De Vis, Pieter; Vlahakis, Catherine; Verma, Aprajita; Dye, Simon; Riechers, Dominik

    2013-10-01

    We propose to obtain redshifts for the four most distant (z_est > 3.8) and luminous galaxies in 90 sq deg of the Herschel-ATLAS southern field. The bright 500 micron fluxes of these sources means they are either gravitationally lensed or are among the rarest, most luminous starbursts in the universe. Creating large and unbiased samples of strong lenses is a key goal for H-ATLAS, allowing us to constrain cosmological parameters and the evolution of dark matter haloes, as well as providing an unprecedented sample of the most actively star forming galaxies in the early universe, able to be studied in exquisite detail thanks to the lensing magnification. The submm photo-z of these objects are 3.8

  5. 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.

  6. 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).

  7. 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.

  8. 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.

  9. Semifluorinated Alkanes at the Air-Water Interface: Tailoring Structure and Rheology at the Molecular Scale.

    PubMed

    Theodoratou, Antigoni; Jonas, Ulrich; Loppinet, Benoit; Geue, Thomas; Stangenberg, Rene; Keller, Rabea; Li, Dan; Berger, Rüdiger; Vermant, Jan; Vlassopoulos, Dimitris

    2016-04-01

    Semifluorinated alkanes form monolayers with interesting properties at the air-water interface due to their pronounced amphi-solvophobic nature and the stiffness of the fluorocarbons. In the present work, using a combination of structural and dynamic probes, we investigated how small molecular changes can be used to control the properties of such an interface, in particular its organization, rheology, and reversibility during compression-expansion cycles. Starting from a reference system perfluor(dodecyl)dodecane, we first retained the linear structure but changed the linkage groups between the alkyl chains and the fluorocarbons, by introducing either a phenyl group or two oxygens. Next, the molecular structure was changed from linear to branched, with four side chains (two fluorocarbons and two hydrocarbons) connected to extended aromatic cores. Neutron reflectivity at the air-water interface and scanning force microscopy on deposited films show how the changes in the molecular structure affect molecular arrangement relative to the interface. Rheological and compression-expansion measurements demonstrate the significant consequences of these changes in molecular structure and interactions on the interfacial properties. Remarkably, even with these simple molecules, a wide range of surface rheological behaviors can be engineered, from viscous over viscoelastic to brittle solids, for very similar values of the surface pressure. PMID:26978461

  10. 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.

  11. 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.

  12. 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. PMID:8196040

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. DIFFUSE HARD X-RAY EMISSION IN STARBURST GALAXIES AS SYNCHROTRON FROM VERY HIGH ENERGY ELECTRONS

    SciTech Connect

    Lacki, Brian C.; Thompson, Todd A.

    2013-01-01

    The origin of the diffuse hard X-ray (2-10 keV) emission from starburst galaxies is a long-standing problem. We suggest that synchrotron emission of 10-100 TeV electrons and positrons (e {sup {+-}}) can contribute to this emission, because starbursts have strong magnetic fields. We consider three sources of e {sup {+-}} at these energies: (1) primary electrons directly accelerated by supernova remnants, (2) pionic secondary e {sup {+-}} created by inelastic collisions between cosmic ray (CR) protons and gas nuclei in the dense interstellar medium of starbursts, and (3) pair e {sup {+-}} produced between the interactions between 10 and 100 TeV {gamma}-rays and the intense far-infrared (FIR) radiation fields of starbursts. We create one-zone steady-state models of the CR population in the Galactic center (R {<=} 112 pc), NGC 253, M82, and Arp 220's nuclei, assuming a power-law injection spectrum for electrons and protons. We consider different injection spectral slopes, magnetic field strengths, CR acceleration efficiencies, and diffusive escape times, and include advective escape, radiative cooling processes, and secondary and pair e {sup {+-}}. We compare these models to extant radio and GeV and TeV {gamma}-ray data for these starbursts, and calculate the diffuse synchrotron X-ray and inverse Compton (IC) luminosities of these starbursts in the models which satisfy multiwavelength constraints. If the primary electron spectrum extends to {approx}PeV energies and has a proton/electron injection ratio similar to the Galactic value, we find that synchrotron emission contributes 2%-20% of their unresolved, diffuse hard X-ray emission. However, there is great uncertainty in this conclusion because of the limited information on the CR electron spectrum at these high energies. IC emission is likewise a minority of the unresolved X-ray emission in these starbursts, from 0.1% in the Galactic center to 10% in Arp 220's nuclei, with the main uncertainty being the starbursts

  18. Diffuse Hard X-Ray Emission in Starburst Galaxies as Synchrotron from Very High Energy Electrons

    NASA Astrophysics Data System (ADS)

    Lacki, Brian C.; Thompson, Todd A.

    2013-01-01

    The origin of the diffuse hard X-ray (2-10 keV) emission from starburst galaxies is a long-standing problem. We suggest that synchrotron emission of 10-100 TeV electrons and positrons (e ±) can contribute to this emission, because starbursts have strong magnetic fields. We consider three sources of e ± at these energies: (1) primary electrons directly accelerated by supernova remnants, (2) pionic secondary e ± created by inelastic collisions between cosmic ray (CR) protons and gas nuclei in the dense interstellar medium of starbursts, and (3) pair e ± produced between the interactions between 10 and 100 TeV γ-rays and the intense far-infrared (FIR) radiation fields of starbursts. We create one-zone steady-state models of the CR population in the Galactic center (R <= 112 pc), NGC 253, M82, and Arp 220's nuclei, assuming a power-law injection spectrum for electrons and protons. We consider different injection spectral slopes, magnetic field strengths, CR acceleration efficiencies, and diffusive escape times, and include advective escape, radiative cooling processes, and secondary and pair e ±. We compare these models to extant radio and GeV and TeV γ-ray data for these starbursts, and calculate the diffuse synchrotron X-ray and inverse Compton (IC) luminosities of these starbursts in the models which satisfy multiwavelength constraints. If the primary electron spectrum extends to ~PeV energies and has a proton/electron injection ratio similar to the Galactic value, we find that synchrotron emission contributes 2%-20% of their unresolved, diffuse hard X-ray emission. However, there is great uncertainty in this conclusion because of the limited information on the CR electron spectrum at these high energies. IC emission is likewise a minority of the unresolved X-ray emission in these starbursts, from 0.1% in the Galactic center to 10% in Arp 220's nuclei, with the main uncertainty being the starbursts' magnetic field. We also model generic starbursts, including

  19. 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.

  20. 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.

  1. Two-dimensional topological insulator molecular networks: dependence on structure, symmetry, and composition

    NASA Astrophysics Data System (ADS)

    Tan, Liang Z.; Louie, Steven G.

    2014-03-01

    2D molecular networks can be fabricated from a wide variety of molecular building blocks, arranged in many different configurations. Interactions between neighboring molecular building blocks result in the formation of new 2D materials. Examples of 2D organic topological insulators, that contain molecular building blocks and heavy elements arranged in a hexagonal lattice, have been recently proposed by Feng Liu and coworkers (Nano Lett., 13, 2842 (2013)). In this work, we present a systematic study of the design space of 2D molecular network topological insulators, elucidating the role of structure, symmetry, and composition of the networks. We show that the magnitude and presence of spin-orbit gaps in the electronic band structure is strongly dependent on the symmetry properties and arrangement of the individual components of the molecular lattice. We present general rules to maximize the magnitude of spin-orbit gaps and perform ab-initio calculations on promising structures derived from these guidelines. This work was supported by National Science Foundation Grant No. DMR10-1006184, the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Computational resources have been provided by the NSF through XSEDE resources at NICS.

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    We present the evolution in the number density and stellar mass functions of photometrically selected post-starburst galaxies in the UKIDSS Deep Survey (UDS), 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% of the total population at z ˜ 2, to <1% 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% 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.

  4. The effect of central starbursts on the interstellar medium of dwarf galaxies

    NASA Technical Reports Server (NTRS)

    De Young, David S.; Heckman, Timothy M.

    1994-01-01

    Major starburst events can last tens of millions of years, and in the process they can deposit significant amounts of energy into the surrounding interstellar medium. This energy from supernova and stellar winds imparts enough momentum to the interstellar medium (ISM) that portions of the ISM can become unbound and leave the parent galaxy, taking the metal-enriched stellar debris along. In dwarf galaxies, starbursts can produce enough total energy to unbind most or all of the ambient ISM. Whether this actually occurs is a strong function of the ellipticity of the ISM distribution, with flat disks and spheres being the limiting cases. We calculate whether 'blow out' along the symmetry axis of 'blow away' of the entire ISM occurs during a central starburst in dwarf galaxies as a function of galactic mass, starburst energy, ISM density, and ISM ellipticity. The calculations cover a range of 10(exp 7) to 10(exp 9) solar mass for dwarf galaxies and include 'normal' galaxies of 10(exp 11) solar mass as well. No massive dark matter halos are assumed to be present. We find that for physically reasonable values of total ISM mass and starburst energy a blow out along the symmetry axis occurs in the majority of cases, though a significant fraction of small dwarf galaxies can lose most of their ISM. As no dark matter halos or clumpy ISM distributions are included, it is apparent that the ISM in most dwarf galaxies may be generally resistant to significant disruption by a central starburst event. The effects of this range of behavi or on the metallicities that would be observed in these galaxies is discussed.

  5. Structural studies of molecular and metallic overlayers using angle- resolved photoemission extended fine structure

    SciTech Connect

    Huang, Z.

    1992-10-01

    Angle-resolved photoemission extended fine structure (ARPEFS) was used to study molecular and metallic overlayers on metal surfaces through analysis of p2mg(2{times}1)CO/Ni(110) and the p(2{times}2)K/Ni(111) adsorption. For the dense p2mg(2{times}1)CO/Ni(110) surface layer, photoemission intensities from C 1s level were measured in three directions at photoelectron kinetic energies 60-400 eV. Using multiple-scattering spherical-wave (MSSW) modeling, it was found that CO molecules are adsorbed on short-bridge sites, with adjacent CO along the [110] direction displaced alternatively in opposite directions towards the [001] azimuths to form a zigzag chain geometry. The tilt angle is 16{plus_minus}2{degree} from the surface normal for the direction linking the C atom and the center of the Ni bridge. The carbon C-Ni interatomic distance was determined to be 1.94{plus_minus}0.02{Angstrom}. The first- to second-layer spacing of Ni is 1.27{plus_minus}0.04{Angstrom}, up from 1.10{Angstrom} for the clean Ni(110) surface, but close to the 1.25{Angstrom} Ni interlayer spacing in the bulk. The C-O bond length and tilt angle were varied within small ranges (1.10--1.20{Angstrom} and 15--23{degrees}) in our MSSW simulations. Best agreement between experiment and simulations was achieved at 1.16{Angstrom} and 19{degrees}. This yields an O-O distance of 2.95{Angstrom} for the two nearest CO molecules, (van der Waals` radius {approximately} 1.5 {Angstrom} for oxygen). Two different partial-wave phase-shifts were used in MSSW, and structural results from both are in very good agreement. For the p(2{times}2)K/Ni(111) overlayer, ARPEFS {chi}(k) curves from K 1s level measured along [111] and [771] at 130K showed that the K atoms are preferentially adsorbed on the atop sites, in agreement with a LEED study of the same system.

  6. Structural studies of molecular and metallic overlayers using angle- resolved photoemission extended fine structure

    SciTech Connect

    Huang, Z.

    1992-10-01

    Angle-resolved photoemission extended fine structure (ARPEFS) was used to study molecular and metallic overlayers on metal surfaces through analysis of p2mg(2[times]1)CO/Ni(110) and the p(2[times]2)K/Ni(111) adsorption. For the dense p2mg(2[times]1)CO/Ni(110) surface layer, photoemission intensities from C 1s level were measured in three directions at photoelectron kinetic energies 60-400 eV. Using multiple-scattering spherical-wave (MSSW) modeling, it was found that CO molecules are adsorbed on short-bridge sites, with adjacent CO along the [110] direction displaced alternatively in opposite directions towards the [001] azimuths to form a zigzag chain geometry. The tilt angle is 16[plus minus]2[degree] from the surface normal for the direction linking the C atom and the center of the Ni bridge. The carbon C-Ni interatomic distance was determined to be 1.94[plus minus]0.02[Angstrom]. The first- to second-layer spacing of Ni is 1.27[plus minus]0.04[Angstrom], up from 1.10[Angstrom] for the clean Ni(110) surface, but close to the 1.25[Angstrom] Ni interlayer spacing in the bulk. The C-O bond length and tilt angle were varied within small ranges (1.10--1.20[Angstrom] and 15--23[degrees]) in our MSSW simulations. Best agreement between experiment and simulations was achieved at 1.16[Angstrom] and 19[degrees]. This yields an O-O distance of 2.95[Angstrom] for the two nearest CO molecules, (van der Waals' radius [approximately] 1.5 [Angstrom] for oxygen). Two different partial-wave phase-shifts were used in MSSW, and structural results from both are in very good agreement. For the p(2[times]2)K/Ni(111) overlayer, ARPEFS [chi](k) curves from K 1s level measured along [111] and [771] at 130K showed that the K atoms are preferentially adsorbed on the atop sites, in agreement with a LEED study of the same system.

  7. A Molecular Structural Basis for the Excitation Properties of Axons

    PubMed Central

    Goldman, David E.

    1964-01-01

    A structural model is suggested for axon membranes consisting of a double layer of lipid and phospholipid molecules in which the polar ends of certain phospholipids change their orientation and combining properties under the influence of an electric field. The phosphate groups act as ion exchange “gates” for the control of ion flow through the membrane. Expressions are developed for the calculation of membrane current components as functions of time, potential, and ionic environment. Approximate solutions show fairly good agreement with existing experimental data in a number of different respects such as steady-state current-voltage relations, the effect of calcium on steady-state current, potassium tracer flux ratios, initial current and rate of change of current, and the dependence of the time constants of current change on membrane potential. PMID:14185580

  8. 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

  9. Mouse alpha-macroglobulin. Structure, function and a molecular model.

    PubMed Central

    Hudson, N W; Kehoe, J M; Koo, P H

    1987-01-01

    Mouse alpha-macroglobulin (M-AMG) is believed to be a functional homologue of human alpha 2-macroglobulin (h-alpha 2M). The subunit composition, the tryptic cleavage pattern before and after methylamine incorporation and the two-dimensional tryptic-peptide mapping, however, indicate that these two proteins are structurally distinct. M-AMG is composed of two major types of polypeptides (Mr 163,000 and 35,000) together with a minor polypeptide (Mr 185,000), whereas h-alpha 2M has only one type of polypeptide (Mr 185,000). After incorporation of methylamine, there is no change in the normal tryptic-cleavage pattern of M-AMG; however, tryptic cleavage of h-alpha 2M is severely retarded [Hudson & Koo (1982) Biochim. Biophys. Acta 704, 290-303]. The N-terminal sequence of the 163,000-Mr polypeptide of M-AMG shows sequence homology with the N-terminal sequence of h-alpha 2M. The amino acid compositions of M-AMG and its two major polypeptide chains are compared. Thermal fragmentation studies show that the 163,000-Mr polypeptide is broken down into 125,000-Mr and 29,000-Mr fragments. Trypsin-binding studies show that M-AMG can bind two molecules of trypsin/molecule. Inactivations of the trypsin-binding property of M-AMG and h-alpha 2M with methylamine show similar kinetics of inhibition at 4 degrees C. A structural model of M-AMG is proposed, based on accumulated data. Images Fig. 3. PMID:2449173

  10. 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

  11. Inhibition of barium sulfate deposition by polycarboxylates of various molecular structures

    SciTech Connect

    van der Leeden, M.C.; van Rosmalen, G.M. )

    1990-02-01

    To establish a relationship between the molecular structure of polycarboxylates and their growth-retarding influence on barium sulfate, seeded-suspension-growth experiments were performed at various inhibitor concentrations and pH values. Two types of polycarboxylates with a molecular structure based on their polyacrylic or maleic acid were studied. The molecular structure of these compounds were varied by particle substitution with monomers containing hydroxyl, amide, and sulfonic acid, as well as hydrophobic groups. Hydrophobic groups are detrimental to good inhibitor performance, whereas the introduction of OH, NH {sub 2}, or SO {sub 3} H groups presents opportunities to enhance the inhibitor effectiveness. The sequence in performance of the compounds on barium sulfate was compared with the sequence formerly obtained for calcium sulfate dihydrate.

  12. Molecular structure and rotary dynamics of Enterococcus hirae V₁-ATPase.

    PubMed

    Iino, Ryota; Minagawa, Yoshihiro; Ueno, Hiroshi; Hara, Mayu; Murata, Takeshi

    2014-09-01

    V1-ATPase is a rotary molecular motor in which the mechanical rotation of the rotor DF subunits against the stator A3B3 ring is driven by the chemical free energy of ATP hydrolysis. Recently, using X-ray crystallography, we solved the high-resolution molecular structure of Enterococcus hirae V1-ATPase (EhV1) and revealed how the three catalytic sites in the stator A3B3 ring change their structure on nucleotide binding and interaction with the rotor DF subunits. Furthermore, recently, we also demonstrated directly the rotary catalysis of EhV1 by using single-molecule high-speed imaging and analyzed the properties of the rotary motion in detail. In this critical review, we introduce the molecular structure and rotary dynamics of EhV1 and discuss a possible model of its chemomechanical coupling scheme. PMID:25229752

  13. 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. PMID:22571663

  14. 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.

  15. The Wolf-Rayet Population and ISM Interaction in Nearby Starbursts

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.; Monreal-Ibero, A.; Vílchez, J. M.; Pérez-Montero, E.; Iglesias-Páramo, J.; Sandin, C.; Relano, M.; Amorín, R.

    The interaction between massive star formation and gas is a key ingredient in galaxy evolution. Given the level of observational detail currently achievable in nearby starbursts, they constitute ideal laboratories to study interaction process that contribute to global evolution in all types of galaxies. Wolf-Rayet (WR) stars, as an observational marker of high mass star formation, play a pivotal role and their winds can strongly influence the surrounding gas. Imaging spectroscopy of two nearby (<4 Mpc) starbursts, both of which show multiple regions with WR stars, are discussed. The relation between the WR content and the physical and chemical properties of the surrounding ionized gas is explored.

  16. Formation of the twin galactic starburst regions NGC6334 and NGC6357

    NASA Astrophysics Data System (ADS)

    Torii, Kazufumi; Hasegawa, Keisuke; Ohama, Akio; Yamamoto, Hiroaki; Tachihara, Kengo; Fukui, Yasuo

    2015-08-01

    Since 2009, several molecular line observations toward the galactic high-mass star forming regions have indicated that cloud-cloud collisions (CCC) play an important role in forming high-mass stars; for example, super star clusters Westerlund2, NGC3603, and RCW38 (Furukawa et al. 2009; Fukui et al. 2014, 2015) and small galactic HII regions M20 and RCW120 which are each excited by a single O star (Torii et al. 2011, 2015). Using the NANTEN2 4-m telescope situated at Atacama, Chile, we have completed a large-scale molecular line mapping toward young galactic starburst regions NGC6334 and NGC6357. The two regions have several clusetrs which are rich in O stars having 30-100 MSun and are suggested to be physically connected with each other, although they are separated by 100 pc. Our new CO observations show that two molecular cloud complexes are distributed toward NGC6334 and NGC6357 at two different velocities, -3 km/s and -18 km/s. They have filamentary distributions elongated for over 100 pc nearly parallel to the galactic plane. The -3km/s complex apparently shows morphological agreements with the nebulosity in NGC6334 and NGC6357, and the -18km/s complex shows complementary distributions with the -3 km/s complex especially toward the O stars. Furthermore, intermediate velocity features which connect the two complexes are seen toward the same direction. These observational signatures indicate the physical association of the two cloud complexes with NGC6334 and NGC6357. We postulate a scenario that a collision between the two filamentary cloud complexes with a colliding velocity ~15 km/s triggered high-mass star formation in NGC6334 and NGC6357. The timescale of the collision, thus the high-mass star formation, is estimated to be less than 0.5 Myrs, which corresponds to a mass accretion rate up to 2×10-4 MSun/yr. Previous known CCC origin objects are the ones in which high-mass star were formed at a very limited volume less than 1pc3. In contrast, the CCC in NGC

  17. Molecular Structure of Aggregated Amyloid-β: Insights from Solid-State Nuclear Magnetic Resonance.

    PubMed

    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 to characterize the molecular structures of Aβ aggregates. Full molecular structural models based primarily on data from measurements using solid-state nuclear magnetic resonance (ssNMR) 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

  18. 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.

  19. 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). PMID:26594569

  20. 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).

  1. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    PubMed Central

    Shi, Fei; Qin, Song; Wang, Yin-Chu

    2011-01-01

    Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions. PMID:21904470

  2. Molecular structure, photophysical and thermal properties of samarium (III) complexes

    NASA Astrophysics Data System (ADS)

    Kumar, Rajeev; Singh, Udai P.

    2008-03-01

    Some 8-coordinated samarium (III) complexes ( 1- 4) having bipy (2,2'-bipyridine), terpy (2,2':6',2″-terpyridine), phen (1,10-phenanthroline) and tp [hydrotris (pyrazol-1-yl) borate] as supporting ligands have been synthesized and structurally characterized by different techniques including X-ray crystallography. The X-ray studies demonstrated that the complexes 1, 2 and 4 crystallized in triclinic space group P1¯ with cell dimensions a = 8.5640(2) Å, b = 8.8696(2) Å, c = 15.8608(4) Å for 1; a = 7.2113(9) Å, b = 11.0737(14) Å, c = 13.6289(18) Å for 2; a = 12.440(3) Å, b = 12.874(3) Å, c = 17.822(4) Å for 4, whereas the complex 3 crystallized in the monoclinic space group P2 1/ c with cell dimensions a = 9.472(3) Å, b = 17.092(5) Å, c = 14.516(5) Å. The IR study suggested that the azide is coordinated in 1, 3-bridging mode in complex 4. The photophysical properties of above complexes have been studied with ultraviolet absorption and emission spectral studies. Thermogravimetric analyses suggested that all these complexes undergo the complete decomposition to form the thermally stable samarium oxide (Sm 2O 3).

  3. Molecular-structure variation of organic materials irradiated with atmospheric pressure plasma

    NASA Astrophysics Data System (ADS)

    Takenaka, K.; Miyazaki, A.; Setsuhara, Y.

    2014-06-01

    The effect of atmospheric pressure He plasma on the molecular structure of polyethylene terephthalate (PET) has been investigated. The plasma composition was analyzed using optical emission spectroscopy. In addition to strong He emission lines, lines due to O and N radicals were also detected. The change in the molecular structure of the PET film surface was investigated using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. It was found that plasma irradiation led to oxidation and degradation of the surface due to chemical and physical effects of the active species. The results demonstrate the feasibility of observing the interaction of plasma with organic material on a local scale.

  4. 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.

  5. Modulated structure and molecular dissociation of solid chlorine at high pressures.

    PubMed

    Li, Peifang; Gao, Guoying; Ma, Yanming

    2012-08-14

    Among diatomic molecular halogen solids, high pressure structures of solid chlorine (Cl(2)) remain elusive and least studied. We here report first-principles structural search on solid Cl(2) 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 Br(2) and I(2), it was suggested that solid Cl(2) 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 Cl(2) into monatomic phases having body centered orthorhombic (bco) and face-centered cubic (fcc) structures, respectively. One unique monatomic structural feature of solid Cl(2) 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 Br(2) and I(2). Electron-phonon coupling calculations revealed that solid Cl(2) 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 A(g) vibrational (rotational) Raman mode in the Cmca phase might be the driving force to initiate the transition. PMID:22897288

  6. 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

  7. Recombinant human betacellulin. Molecular structure, biological activities, and receptor interaction.

    PubMed

    Watanabe, T; Shintani, A; Nakata, M; Shing, Y; Folkman, J; Igarashi, K; Sasada, R

    1994-04-01

    Soluble forms of human betacellulin (BTC) were purified to homogeneity from the conditioned medium of mouse A9 cells transfected with the BTC precursor cDNA. Three types of soluble BTC, designated BTC-1a, BTC-1b and BTC-2, were resolved by cation-exchange and size-exclusion column chromatography. Physicochemical analysis has revealed that BTC-1a represents the glycosylated, intact molecule composed of 80 amino acid residues (Asp32 to Tyr111 of the precursor molecule). BTC-1b appears to be a truncated molecule lacking 12 amino acid residues from the amino terminus of BTC-1a. BTC-2 was found to be a 50-amino acid molecule (Arg62 to Tyr111) that corresponds to the epidermal growth factor (EGF) structural unit. The biological activities of these BTC molecules were essentially identical as judged by their mitogenicity on Balb/c 3T3 fibroblasts. BTC and EGF were equipotent in stimulating Balb/c 3T3 cell proliferation and rat mesangial cell Ca2+ mobilization as well as in inhibiting the growth of human epidermoid carcinoma A431 cells. BTC and EGF antagonized each other with similar dose dependence for binding to A431 cells, indicating that these factors bind the same receptor molecules with equivalent avidity. The Kd value of EGF receptor (EGFR) and BTC is 0.5 nM as determined on Balb/c 3T3 cells. In addition, human mammary carcinoma MDA-MB-453 cells, which express multiple members of the EGFR family, were found to possess 2.7 x 10(3) BTC binding sites/cell, and the binding was readily quenched by EGF. These results suggest that the primary receptor for BTC is EGFR. PMID:8144591

  8. 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.

  9. 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

  10. 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. PMID:24676684