Science.gov

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. Feedback Mechanisms of Starbursts and AGNs through Molecular Outflows

    NASA Astrophysics Data System (ADS)

    Matsushita, S.; Krips, M.; Lim, J.; Muller, S.; Tsai, A.-L.

    2013-10-01

    Our deep molecular line images of nearby starburst galaxies and AGNs exhibit molecular outflows in most galaxies, and have revealed that the molecular outflows co-exist with outflows or jets seen in other wavelengths. In case of starbursts, X-ray outflows have higher energy and pressure than those of molecular outflows, suggesting that plasma outflows are blowing the molecular gas away from starburst regions, which suggests a strong negative feedback. On the other hand, current starburst regions in M82 can be seen at the inner edge of an expanding molecular bubble, suggesting a positive feedback. In case of AGNs, jets seem to entrain the surrounding molecular gas away from the AGNs, suggesting a negative feedback.

  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. Kinematics and Structure of the Starburst Galaxy NGC 7673

    NASA Astrophysics Data System (ADS)

    Homeier, N. L.; Gallagher, J. S.

    1999-09-01

    The morphology and kinematics of the luminous blue starburst galaxy NGC 7673 are explored using the WIYN (Wisconsin-Indiana-Yale-NOAO) 3.5 m telescope. Signs of a past kinematic disturbance are detected in the outer galaxy; the most notable feature is a luminous ripple located 1.55 arcmin from the center of NGC 7673. Subarcsecond imaging in B and R filters also reveals red dust lanes and blue star clusters that delineate spiral arms in the bright inner disk, and narrowband Hα imaging shows that the luminous star clusters are associated with giant H II regions. The Hα kinematics measured with echelle imaging spectroscopy using the WIYN DensePak fiber array imply that these H II regions are confined to a smoothly rotating disk. The velocity dispersion in ionized gas in the disk is σ~24 km s-1, which sets an upper boundary on the dispersion of young stellar populations. Broad emission components with σ~63 km s-1 found in some regions are likely produced by mechanical power supplied by massive, young stars; a violent starburst is occurring in a kinematically calm disk. Although the asymmetric outer features point to a merger or interaction as the starburst trigger, the inner disk structure constrains the strength of the event to the scale of a minor merger or weak interaction that occurred at least an outer disk dynamical timescale in the past.

  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. 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.

  7. 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.

  8. Resolving the Chemistry of Molecular Gas that Fuels Luminous Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Meier, David; Turner, Jean; Anderson, Crystal

    2012-10-01

    Energy input from massive stars profoundly impact on how starburst galaxies evolve. Both the triggers of and feedback from star formation manifest themselves in the gas chemistry. We use millimeter interferometry to obtain high spatial resolution maps of CO, HCO^+, CCH, NNH^+, HNCO, CH3OH and SiO, toward the starbursts, Maffei 2, M 82, IRAS 04296+2923 and Arp 220. Dramatic variations in gas chemistry are observed both within the individual galaxies and from galaxy to galaxy. These variations correlate with star formation and gas dynamics. CO isotopologues are used to constrain the evolutionary history of star formation. Species preferentially formed (CCH) and destroyed (NNH^+) in the presence of strong UV radiation map out where energy input from the massive stars dominate. CCH abundances are correlated with star formation rate, except in the most extreme starburst, Arp 220, whereas NNH^+ abundances drop, except for Arp 220. The abundance anomalies in Arp 220 hint that the molecular medium in the most extreme starbursts is different. HNCO, CH3OH and SiO locate shocks due to bars and galaxy-galaxy mergers in these systems. Comparisons between these species suggest shock strength does not change across bars, but does for merger remnants.

  9. Warm, Dense Molecular Gas in the ISM of Starbursts, LIRGs, and ULIRGs

    NASA Astrophysics Data System (ADS)

    Narayanan, Desika; Groppi, Christopher E.; Kulesa, Craig A.; Walker, Christopher K.

    2005-09-01

    The role of star formation in luminous and ultraluminous infrared galaxies (LIRGs, LIR>=1011 Lsolar ULIRGs, LIR>=1012 Lsolar) is a hotly debated issue: while it is clear that starbursts play a large role in powering the IR luminosity in these galaxies, the relative importance of possible enshrouded AGNs is unknown. It is therefore important to better understand the role of star-forming gas in contributing to the infrared luminosity in IR-bright galaxies. The J=3 level of 12CO lies 33 K above ground and has a critical density of ~1.5×104 cm-3. The 12CO J=3-2 line serves as an effective tracer for warm, dense molecular gas heated by active star formation. Here we report on 12CO J=3-2 observations of 17 starburst spiral galaxies, LIRGs, and ULIRGs, which we obtained with the Heinrich Hertz Submillimeter Telescope on Mount Graham, Arizona. Our main results are as follows. (1) We find a nearly linear relation between the infrared luminosity and warm, dense molecular gas such that the infrared luminosity increases as the warm, dense molecular gas to the power 0.92; we interpret this to be roughly consistent with the recent results of Gao & Solomon. (2) We find LIR/MH2warm,dense ratios ranging from ~38 to ~482 Lsolar/Msolar using a modified CO-H2 conversion factor of 8.3×1019 cm-2 (K km s-1)-1 derived in this paper.

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

    SciTech Connect

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

    2013-05-01

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

  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. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  14. 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.

  15. 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.

  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.

  17. The infrared structure and the origin of the starburst disk in NGC 1068

    NASA Technical Reports Server (NTRS)

    Telesco, C. M.; Decher, R.

    1988-01-01

    A detailed map of the extranuclear IR emission in the central 4 kpc of the luminous Seyfert galaxy NGC 1068 is presented. The relationship of the IR emission with low-excitation, visible H II regions implies that the IR luminosity is powered by recent star formation. The observations show that the star formation is distributed across the central 3.5 kpc primarily in two very extended complexes, one located to the north of the nucleus and the other to the southwest. These two complexes coincide with the two dominant CO features. It is shown that there are two inner Lindblad resonances which occur near the ends of the bar which approximately bound the IR-luminous star-forming regions, the CO complexes, and the visually bright spiral arms. It is proposed that the starburst results from a bar-driven density wave which also includes the effects of shock focusing.

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

    NASA Astrophysics Data System (ADS)

    Noeske, K. G.

    2003-03-01

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

  19. 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.

  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

    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.

  3. The Optical Structure of the Starburst Galaxy M82. I. Dynamics of the Disk and Inner-Wind

    NASA Astrophysics Data System (ADS)

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

    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 × 0.9 kpc of the disk. These cover the emission lines of Hα, [N II], [S II], and [S III] at a spectral resolution of 45-80 km s-1. The high signal-to-noise of the data is sufficient to accurately decompose the emission line profiles into multiple narrow components (FWHM ~ 30-130 km s-1) superimposed on a broad (FWHM ~ 150-350 km s-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-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 implications of this. We confirm that the

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Umehata, Hideki

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

  6. Understanding molecular structure from molecular mechanics.

    PubMed

    Allinger, Norman L

    2011-04-01

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

  7. 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

  8. 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.

  9. The IMACS Cluster Building Survey. V. Further Evidence for Starburst Recycling from Quantitative Galaxy Morphologies

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    Using J- and K 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. Data were obtained using the 6.5 m Magellan Telescopes at Las Campanas Observatory, Chile.

  10. 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.

  11. 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%.

  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. 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

  14. Rotating Nuclear Rings and Extreme Starbursts in Ultraluminous Galaxies

    NASA Astrophysics Data System (ADS)

    Downes, D.; Solomon, P. M.

    1998-11-01

    outer disk. The narrow CO line width, the single-peak line profile, the equality of the major and minor axes, and the observed velocity gradients all imply that the molecular disk is nearly face-on, yielding low optical and UV extinction to the active galactic nucleus (AGN). Such a geometry means that the molecular disk cannot be heated by the AGN; the far-infrared (FIR) luminosity of Mrk 231 is powered by a starburst, not the AGN. In Mrk 273, the CO (1-0) maps show long streamers of radius 5 kpc (7") with velocity gradients north-south, and a nuclear disk of radius 400 pc (0.6") with velocity gradients east-west. The nuclear disk contains a bright CO core of radius 120 pc (0.2"). In Arp 220, the CO and 1.3 mm continuum maps show the two ``nuclei'' embedded in a central ring or disk at P.A. 50° and a fainter structure extending 7" (3 kpc) to the east, normal to the nuclear disk. Models of the CO and dust flux indicate that the two K-band sources contain high-density gas, with n(H2) = 2 × 104 cm-3. There is no evidence that these sources really are the premerger nuclei. They are more likely to be compact extreme starburst regions, containing 109 M⊙ of dense molecular gas and new stars, but no old stars. Most of the HCN emission arises in the two nuclei. The luminosity-to-mass ratios for the CO sources in Arp 220 are compatible with the early phases of compact starbursts. There is a large mass of molecular gas currently forming stars with plenty of ionizing photons, and no obvious AGN. The entire bolometric luminosity of Arp 220 comes from starbursts, not an AGN. The CO maps show that the gas in ultraluminous IR galaxies is in extended disks that cannot intercept all the power of central AGNs, even if they exist. We conclude that in ultraluminous IR galaxies--even in Mrk 231, which hosts a quasar--the FIR luminosity is powered by extreme starbursts in the molecular rings or disks, not by dust-enshrouded quasars.

  15. 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.

  16. (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.

  17. 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.

  18. 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

  19. Chandra Observations of Starburst Galaxies

    NASA Technical Reports Server (NTRS)

    Prestwich, Andrea; Lavoie, Anthony R. (Technical Monitor)

    2000-01-01

    We present early X-ray results from Chandra for two starburst galaxies, M82 and NGC3256, obtained using AXAF CCD Imaging Spectrometer (ACIS-I) and the HRC. For M82 the arcsecond spatial resolution enables us to separate the point source component from the extended emission for the first time. Astrometry reveals that most of the X-ray sources are not coincident with the family of compact radio sources believed to be Super Nova Remnants (SNRs). In addition, based on three epoch Chandra observations, several of the X-ray sources are clearly variable indicating that they are binaries. When we deconvolve the extended and point source components detected in the hard X-ray band, we find that 50 percent arises from the extended component. This fact, together with its morphology, constrains the various models proposed to explain the hard X-ray emission. For NGC3256 we resolve two closely separated nuclei. These new data support a pure starburst origin for the total X-ray emission rather than a composite AGN/starburst, thereby making NGC3256 one of the most X-ray luminous starburst galaxies known.

  20. 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

  1. Understanding post-starburst quasars

    NASA Astrophysics Data System (ADS)

    Cales, Sabrina L.

    Post-starburst quasars (PSQs) are an interesting type of hybrid galaxy that harbor both a post-starburst stellar population and luminous AGN. The starburst is hundreds of millions of years old with a mass on the order of 10 billion solar masses. This type of hybrid galaxy provides a natural breading ground for studying the role active galactic nuclei (AGN) play in galaxy evolution (i.e., the black hole mass-galaxy bulge mass relation). My thesis work has centered on testing the idea that, at z ˜ 0.3, PSQs are a phase in the life of galaxies triggered by external events (e.g., mergers, tidal interactions) or whether they are a more heterogeneous population in which multiple mechanisms can contribute to the class (i.e., external events and internal processes). This project is devoted to understanding the properties of PSQs and is comprised of three sub-projects: (i) two-dimensional image analysis with HST imaging and characterization of PSQ morphologies, (ii) determination of stellar population ages and masses and quasar black hole masses and accretion rates via spectral modeling of Keck and KPNO spectroscopy, (iii) comparisons of PSQ properties with other galaxy types and models. Finally, I briefly outline my conclusions in the context of AGN/galaxy evolution.

  2. Band Spectra and Molecular Structure

    NASA Astrophysics Data System (ADS)

    Kronig, R. De L.

    2011-06-01

    Introduction; Part I. The Energy Levels of Diatomic Molecules and their Classification by Means of Quantum Numbers: 1. General foundations; 2. Wave mechanics of diatomic molecules; 3. Electronic levels; 4. Vibrational levels; 5. Rotational levels; 6. Stark and Zeeman effect; 7. Energy levels of polyatomic molecules; Part II. Fine Structure and Wave Mechanical Properties of the Energy Levels of Diatomic Molecules: 8. The perturbation function; 9. Rotational distortion of spin multiplets; 10. Fine structure; 11. Perturbations and predissociation; 12. Even and odd levels; 13. Symmetrical and antisymmetrical levels; Part III. Selection Rules and Intensities in Diatomic Molecules: 14. General foundations; 15. Electronic bands; 16. Vibrational bands; 17. Rotational bands; 18. Band spectra and nuclear structure; 19. Transitions in the Stark and Zeeman effect; Part IV. Macroscopic Properties of Molecular Gases: 20. Scattering; 21. Dispersion; 22. Kerr and Faraday effect; 23. Dielectric constants; 24. Magnetic susceptibilities; 25. Specific heats; Part V. Molecule Formation and Chemical Binding: 26. Heteropolar molecules; 27. Homopolar molecules. Chemical forces between two H-atoms and two He-atoms; 28. The general theory of homopolar compounds; Bibliography; Subject index.

  3. 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.

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

    NASA Technical Reports Server (NTRS)

    Jackson, James M.; Marscher, Alan M.

    1996-01-01

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

  5. The nature of starburst activity in M 82

    NASA Astrophysics Data System (ADS)

    Förster Schreiber, Natascha M.

    2000-07-01

    Results of near-infrared integral field spectroscopy of the starburst galaxy M 82, obtained with the MPE (Max-Planck-Institut für Extraterrestrische Physik, Garching, Germany) 3D instrument, are presented. These data provide the spatial distribution of key diagnostics (e.g. HI and HeI nebular emission lines, atomic and molecular stellar absorption features) for the composition of the populations of hot massive stars and cool evolved stars, on scales of 20-25 pc . Together with mid-infrared spectroscopy from the Short Wavelength Spectrometer (SWS) on board the ISO satellite ( ISO is an ESA project with instruments funded by ESA member States (especially the PI countries: France, Germany, the Netherlands and the United Kingdom) with the participation of ISAS and NASA. SWS is a joint project of SRON and MPE) and data from the literature, the 3D data are analyzed with a starburst model to constrain quantitatively the cutoffs of the initial mass function, and the spatial and chronological evolution of starburst activity.

  6. Molecular and Supermolecular Structure of Commercial Pyrodextrins.

    PubMed

    Le Thanh-Blicharz, Joanna; Błaszczak, Wioletta; Szwengiel, Artur; Paukszta, Dominik; Lewandowicz, Grażyna

    2016-09-01

    Size exclusion chromatography with triple detection as well as infrared spectroscopy studies of commercially available pyrodextrins proved that these molecules are characterized not only by significantly lower molecular mass, in comparison to that of native starch, but also by increased branching. Therefore, pyrodextrins adopt a very compact structure in solution and show Newtonian behavior under shear in spite of their molecular masses of tens of thousands Daltons. The results also indicate that 50% reduction of digestibility of pyrodextrins is, to a minor extent, caused by formation of low-molecular color compounds containing carbonyl functional groups. The main reason is, as postulated in the literature, transglycosidation that leads to decreased occurrence of α-1,4-glycoside bonds in the molecular structure. In the process of dextrinization starch also undergoes changes in supermolecular structure, which, however, have no influence on digestibility. Likewise, the effect of formation of low-molecular colorful compounds containing carbonyl groups is not crucial.

  7. Molecular and Supermolecular Structure of Commercial Pyrodextrins.

    PubMed

    Le Thanh-Blicharz, Joanna; Błaszczak, Wioletta; Szwengiel, Artur; Paukszta, Dominik; Lewandowicz, Grażyna

    2016-09-01

    Size exclusion chromatography with triple detection as well as infrared spectroscopy studies of commercially available pyrodextrins proved that these molecules are characterized not only by significantly lower molecular mass, in comparison to that of native starch, but also by increased branching. Therefore, pyrodextrins adopt a very compact structure in solution and show Newtonian behavior under shear in spite of their molecular masses of tens of thousands Daltons. The results also indicate that 50% reduction of digestibility of pyrodextrins is, to a minor extent, caused by formation of low-molecular color compounds containing carbonyl functional groups. The main reason is, as postulated in the literature, transglycosidation that leads to decreased occurrence of α-1,4-glycoside bonds in the molecular structure. In the process of dextrinization starch also undergoes changes in supermolecular structure, which, however, have no influence on digestibility. Likewise, the effect of formation of low-molecular colorful compounds containing carbonyl groups is not crucial. PMID:27447364

  8. 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.

  9. The gas content in starburst galaxies

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

  10. 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.

  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. Exploring the Limits of Star Formation from the Extreme Environment of Starbursts to the Milky Way

    NASA Astrophysics Data System (ADS)

    Heiderman, Amanda L.

    2012-01-01

    We investigate the relation between star formation rate (SFR) and gas surface densities in Galactic star forming regions and integral field unit (IFU) spatially resolved regions in nearby interacting/starburst galaxies. Our Galactic study uses a sample of 20 molecular clouds from the Spitzer c2d and Gould's Belt surveys. These data allow us to probe the low mass star formation regime that is essentially invisible to tracers (such as H-alpha emission) used to establish extragalactic relations (eg., Schmidt-Kennicutt relation). We find Galactic clouds above a threshold of 129 Msun/pc2 lie on a linear relation above extragalactic relations. Our extragalactic IFU survey is the VIRUS-P Investigation of the eXtreme ENvironments of Starbursts (VIXENS) which includes 15 nearby interacting/starburst galaxies that span a range of interaction phases: from close pairs to late stage mergers. The main goal of VIXENS is to investigate the Schmidt-Kennicutt relation on spatial scales of 0.1-0.9 kpc and test theoretical predictions at high SFR and gas surface densities in starburst galaxies. If a starburst CO-to-H2 conversion factor is used, we find sub-kpc scale starburst regions lie above extragalactic relations, overlapping with global measurements of high-z mergers as well as Galactic star forming regions. The overlap with Galactic star forming regions suggests that the bulk of gas in mergers is efficiently forming stars. These unique data sets allow us to compare SFR-gas surface density relations from Galactic clouds to extreme starbursts on spatially resolved scales for the first time.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. [Oligoglycine surface structures: molecular dynamics simulation].

    PubMed

    Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V

    2010-01-01

    The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

  2. 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

  3. 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 -}.

  4. 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.

  5. 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.

  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. 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)

  8. 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…

  9. Students' Understanding of Molecular Structure Representations

    ERIC Educational Resources Information Center

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

    2003-01-01

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

  10. Mapping CS in starburst galaxies: Disentangling and characterising dense gas

    NASA Astrophysics Data System (ADS)

    Kelly, G.; Viti, S.; Bayet, E.; Aladro, R.; Yates, J.

    2015-06-01

    Aims: We observe the dense gas tracer CS in two nearby starburst galaxies to determine how the conditions of the dense gas varies across the circumnuclear regions in starburst galaxies. Methods: Using the IRAM-30m telescope, we mapped the distribution of the CS(2-1) and CS(3-2) lines in the circumnuclear regions of the nearby starburst galaxies NGC 3079 and NGC 6946. We also detected formaldehyde (H2CO) and methanol (CH3OH) in both galaxies. We marginally detect the isotopologue C34S. Results: We calculate column densities under LTE conditions for CS and CH3OH. Using the detections accumulated here to guide our inputs, we link a time and depth dependent chemical model with a molecular line radiative transfer model; we reproduce the observations, showing how conditions where CS is present are likely to vary away from the galactic centres. Conclusions: Using the rotational diagram method for CH3OH, we obtain a lower limit temperature of 14 K. In addition to this, by comparing the chemical and radiative transfer models to observations, we determine the properties of the dense gas as traced by CS (and CH3OH). We also estimate the quantity of the dense gas. We find that, provided there are between 105 and 106 dense cores in our beam, for both target galaxies, emission of CS from warm (T = 100-400 K), dense (n(H2) = 105-6 cm-3) cores, possibly with a high cosmic ray ionisation rate (ζ = 100ζ0) best describes conditions for our central pointing. In NGC 6946, conditions are generally cooler and/or less dense further from the centre, whereas in NGC 3079, conditions are more uniform. The inclusion of shocks allows for more efficient CS formation, which means that gas that is less dense by an order of magnitude is required to replicate observations in some cases.

  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. Molecular and structural analysis of viscoelastic properties

    NASA Astrophysics Data System (ADS)

    Yapp, Rebecca D.; Kalyanam, Sureshkumar; Insana, Michael F.

    2007-03-01

    Elasticity imaging is emerging as an important tool for breast cancer detection and monitoring of treatment. Viscoelastic image contrast in breast lesions is generated by disease specific processes that modify the molecular structure of connective tissues. We showed previously that gelatin hydrogels exhibit mechanical behavior similar to native collagen found in breast tissue and therefore are suitable as phantoms for elasticity imaging. This paper summarizes our study of the viscoelastic properties of hydrogels designed to discover molecular-scale sources of elasticity image contrast.

  13. 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.

  14. 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

  15. Ultraviolet imaging of the AGN+starburst galaxy NGC 1068

    NASA Technical Reports Server (NTRS)

    Neff, Susan G.; Fanelli, Michael N.; Roberts, Laura J.; O'Connell, Robert W.; Bohlin, Ralph; Roberts, Morton S.; Smith, Andrew M.; Stecher, Theodore P.

    1994-01-01

    Images of the Seyfert 2 galaxy NGC 1068 were obtained at two ultraviolet wavelengths by the Ultraviolet Imaging Telescope (UIT). These data represent the first detailed UV imagery of a composite (active galactic nucleus + starburst) disk galaxy. NGC 1068 cotains multiple components at UV wavelengths: the central active galactic nucleus; a population of very luminous starburst knots; a bright oval inner disk; and a fainter, more circular halo. The most luminous knot, which is located approximately 750 pc from the nucleus at PA 315 deg, is approximately 80 times the luminosity of 30 Doradus and gives NGC 1068 a 'double nucleus' appearance in the UV. Significant extended emission is observed throughout the disk, unlike other disk galaxies so far observed in the UV. The radial brightness profile in both UV bandpasses generally follows an exponential decline to approximately 5 kpc. A faint halo extending to approximately 13 kpc is likely to be a galaxian-sized reflection nebula where ambient dust scatters the intense UV continuum from the inner galaxy. UV colors show a striking asymmetric morphology, which is correlated with the observed molecular CO emission.

  16. 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.

  17. Silylated carbodiimides in molecular and extended structures

    NASA Astrophysics Data System (ADS)

    Kroll, Peter; Riedel, Ralf; Hoffmann, Roald

    1999-08-01

    This work studies the ternary Si-C-N phases SiC2N4 and Si2CN4,exploiting an analogy between the NCN and O groups. Starting from the molecular model of N,N'-bis(trimethylsilyl)-carbodiimide and proceeding to extended models, we calculate that the energy hypersurface associated with the Si-N=C bond angle φN is very shallow, for both molecular and extended structures. We propose a crystal structure for the low-temperature modification α-SiC2N4 in space group P4322 (95), which is 40 meV (~4 kJ/mol) lower in energy than an ideal cubic arrangement in space group Pn3¯m.A second structure, β-SiC2N4 [space group P4¯n2 (118)], is slightly higher in energy than α-SiC2N4,but still more stable than the cubic structure, and may be the high-temperature structure of SiC2N4.Both variants of SiC2N4 show a small bulk modulus of about 8 GPa (~0.13 Mbar),suggesting a high compressibility of these nonoxide covalently bonded materials. For Si2CN4 we refined the crystal structure of the compound within the experimentally determined space group Aba2 (41). We also found a second candidate nearly equal in energy, with space group Cmc21,differing only in the connection pattern of the SiN2 layered sheets. Both ternary compounds appear to be thermodynamically unstable with respect to decomposition into Si3N4,C, and molecular N2.

  18. ROSAT HRI Observations of the Starburst Galaxy M82

    NASA Astrophysics Data System (ADS)

    Schulman, E.; Bregman, J. N.

    1992-12-01

    Gas-dynamical models of starburst galaxies predict that supernova heating creates a bubble of hot gas which breaks out of the disk. Some models predict a polar outflow in which the hot gas escapes along an edge-brightened chimney-like structure, while others predict spherical galactic winds. In order to test these models we have obtained a 25 ksec ROSAT HRI image of the starburst galaxy M82. Our HRI image has a resolution of about 5''(70 pc) and a field of view of about 30' (20 kpc). The image includes photons with energies between 0.2 and 1.5 keV and is almost an order of magnitude more sensitive than previous images. The X-ray emission extends perpendicular to the disk 3-4 kpc which is comparable to the extent of the emission detected with the Einstein IPC, although our resolution is more than a factor of 10 better. The emission is neither collimated nor spherically distributed, but has a conical distribution in which the emission close to the center of the galaxy is more compact than the emission farther away from the disk. The X-ray emission is not edge-brightened and decreases in hardness with distance from the center of the galaxy. The mean energy in the core is about 0.85 keV, while the mean energy a few kpc from the disk is about 0.25 keV. The shape, temperature, and lack of edge-brightening of the emission is in conflict with some starburst models. ES wishes to acknowledge support from a NASA Graduate Student Research Program Fellowship.

  19. Radiation Pressure-supported Starburst Disks and Active Galactic Nucleus Fueling

    NASA Astrophysics Data System (ADS)

    Thompson, Todd A.; Quataert, Eliot; Murray, Norman

    2005-09-01

    We consider the structure of marginally Toomre-stable starburst disks under the assumption that radiation pressure on dust grains provides the dominant vertical support against gravity. This assumption is particularly appropriate when the disk is optically thick to its own infrared radiation, as in the central regions of ULIRGs. We argue that because the disk radiates at its Eddington limit (for dust), the ``Schmidt law'' for star formation changes in the optically thick limit, with the star formation rate per unit area scaling as Σ˙*~Σg/κ, where Σg is the gas surface density and κ is the mean opacity of the disk. Our calculations further show that optically thick starburst disks have a characteristic flux, star formation rate per unit area, and dust effective temperature of F~1013 Lsolar kpc-2, Σ˙*~103 Msolar yr-1 kpc-2, and Teff~90 K, respectively. We compare our model predictions with observations of ULIRGs and find good agreement. We extend our model of starburst disks from many hundred parsec scales to subparsec scales and address the problem of fueling AGNs. We assume that angular momentum transport proceeds via global torques (e.g., spiral waves, winds, or a central bar) rather than a local viscosity. We consistently account for the radial depletion of gas due to star formation and find a strong bifurcation between two classes of disk models: (1) solutions with a starburst on large scales that consumes all of the gas with little or no fueling of a central AGN and (2) models with an outer large-scale starburst accompanied by a more compact starburst on 1-10 pc scales and a bright central AGN. The luminosity of the latter models is in many cases dominated by the AGN, although these disk solutions exhibit a broad mid- to far-infrared peak from star formation. We show that the vertical thickness of the starburst disk on parsec scales can approach h~r, perhaps accounting for the nuclear obscuration in some type 2 AGNs. We also argue that the disk of young

  20. 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

  1. 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.

  2. Magnetic field surrounding the starburst nucleus of the galaxy M82 from polarized dust emission

    PubMed

    Greaves; Holland; Jenness; Hawarden

    2000-04-13

    Magnetic fields may play an important role in the star-formation process, especially in the central regions of 'starburst' galaxies where star formation is vigorous. But the field directions are very difficult to determine in the dense molecular gas out of which the stars form, so it has hitherto been impossible to test this hypothesis. Dust grains in interstellar clouds tend to be magnetically aligned, and it is possible to determine the alignment direction based on the polarization of optical light due to preferential extinction along the long axes of the aligned grains. This technique works, however, only for diffuse gas, not for the dense molecular gas. Here we report observations of polarized thermal emission from the aligned dust grains in the central region of M82, which directly traces the magnetic field structure (as projected onto the plane of the sky). Organized field lines are seen around the brightest star-forming regions, while in the dusty halo the field lines form a giant magnetic bubble possibly blown out by the galaxy's 'superwind'.

  3. Infrared Line Ratios in Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Guiles, S.; Devost, D.; Houck, J. R.

    2004-12-01

    Infrared line ratios are especially well suited to probe the physical conditions in starburst galaxies because they are sensitive to the hardness of the stellar ionizing radiation and are less affected by interstellar extinction than lines at shorter wavelengths. We compare IR line ratios in starburst galaxies obtained by the Infrared Spectrograph (IRS)* on the Spitzer Space Telescope with theoretical models. The models use the STARBURST99 code to generate a spectral energy distribution of a stellar cluster which then serves as the input to the MAPPINGS III photoionization code. We explore various model parameters such as the initial mass function and star formation mode, and we present preliminary results for a number of galaxies in our sample. This work is based in part on observations made with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under NASA contract 1407. Support for this work was provided by NASA through Contract Number 1257184 issued by JPL/Caltech. * The IRS was a collaborative venture between Cornell University and Ball Aerospace Corporation funded by NASA through the Jet Propulsion Laboratory and the Ames Research Center.

  4. An Atlas of Starburst Galaxy Emission Lines

    NASA Astrophysics Data System (ADS)

    Meskhidze, Helen; Richardson, Chris T.; Ferland, Gary J.

    2015-01-01

    Recent observations of high ionization lines (e.g. [Ne V] and He II λ4686) from star-forming regions have prompted a need to study the production mechanisms of these high ionization lines. Our study addresses the following questions: 1. What are specific cloud parameters that influence the strength of emission lines in starburst galaxies? 2. How can these parameters be tuned in simulations to match observations? We adopt the locally optimally emitting cloud model, a model previously used to study AGN, for our study of star-forming regions. We present the results of hundreds of photoionization simulations spanning 15 orders of magnitude in hydrogen ionizing photon flux and 10 orders of magnitude in hydrogen density. We vary both properties of the starbursts (SEDs, evolutionary histories, ages), as well as cloud properties (such as the abundances and metallicity), tracking nearly 100 emission lines ranging from the UV to the near IR. Finally, we compare these results to the results of other studies on star-forming regions. The results of our photoionization calculations should prove useful for the analysis of starburst galaxy emission-line data.

  5. THE IMPACT OF STARBURSTS ON THE CIRCUMGALACTIC MEDIUM

    SciTech Connect

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

    2013-05-01

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

  6. 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.

  7. The Nature of Starbursts. II. The Duration of Starbursts in 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

    2010-11-01

    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 1053.9-1057.2 erg of energy into the interstellar medium through stellar winds and supernovae, and produced 3%-26% of the host galaxy's mass. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the Data Archive at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

  8. 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.

  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. Molecular composition, structure, and sensitivity of explosives

    SciTech Connect

    Storm, C.B.; Travis, J.R.

    1992-01-01

    High explosives, blasting agents, propellants, and pyrotechnics are all metastable relative to reaction products and are termed energetic materials. They are thermodynamically unstable but the kinetics of decomposition at ambient conditions are sufficiently slow that they can be handled safely under controlled conditions. The ease with which an energetic material can be caused to undergo a violent reaction or detonation is called its sensitivity. Sensitivity tests for energetic materials are aimed at defining the response of the material to a specific situation, usually prompt shock initiation or a delayed reaction in an accident. The observed response is always due to a combination of the physical state and the molecular structure of the material. Modeling of any initiation process must consider both factors. The physical state of the material determines how and where the energy is deposited in the material. The molecular structure determines the mechanism of decomposition of the material and the rate of energy release. Slower inherent reaction chemistry leads to longer reaction zones in detonation and inherently safer materials. Slower chemistry also requires hot spots involved in initiation to be hotter and to survive for longer periods of time. High thermal conductivity also leads to quenching of small hot spots and makes a material more difficult to initiate. Early endothermic decomposition chemistry also delays initiation by delaying heat release to support hot spot growth. The growth to violent reaction or detonation also depends on the nature of the early reaction products. If chemical intermediates are produced that drive further accelerating autocatalytic decomposition the initiation will grow rapidly to a violent reaction.

  11. 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

  12. 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

  13. Molecular structure input on the web.

    PubMed

    Ertl, Peter

    2010-02-02

    A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.)

  1. 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.

  2. Direct Measurement of the Supernova Rate in Starburst Galaxies

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

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

  3. 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

  4. 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.

  5. 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.

  6. DIFFERENT STAR FORMATION LAWS FOR DISKS VERSUS STARBURSTS AT LOW AND HIGH REDSHIFTS

    SciTech Connect

    Daddi, E.; Elbaz, D.; Bournaud, F.; Salmi, F.; Dannerbauer, H.; Carilli, C.; Dickinson, M.; Monaco, P.; Riechers, D.

    2010-05-01

    We present evidence that bona fide disks and starburst systems occupy distinct regions in the gas mass versus star formation rate (SFR) plane, both for the integrated quantities and for the respective surface densities. This result is based on carbon monoxide (CO) observations of galaxy populations at low and high redshifts, and on the current consensus for the CO luminosity to gas mass conversion factors. The data suggest the existence of two different SF regimes: a long-lasting mode for disks and a more rapid mode for starbursts, the latter probably occurring during major mergers or in dense nuclear SF regions. Both modes are observable over a large range of SFRs. The detection of CO emission from distant near-IR selected galaxies reveals such bimodal behavior for the first time, as they allow us to probe gas in disk galaxies with much higher SFRs than are seen locally. The different regimes can potentially be interpreted as the effect of a top-heavy initial mass function in starbursts. However, we favor a different physical origin related to the fraction of molecular gas in dense clouds. The IR luminosity to gas mass ratio (i.e., the SF efficiency) appears to be inversely proportional to the dynamical (rotation) timescale. Only when accounting for the dynamical timescale, a universal SF law is obtained, suggesting a direct link between global galaxy properties and the local SFR.

  7. Starbursts: From 30 Doradus to Lyman Break Galaxies

    NASA Astrophysics Data System (ADS)

    de Grijs, R.; González Delgado, R. M.

    2005-05-01

    Starbursts are important features of early galaxy evolution. Many of the distant, high-redshift galaxies we are able to detect are in a starbursting phase, often apparently provoked by a violent gravitational interaction with another galaxy. In fact, if we did not know that major starbursts existed, these conference proceedings testify that we would indeed have difficulties explaining the key properties of the Universe! The enhanced synergy facilitated by the collaboration among observers using cutting-edge ground and space-based facilities, theorists and modellers has made these proceedings into a true reflection of the state of the art in this very rapidly evolving field.

  8. Evidence of nuclear disks in starburst galaxies from their radial distribution of supernovae

    NASA Astrophysics Data System (ADS)

    Herrero-Illana, R.; Pérez-Torres, M. Á.; Alberdi, A.

    2012-04-01

    Galaxy-galaxy interactions are expected to be responsible for triggering massive star formation and possibly accretion onto a supermassive black hole, by providing large amounts of dense molecular gas down to the central kiloparsec region. Several scenarios to drive the gas further down to the central ~100 pc, have been proposed, including the formation of a nuclear disk around the black hole, where massive stars would produce supernovae. Here, we probe the radial distribution of supernovae and supernova remnants in the nuclear regions of the starburst galaxies M 82, Arp 299-A, and Arp 220, by using high-angular resolution (≲ 0.''1) radio observations published in the literature (for M 82 and Arp 220), or obtained by ourselves from the European VLBI Network (Arp 299-A). Our main goal was to characterize the nuclear starbursts in those galaxies and thus test scenarios that propose that nuclear disks of sizes ~100 pc form in the central regions of starburst galaxies. We obtained the radial distribution of supernovae (SNe) in the nuclear starbursts of M 82, Arp 299-A, and Arp 220, and derived scale-length values for the putative nuclear disks powering the bursts in those central regions. The scale lengths for the (exponential) disks range from ~20-30 pc for Arp 299-A and Arp 220, up to ~140 pc for M 82. The radial distribution of SNe for the nuclear disks in Arp 299-A and Arp 220 is also consistent with a power-law surface density profile of exponent γ = 1, as expected from detailed hydrodynamical simulations of nuclear disks. Our results support scenarios where a nuclear disk of size ~100 pc is formed in (U)LIRGs, and sustained by gas pressure, in which case the accretion onto the black hole could be lowered by supernova feedback. Appendices are available in electronic form at http://www.aanda.org

  9. Molecular clouds and galactic spiral structure

    NASA Technical Reports Server (NTRS)

    Dame, T. M.

    1984-01-01

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

  10. 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.

  11. Obscured starbursts in galaxy clusters: a MIPS survey of z=0.5 clusters

    NASA Astrophysics Data System (ADS)

    Smail, Ian; Ebeling, Harald; Edge, Alastair; Geach, Jim; Ma, Cheng-Jiun; Wardlow, Julie

    2008-03-01

    We propose panoramic MIPS 24um imaging of four intermediate redshift (z~0.5) clusters selected from the MACS X-ray Survey. We will combine these with observations of four clusters at the same epoch from our pilot study (which span a broader range in mass) to parameterize the evolutionary sequence of infalling field galaxies in terms of the cluster global structure. This analysis will distinguish between the role of global and local environment in determining the star formation histories of starburst galaxies entering the cluster potential from the low-density field. Our previous successful MIPS project has yielded some exciting results - in particular the existence of large populations of starburst galaxies in z~0.5 clusters with strong PAH emission - which have been completely overlooked by previous optical/near-IR surveys of these well-studied systems. These are potentially the missing link between distant spirals and the local passive S0 galaxies which are the dominant population in local clusters. Our initial results point to a strong dependence of star formation on specific cluster properties - either the dynamical state or the cluster mass (or equivalently temperature of the ICM). By specifically targeting four clusters with a narrow range in mass, but a wide range of structures, we aim to determine the key drivers of the variation in the starburst population within clusters. This will provide vital clues as to the physics of environmental transformations of galaxies: an important ingredient of current galaxy evolution models.

  12. 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.

  13. The radial distribution of supernovae in nuclear starbursts

    NASA Astrophysics Data System (ADS)

    Herrero-Illana, R.; Pérez-Torres, M. A.; Alberdi, A.

    2013-05-01

    Galaxy-galaxy interactions are expected to be responsible for triggering massive star formation and possibly accretion onto a supermassive black hole, by providing large amounts of dense molecular gas down to the central kiloparsec region. Several scenarios to drive the gas further down to the central ˜100 pc, have been proposed, including the formation of a nuclear disk around the black hole, where massive stars would produce supernovae. Here, we probe the radial distribution of supernovae and supernova remnants in the nuclear regions of the starburst galaxies M82, Arp 299-A, and Arp 220, by using high-angular resolution (≲ 0.''1) radio observations. We derived scale-length values for the putative nuclear disks, which range from ˜20-30 pc for Arp 299-A and Arp 220, up to ˜140 pc for M82. The radial distribution of SNe for the nuclear disks in Arp 299-A and Arp 220 is also consistent with a power-law surface density profile of exponent γ = 1, as expected from detailed hydrodynamical simulations of nuclear disks. This study is detailed in te{herrero-illana12}.

  14. HNCO Abundances in Galaxies: Tracing the Evolutionary State of Starbursts

    NASA Astrophysics Data System (ADS)

    Martín, Sergio; Martín-Pintado, J.; Mauersberger, R.

    2009-03-01

    The chemistry in the central regions of galaxies is expected to be strongly influenced by their nuclear activity. To find the best tracers of nuclear activity is of key importance to understand the processes taking place in the most obscured regions of galactic nuclei. In this work, we present multiline observations of CS, C34S, HNCO, and C18O in a sample of 11 bright galaxies prototypical for different types of activity. The 32S/34S isotopic ratio is ~10, supporting the idea of an isotopical 34S enrichment due to massive star formation in the nuclear regions of galaxies. Although C32S and C34S do not seem to be significantly affected by the activity type, the HNCO abundance appears highly contrasted among starbursts (SBs). We observed HNCO abundance variations of nearly 2 orders of magnitude. The HNCO molecule is shown to be a good tracer of the amount of molecular material fueling the SB and therefore can be used as a diagnostics of the evolutionary state of a nuclear SB.

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

    SciTech Connect

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

    2009-09-20

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

  16. The molecular structure of 1-methyl- trans-cyclooctene

    NASA Astrophysics Data System (ADS)

    Traetteberg, M.; Bakken, P.; Almenningen, A.

    1981-07-01

    The molecular structure of 1 -methyl- trans-cyclooctene has been studied by the gas electron diffraction method. A molecular mechanics calculation has been done for the title compound and for trans-cyclooctene and 1,2-dimethyl- trans-cyclooctene.

  17. Structures of High Density Molecular Fluids

    SciTech Connect

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

    2002-02-01

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

  18. 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)

  19. 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.

  20. 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.

  1. Spectro-imaging of M 82 at 3.3μm: evidence for dissociation of carriers in the starburst.

    NASA Astrophysics Data System (ADS)

    Normand, P.; Rouan, D.; Lacombe, F.; Tiphene, D.

    1995-05-01

    We present subarcsecond infrared images in the 3.3μm PAH feature of M 82, the prototype of starburst galaxies. Observations were done using the Paris-Meudon Observatory CIRCUS IR Camera at the CFHT 3m60 telescope. The most interesting results derive from the map of line-to-continuum ratio (R=[3.3μm]/Cont) which exhibits very peculiar features: i) a strong anti-correlation, at large scale, with the continuum intensity, the line being practically lacking in the central lane where peaks the continuum emission, a clear indication of the destruction of the carrier of the line by some process associated to the starburst phenomenon; ii) the region where R is maximum is found essentially in an extended bow (540x240pc) south of the starburst region and coinciding tightly with the external part of the molecular disk traced by CO and HCN emission; iii) on smaller scales a rather complex and clumpy structure is found, both in the bow of enhanced R and at center, where almost total depletion of PAH (lowest value of R) is found in several bubbles, a few of them at location of strong radio SNR, and in a channel, north of the nucleus, that coincides rather precisely with the superwind direction. There is indication of two different regimes of depletion: a partial depletion and a quasi-complete depletion in the central lane around the nucleus. It is shown that the 3-4μm continuum emission cannot be explained by reddened starlight or by classical dust thermal emission, and is larger than predicted by models. The ratio R should give a fair estimate of the local 3.3μm line carrier abundance. Mechanisms of destruction and production of PAHs are investigated; in particular, we show that the two regimes of depletion may correspond to two different destructive processes: one, more efficient, that may correspond to electron bombardment in the SN dominated central region and one driven by UV photons in the molecular disk. For the later, we show that three competitive mechanisms are

  2. 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)

  3. 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

  4. An excess of dusty starbursts related to the Spiderweb galaxy

    NASA Astrophysics Data System (ADS)

    Dannerbauer, H.; Kurk, J. D.; De Breuck, C.; Wylezalek, D.; Santos, J. S.; Koyama, Y.; Seymour, N.; Tanaka, M.; Hatch, N.; Altieri, B.; Coia, D.; Galametz, A.; Kodama, T.; Miley, G.; Röttgering, H.; Sanchez-Portal, M.; Valtchanov, I.; Venemans, B.; Ziegler, B.

    2014-10-01

    We present APEX LABOCA 870 μm observations of the field around the high-redshift radio galaxy MRC1138-262 at z = 2.16. We detect 16 submillimeter galaxies (SMGs) in this ~140 arcmin2 bolometer map with flux densities in the range 3-11 mJy. The raw number counts indicate a density of SMGs that is up to four times that of blank field surveys. Based on an exquisite multiwavelength database, including VLA 1.4 GHz radio and infrared observations, we investigate whether these sources are members of the protocluster structure at z ≈ 2.2. Using Herschel PACS and SPIRE and Spitzer MIPS photometry, we derive reliable far-infrared (FIR) photometric redshifts for all sources. Follow-up VLT ISAAC and SINFONI NIR spectra confirm that four of these SMGs have redshifts of z ≈ 2.2. We also present evidence that another SMG in this field, detected earlier at 850 μm, has a counterpart that exhibits Hα and CO(1-0) emission at z = 2.15. Including the radio galaxy and two SMGs with FIR photometric redshifts at z = 2.2, we conclude that at least eight submm sources are part of the protocluster at z = 2.16 associated with the radio galaxy MRC1138-262. We measure a star formation rate density SFRD ~1500 M⊙ yr-1 Mpc-3, four magnitudes higher than the global SFRD of blank fields at this redshift. Strikingly, these eight sources are concentrated within a region of 2 Mpc (the typical size of clusters in the local universe) and are distributed within the filaments traced by the HAEs at z ≈ 2.2. This concentration of massive, dusty starbursts is not centered on the submillimeter-bright radio galaxy which could support the infalling of these sources into the cluster center. Approximately half (6/11) of the SMGs that are covered by the Hα imaging data are associated with HAEs, demonstrating the potential of tracing SMG counterparts with this population. To summarize, our results demonstrate that submillimeter observations may enable us to study (proto)clusters of massive, dusty

  5. Molecular and cluster structures in 18O

    NASA Astrophysics Data System (ADS)

    von Oertzen, W.; Dorsch, T.; Bohlen, H. G.; Krücken, R.; Faestermann, T.; Hertenberger, R.; Kokalova, Tz.; Mahgoub, M.; Milin, M.; Wheldon, C.; Wirth, H.-F.

    2010-01-01

    We have studied the multi-nucleon transfer reaction 12C ( 7Li ,p) at E lab = 44 MeV, populating states in the oxygen isotope 18O . The experiments were performed at the Tandem accelerator of the Maier-Leibniz Laboratory in Munich using the high-resolution Q3D magnetic spectrograph. States were populated up to an excitation energy of 21.2MeV with an overall energy resolution of 45keV, and 30 new states of 18O have been identified. The structure of the rotational bands observed is discussed in terms of cluster bands with the underlying cluster structures: 14C ⊗ α and 12C ⊗ 2 n ⊗ α . Because of the broken intrinsic reflection symmetry in these structures the corresponding rotational bands appear as parity doublets.

  6. 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.

  7. Molecular Eigensolution Symmetry Analysis and Fine Structure

    PubMed Central

    Harter, William G.; Mitchell, Justin C.

    2013-01-01

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

  8. 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.

  9. 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

  10. Linking numerical simulations of molecular cloud structure with observations.

    NASA Astrophysics Data System (ADS)

    Kainulainen, Jouni

    2015-08-01

    Understanding the physical processes that control the life-cycle of the cold interstellar medium (ISM) is one of the key themes in the astrophysics of galaxies today. This importance derives from the role of the cold ISM as the birthplace of new stars, and consequently, as an indivisible constituent of galaxy evolution. In the current paradigm of turbulence-regulated ISM, star formation is controlled by the internal structure of individual molecular clouds, which in turn is set by a complex interplay of turbulence, gravity, and magnetic fields in the clouds. It is in the very focus of the field to determine how these processes give rise to the observed structure of molecular clouds. In this talk, I will review our current efforts to confront this paradigm with the goal of observationally constraining how different processes regulate molecular cloud structure and star formation. At the heart of these efforts lies the use of numerical simulations of gravo-turbulent media to A) define physically meaningful characteristics that are sensitive to the different cloud-shaping processes, and B) determine if and how such characteristics can be recovered by observations. I will show in my talk how this approach has recently led to new constraints for some fundamental measures of the molecular cloud structure. Such constraints allow us to assess the roles of turbulence and gravity in controlling the ISM structure and star formation. I will also highlight specific recent results, focusing on the nature of filamentary structures within molecular clouds. These results may provide a novel set of observational constraints with which to challenge the turbulence-regulated ISM paradigm. Finally, I will discuss the current challenges and open questions in understanding the link between molecular cloud structure and star formation, and speculate on key directions to aim the near-future studies.

  11. 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.

  12. Molecular information structures in the brain.

    PubMed

    Conrad, M

    1976-01-01

    This paper presents a theory of memory and memory mediated learning based on the manipulation of macromolecular conformations. The main features of the theory are: 1) the brain contains primary and reference neurons; 2) inputs from the external environment produce particular patterns of primary firing; 3) the firing of a primary neuron sensitizes certain of its dendrites; 4) the sensitized primaries are loaded by the reference neuron active at the time and in such a way that they fire when called by this reference neuron, thus reconstructing the original pattern of primary activity. The reference neurons may also be loaded by primaries, thus making it possible for the reconstruction process to be initiated by some feature of the initial input. Each reference neuron loads and calls at most one primary pattern of activity, thereby preventing superposition of memories. If the primaries are loadable by sequences of impulses, this makes it possible to increase the connectivity among the various types of neurons by using party-line organization. The loading and calling processes themselves are mediated by call molecules. These are allosteric enzymes, located in the dendrites of primary and reference neurons, whose states are set either by an impulse or sequence of impulses and which catalyze events leading to impulse formation whenever this input recurs. The call molecules are capable of duplicating their setting (or conformation) using either intra- or interneuronal potentials, thereby ensuring stability of the memory trace. The theory allows for general powers of memory manipulation (by rememorization), for the construction of time ordered, content ordered, and associative data structures, and for computation with global representations of the environment. It makes a large number of testable predictions, provides a natural interpretation for the structure of the cerebral cortex, and accounts for: resistance to cooling, differential effects of chemical agents on short

  13. 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.

  14. Molecular structure of vapor-deposited amorphous selenium

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  15. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments

    PubMed Central

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M.; Schulten, Klaus; Roux, Benoît

    2015-01-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

  16. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    PubMed

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

    2015-10-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

  17. 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.

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

    PubMed

    Kumar, Pardeep; Goswami, Debabrata

    2014-12-26

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

  1. Hubble Space Telescope Imaging of the Post-starburst Quasar UN J1025-0040: ``Post''-starburst No More?

    NASA Astrophysics Data System (ADS)

    Grabelsky, M. A.; Brotherton, M. S.; Canalizo, G.; Breugel, W.; Croom, S. M.; Filippenko, A. V.; Stockton, A.; Smith, R. J.; Boyle, B. J.; Miller, L.; Shanks, T.

    2001-12-01

    We present new HST WFPC2 images of the post-starburst quasar UN J1025-0040, which contains both an AGN and a 400-Myr-old nuclear starburst of similar bolometric luminosity ( ~1011.6 solar luminosities). The F450W and F814W images fail to clearly separate the starburst and quasar components, but do show that the bulk of the stars (7 x 1010 solar masses) are contained within a central radius of about 600 parsecs. Equating the point-source light in each image with the AGN contribution, we determined the ratio of AGN-to-starburst light. This ratio is 68% in the red F814W image, consistent with our previous spectral analysis, but < 50% in the blue F450W image whereas we had predicted 76%. The HST images are consistent with previous photometry ruling out variability (a fading AGN) as a cause for this result. We can explain the new data if there is a previously unknown young stellar population present, 40 Myr or younger, with as much as 10% of the mass of the dominant 400-Myr-old population. This younger starburst may represent the trigger for the current nuclear activity. The multiple starburst ages seen in UN J1025-0040 and its companion galaxy indicate a complex interaction and star formation history. Matthew Grabelsky acknowledges support from the NOAO/KPNO Research Experiences for Undergraduates program funded by the National Science Foundation. Support for proposal GO-08703 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  3. ALMA Multi-line Imaging of the Nearby Starburst NGC 253

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    We present spatially resolved (~50 pc) imaging of molecular gas species in the central kiloparsec of the nearby starburst galaxy NGC 253, based on observations taken with the Atacama Large Millimeter/submillimeter Array. A total of 50 molecular lines are detected over a 13 GHz bandwidth imaged in the 3 mm band. Unambiguous identifications are assigned for 27 lines. Based on the measured high CO/C17O isotopic line ratio (gsim350), we show that 12CO(1-0) has moderate optical depths. A comparison of the HCN and HCO+ with their 13C-substituted isotopologues shows that the HCN(1-0) and HCO+(1-0) lines have optical depths at least comparable to CO(1-0). H13CN/H13CO+ (and H13CN/HN13C) line ratios provide tighter constraints on dense gas properties in this starburst. SiO has elevated abundances across the nucleus. HNCO has the most distinctive morphology of all the bright lines, with its global luminosity dominated by the outer parts of the central region. The dramatic variation seen in the HNCO/SiO line ratio suggests that some of the chemical signatures of shocked gas are being erased in the presence of dominating central radiation fields (traced by C2H and CN). High density molecular gas tracers (including HCN, HCO+, and CN) are detected at the base of the molecular outflow. We also detect hydrogen β recombination lines that, like their α counterparts, show compact, centrally peaked morphologies, distinct from the molecular gas tracers. A number of sulfur based species are mapped (CS, SO, NS, C2S, H2CS, and CH3SH) and have morphologies similar to SiO.

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

    SciTech Connect

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

    2015-03-01

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

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

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1989-01-01

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

  6. 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.

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

    PubMed

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

    2013-07-19

    Connecting molecular structure and exciton diffusion length in rubrene derivatives demonstrates how the diffusion length of rubrene can be enhanced through targeted functionalization aiming to enhance self-Förster energy transfer. Functionalization adds steric bulk, forcing the molecules farther apart on average, and leading to increased photoluminescence efficiency. A diffusion length enhancement greater than 50% is realized over unsubstituted rubrene. PMID:23754475

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Are starbursts really mergers at high redshift? A kinematic investigation

    NASA Astrophysics Data System (ADS)

    Dickinson, Mark; Kartaltepe, Jeyhan; Weiner, Ben; Kassin, Susan; Bournaud, Frederic; Eisenhardt, Peter; Inami, Hanae; Pforr, Janine

    2014-02-01

    Star-forming galaxies obey a remarkable ``main sequence'' correlation between their star formation rates (SFR) and stellar masses (M^ast), whose normalization (the specific star formation rate, SSFR) evolves with redshift. A minority of starbursts, with much higher SSFR, are found at all redshifts, and may be an important evolutionary stage, fueling AGN activity and building bulges and spheroids. Locally, starbursting ultraluminous infrared galaxies are the product of galaxy mergers, but this is not so clear at z > 1, where ULIRGs are hundreds of times more common, but where HST images reveal only loose correlations between irregular/disturbed morphology and starburst activity. We propose to use MOSFIRE spectroscopy to measure kinematics for 80 Herschel far-IR-selected galaxies at z 1.5, distributed over the SFR-M^ast plane. We will look for kinematic differences (larger σ_V or σ/V_rot at fixed M^ast; increased line asymmetry, and a new kinematic irregularity index optimized from numerical simulations) between main sequence and starburst galaxies that would indicate a prevalence of merger activity at higher SSFR. This program was allocated 1 night in 2013B, but was scheduled so that it will be impossible to observe our fields in 3 position angles as required. We request additional time in 2014A to complete the observations as planned.

  14. Are starbursts really mergers at high redshift? A kinematic investigation

    NASA Astrophysics Data System (ADS)

    Dickinson, Mark; Kartaltepe, Jeyhan; Weiner, Ben; Kassin, Susan; Bournaud, Frederic; Eisenhardt, Peter; Inami, Hanae; Pforr, Janine

    2013-08-01

    Star-forming galaxies obey a remarkable ``main sequence'' correlation between their star formation rates (SFR) and stellar masses (M^ast), whose normalization (the specific star formation rate or SSFR) evolves with redshift. A minority population of starbursts with much higher SSFR are found at all redshifts, and may represent an important stage in the transformation and evolution of galaxies, fueling AGN activity and building bulges and spheroids. Locally, starbursting ultraluminous infrared galaxies are clearly the product of galaxy mergers, but this is much less clear at z > 1, where ULIRGs are hundreds of times more common than today, but where HST observations reveal only loose correlations between irregular/disturbed morphology and starburst activity. We propose to use MOSFIRE spectroscopy to measure kinematics for >80 Herschel far-IR-selected galaxies at z 1.5, distributed over the SFR-M^ast plane. We will look for kinematic differences (larger σ_V or σ/V_rot at fixed M^ast; increased line asymmetry, and a new kinematic irregularity index optimized from numerical simulations) between main sequence and starburst galaxies that would indicate a prevalence of merger activity at higher SSFR.

  15. 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.

  16. The role of massive stars in young starburst galaxies

    NASA Astrophysics Data System (ADS)

    Norris, Richard Paul Furber

    Starburst galaxies are defined as those galaxies undergoing violent star formation over relatively short periods of time (10 to 100 Myr). These objects may form stellar populations of > 106 Msun, containing massive stars with masses > 100 Msun. Although most starburst galaxies are observed at relatively low redshift, recent evidence suggests that these types of galaxies were far more important in the high redshift past. It is believed that the chemical evolution of the Universe has been strongly influenced by this mode of star formation through the dense winds from massive stars and supernovae ejecta. Our understanding of starbursts is still relatively poor, since most are too distant to be resolved. We can gain some understanding of starbursts indirectly through the modelling of associated nebulae via the calculation of theoretical spectral energy distributions (SEDs) and photoionization modelling. This technique heavily relies upon the accuracy of the predicted far UV continuum of the massive star population. This thesis presents a new grid of SEDs for O stars, early B supergiants and Wolf-Rayet stars which have been incorporated into the evolutionary synthesis code Starburst99 (Leitherer et al. 1999). A total of 285 expanding, non-LTE, line-blanketed model atmospheres have been calculated to replace old, inaccurate LTE models for O stars, and pure helium, unblanketed models for W-R stars. These new grids cover five metallicities and the wind parameters are scaled with metallicity. We find that the new models yield significantly less ionizing flux below the He 0 ionizing edge at early phases and as a consequence, nebular He II lambda4686 will not be observable in young starbursts. We use the photoionization code CLOUDY to test the accuracy of the predicted ionizing fluxes from our new models. We find that they are in much better agreement with observed optical and IR nebular line diagnostics than any previous models. The new W-R atmospheres are used in

  17. Direction selectivity in a model of the starburst amacrine cell.

    PubMed

    Tukker, John J; Taylor, W Rowland; Smith, Robert G

    2004-01-01

    The starburst amacrine cell (SBAC), found in all mammalian retinas, is thought to provide the directional inhibitory input recorded in On-Off direction-selective ganglion cells (DSGCs). While voltage recordings from the somas of SBACs have not shown robust direction selectivity (DS), the dendritic tips of these cells display direction-selective calcium signals, even when gamma-aminobutyric acid (GABAa,c) channels are blocked, implying that inhibition is not necessary to generate DS. This suggested that the distinctive morphology of the SBAC could generate a DS signal at the dendritic tips, where most of its synaptic output is located. To explore this possibility, we constructed a compartmental model incorporating realistic morphological structure, passive membrane properties, and excitatory inputs. We found robust DS at the dendritic tips but not at the soma. Two-spot apparent motion and annulus radial motion produced weak DS, but thin bars produced robust DS. For these stimuli, DS was caused by the interaction of a local synaptic input signal with a temporally delayed "global" signal, that is, an excitatory postsynaptic potential (EPSP) that spread from the activated inputs into the soma and throughout the dendritic tree. In the preferred direction the signals in the dendritic tips coincided, allowing summation, whereas in the null direction the local signal preceded the global signal, preventing summation. Sine-wave grating stimuli produced the greatest amount of DS, especially at high velocities and low spatial frequencies. The sine-wave DS responses could be accounted for by a simple mathematical model, which summed phase-shifted signals from soma and dendritic tip. By testing different artificial morphologies, we discovered DS was relatively independent of the morphological details, but depended on having a sufficient number of inputs at the distal tips and a limited electrotonic isolation. Adding voltage-gated calcium channels to the model showed that their

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

    PubMed

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

    2013-03-21

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

  19. 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 (\

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

    PubMed

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

    2016-06-01

    Major depressive disorder (MDD) is a significant cause of morbidity and mortality worldwide, correlating with genetic susceptibility and environmental risk factors. Molecular, functional, and structural imaging approaches have been increasingly used to detect neurobiological changes, analyze neurochemical correlates, and parse pathophysiological mechanisms underlying MDD. We reviewed recent neuroimaging publications on MDD in terms of molecular, functional, and structural alterations as detected mainly by magnetic resonance imaging (MRI) and positron emission tomography. Altered structure and function of brain regions involved in the cognitive control of affective state have been demonstrated. An abnormal default mode network, as revealed by resting-state functional MRI, is likely associated with aberrant metabolic and serotonergic function revealed by radionuclide imaging. Further multi-modal investigations are essential to clarify the characteristics of the cortical network and serotonergic system associated with behavioral and genetic variations in MDD. PMID:27142698

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. Molecular docking and structure-based drug design strategies.

    PubMed

    Ferreira, Leonardo G; Dos Santos, Ricardo N; Oliva, Glaucius; Andricopulo, Adriano D

    2015-07-22

    Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  6. Improving structure-based function prediction using molecular dynamics

    PubMed Central

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

    2009-01-01

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

  7. 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.

  8. Efficient transfer of genetic material into mammalian cells using Starburst polyamidoamine dendrimers.

    PubMed Central

    Kukowska-Latallo, J F; Bielinska, A U; Johnson, J; Spindler, R; Tomalia, D A; Baker, J R

    1996-01-01

    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 beta-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. Images Fig. 1 Fig. 2 Fig. 4 PMID:8643500

  9. Detection of internal molecular structural motions using anisotropic spectroscopy

    NASA Astrophysics Data System (ADS)

    Singh, Rohit; George, Deepu; Korter, Timothy; Markelz, Andrea

    2012-02-01

    The far infrared spectroscopy of molecular crystals reveals both intra and inter molecular vibrational modes [1,2]. With the significant increase in complexity of structures, one finds increasing overlap in the internal modes. As an overall strategy to measure the correlated structural motions in protein, we use anisotropic and birefringent behavior of molecular crystals to develop a new technique called MOSTS (Modulated Orientation Sensitive THz Spectroscopy). We achieve high sensitivity and mode separation by using single molecular crystal such as sucrose and rapid modulation of the relative alignment of the terahertz polarization and the crystal axes by rotating the sample. By locking into the signal at the rotation frequency we determine the polarization sensitive signal and map out the optically active vibrational resonances. To illustrate the technique we compare our measured spectra with the calculated and find a close agreement. [4pt] [1] D.G. Allis, J.A. Zeitler, P.F.Taday and T.M.Korter, Chem. Phys. Lett., 463, 84 (2008).[0pt] [2] P.U. Jepsen and J.C. Stewart, Chem. Phys. Lett., 442, 275 (2007).

  10. 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

  11. Structure, subunit composition, and molecular weight of RD-114 RNA.

    PubMed Central

    Kung, H J; Bailey, J M; Davidson, N; Nicolson, M O; McAllister, R M

    1975-01-01

    The properties and subunit composition of the RNA extracted from RD-114 virions have been studied. The RNA extracted from the virion has a sedimentation coefficient of 52S in a nondenaturing aqueous electrolyte. The estimated molecular weight by sedimentation in nondenaturing and weakly denaturing media is in the range 5.7 X 10(6) to 7.0 X 10(6). By electron microscopy, under moderately denaturing conditions, the 52S molecule is seen to be an extended single strand with a contour length of about 4.0 mum corresponding to a molecular weight of 5.74 X 10(6). It contains two characteristic secondary structure features: (i) a central Y- or T-shaped structure (the rabbit ears) with a molecular weight of 0.3 X 10(6), (ii) two symmetreically disposed loops on each side of and at equal distance from the center. The 52S molecule consists of two half-size molecules, with molecular weight 2.8 X 10(6), joined together within the central rabbit ears feature. Melting of the rabbit ears with concomitant dissociation of the 52S molecule into subunits, has been caused by either one of two strongly denaturing treatments: incubation in a mixture of CH3HgOH and glyoxal at room temperature, or thermal dissociation in a urea-formamide solvent. When half-size molecules are quenched from denaturing temperatures, a new off-center secondary structure feature termed the branch-like structure is seen. The dissociation behavior of the 52S complex and the molecular weight of the subunits have been confirmed by gel electrophoresis studies. The loop structures melt at fairly low temperatures; the dissociation of the 52S molecule into its two subunits occurs at a higher temperature corresponding to a base composition of about 63% guanosine plus cytosine. Polyadenylic acid mapping by electron microscopy shows that the 52S molecule contains two polyadenylic acid segments, one at each end. It thus appears that 52S RD-114 RNA consists of two 2.8 X 10(6) dalton subunits, each with a characteristic

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

    SciTech Connect

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

    2014-01-01

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

  13. Effects of amine molecular structure on carbon nanotubes functionalization.

    PubMed

    Jimeno, A; Goyanes, S; Eceiza, A; Kortaberria, G; Mondragon, I; Corcuera, M A

    2009-10-01

    Three amines with different molecular structure, triethylenetetramine (TETA) and two polyetheramines (Jeffamine D-230 and Jeffamine T-403) were employed to functionalize multi-walled carbon nanotubes (MWCNT) previously oxidized by acid treatment. The functionalized MWCNT were characterized by Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, UV-vis spectroscopy and the surface modification was investigated by field emission scanning electron microscopy (FE-SEM). Thermogravimetric analysis (TGA) was employed to quantify the amount of amine groups anchored to MWCNTs. The results have shown that the efficiency of amine functionalization is in the order TETA > D-230 > T-403, thus showing that amine chemical structure and molecular weight are important parameters on functionalization of carbon nanotubes. PMID:19908518

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  16. 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.

  17. 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

  18. 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

  19. Hybrid Molecular Structure of the Giant Protease Tripeptidyl Peptidase II

    PubMed Central

    Chuang, Crystal K.; Rockel, Beate; Seyit, Gönül; Walian, Peter J.; Schönegge, Anne–Marie; Peters, Jürgen; Zwart, Petrus H.; Baumeister, Wolfgang; Jap, Bing K.

    2010-01-01

    Tripeptidyl peptidase II (TPP II) is the largest known eukaryotic protease (6MDa). It is believed to act downstream of the 26S proteasome cleaving tripeptides from the N– termini of longer peptides and it is implicated in numerous cellular processes. Here we report the structure of Drosophila TPP II determined by a hybrid approach: The structure of the dimer was solved by x–ray crystallography and docked into the three– dimensional map of the holocomplex obtained by single-particle cryo-electron microscopy. The resulting structure reveals the compartmentalization of the active sites inside a system of chambers and suggests the existence of a molecular ruler determining the size of the cleavage products. Furthermore, the structure suggests a model for activation of TPP II involving the relocation of a flexible loop and a repositioning of the active–site serine, coupling it to holocomplex assembly and active site sequestration. PMID:20676100

  20. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    SciTech Connect

    Splettstoesser, Thomas; Holmes, Kenneth; Noe, Frank; Smith, Jeremy C

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  7. IUE observations of NGC 1068 - The extremely luminous starburst knots

    NASA Technical Reports Server (NTRS)

    Bruhweiler, F. C.; Truong, K. Q.; Altner, B.

    1991-01-01

    A complete investigation of the UV characteristics of the starburst knots in the inner 3 kpc region of NGC 1068 mapped by the IUE is presented. It is noted that these knots probably represent the most luminous H II regions yet studied at optical and UV wavelengths. Comparisons suggest that the brightest knot, knot 1, is 30 times brighter than NGC 604 in M33 and has a total luminosity of not less than 10 to the 43rd ergs/s.

  8. 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.

  9. A developmental switch in the excitability and function of the starburst network in the mammalian retina.

    PubMed

    Zheng, Ji-Jian; Lee, Seunghoon; Zhou, Z Jimmy

    2004-12-01

    Dual patch-clamp recording and Ca2+ uncaging revealed Ca2+-dependent corelease of ACh and GABA from, and the presence of reciprocal nicotinic and GABAergic synapses between, starburst cells in the perinatal rabbit retina. With maturation, the nicotinic synapses between starburst cells dramatically diminished, whereas the GABAergic synapses remained and changed from excitatory to inhibitory, indicating a coordinated conversion of the starburst network excitability from an early hyperexcitatory to a mature nonepileptic state. We show that this transition allows the starburst cells to use their neurotransmitters for two completely different functions. During early development, the starburst network mediates recurrent excitation and spontaneous retinal waves, which are important for visual system development. After vision begins, starburst cells release GABA in a prolonged and Ca2+-dependent manner and inhibit each other laterally via direct GABAergic synapses, which may be important for visual integration, such as the detection of motion direction.

  10. 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

  11. HST/COS Probes the Starburst Wind of NGC 2611

    NASA Astrophysics Data System (ADS)

    Keeney, Brian A.; Stocke, J. T.

    2011-05-01

    We present moderate-resolution Cosmic Origins Spectrograph (COS) far-UV spectra of the QSO PG 0832+251, which probes the starburst galaxy NGC 2611 (z = 0.0175) along its minor axis at a distance of 2.5 arcmin (54 kpc in projection). An 11-ksec FUSE spectrum of PG 0832+251 revealed Lyβ and O VI absorption associated with NGC 2611; our COS G130M and G160M spectra span the wavelength range 1136-1797 Å with a spectral resolution of 18,000 and cover low- (H I, O I, N I, C II, Si II, Fe II, S II, Al II) and intermediate-ions (Si III/IV, C IV, N V) associated with NGC 2611. Probing starburst winds at appreciable distances along the galaxy's minor axis is the most straightforward way of determining whether gas entrained in the wind will escape the galaxy's gravitational potential to enrich the intergalactic medium, since absorption-line studies which use the starburst continuum itself as a background source suffer from large ambiguities in the location of the absorbing gas. However, the interpretation of the absorption lines in the PG 0832+251 spectrum are complicated by the presence of a small galaxy group, of which NGC 2611 is the largest member.

  12. 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.

  13. 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

  14. 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.

  15. 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.

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

    PubMed

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

    2014-11-07

    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.

  17. Structure of a molecular liquid GeI4

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  18. Structure of a molecular liquid GeI4.

    PubMed

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

    2016-11-01

    A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ∼1 Å(-1) in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak's height is confirmed by a simulation, in which the molecular size is changed. PMID:27605016

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

    PubMed

    Müller, Klaus

    2014-01-01

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

  20. 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).

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  7. MAXIMALLY STAR-FORMING GALACTIC DISKS. I. STARBURST REGULATION VIA FEEDBACK-DRIVEN TURBULENCE

    SciTech Connect

    Ostriker, Eve C.; Shetty, Rahul E-mail: rshetty@ita.uni-heidelberg.de

    2011-04-10

    Star formation rates in the centers of disk galaxies often vastly exceed those at larger radii, whether measured by the surface density of star formation {Sigma}{sub SFR}, by the star formation rate per unit gas mass, {Sigma}{sub SFR}/{Sigma}, or even by total output. In this paper, we investigate the idea that central starbursts are self-regulated systems in which the momentum flux injected to the interstellar medium (ISM) by star formation balances the gravitational force confining the ISM gas in the disk. For most starbursts, supernovae are the largest contributor to the momentum flux, and turbulence provides the main pressure support for the predominantly molecular ISM. If the momentum feedback per stellar mass formed is p{sub *}/m{sub *} {approx} 3000 km s{sup -1}, the predicted star formation rate is {Sigma}{sub SFR} {approx} 2{pi}G{Sigma}{sup 2} m{sub *}/p{sub *} {approx} 0.1 M{sub sun} kpc{sup -2} yr{sup -1}({Sigma}/100 M{sub sun} pc{sup -2}){sup 2} in regions where gas dominates the vertical gravity. We compare this prediction with numerical simulations of vertically resolved disks that model star formation including feedback, finding good agreement for gas surface densities in the range {Sigma} {approx} 10{sup 2}-10{sup 3} M{sub sun} pc{sup -2}. We also compare to a compilation of star formation rates and gas contents from local and high-redshift galaxies (both mergers and normal galaxies), finding good agreement provided that the conversion factor X{sub CO} from integrated CO emission to H{sub 2} surface density decreases modestly as {Sigma} and {Sigma}{sub SFR} increase. Star formation rates in dense, turbulent gas are also expected to depend on the gravitational free-fall time at the corresponding mean ISM density {rho}{sub 0}; if the star formation efficiency per free-fall time is {epsilon}{sub ff}({rho}{sub 0}) {approx} 0.01, the turbulent velocity dispersion driven by feedback is expected to be v{sub z} = 0.4 {epsilon}{sub ff}({rho}{sub 0})p

  8. Maximally Star-forming Galactic Disks. I. Starburst Regulation Via Feedback-driven Turbulence

    NASA Astrophysics Data System (ADS)

    Ostriker, Eve C.; Shetty, Rahul

    2011-04-01

    Star formation rates in the centers of disk galaxies often vastly exceed those at larger radii, whether measured by the surface density of star formation ΣSFR, by the star formation rate per unit gas mass, ΣSFR/Σ, or even by total output. In this paper, we investigate the idea that central starbursts are self-regulated systems in which the momentum flux injected to the interstellar medium (ISM) by star formation balances the gravitational force confining the ISM gas in the disk. For most starbursts, supernovae are the largest contributor to the momentum flux, and turbulence provides the main pressure support for the predominantly molecular ISM. If the momentum feedback per stellar mass formed is p*/m* ~ 3000 km s-1, the predicted star formation rate is ΣSFR ~ 2πGΣ2 m*/p* ~ 0.1 Msun kpc-2 yr-1(Σ/100 Msun pc-2)2 in regions where gas dominates the vertical gravity. We compare this prediction with numerical simulations of vertically resolved disks that model star formation including feedback, finding good agreement for gas surface densities in the range Σ ~ 102-103 Msun pc-2. We also compare to a compilation of star formation rates and gas contents from local and high-redshift galaxies (both mergers and normal galaxies), finding good agreement provided that the conversion factor X CO from integrated CO emission to H2 surface density decreases modestly as Σ and ΣSFR increase. Star formation rates in dense, turbulent gas are also expected to depend on the gravitational free-fall time at the corresponding mean ISM density ρ0 if the star formation efficiency per free-fall time is ɛff(ρ0) ~ 0.01, the turbulent velocity dispersion driven by feedback is expected to be vz = 0.4 ɛff(ρ0)p*/m* ~ 10 km s-1, relatively independent of Σ or ΣSFR. Turbulence-regulated starbursts (controlled by kinetic momentum feedback) are part of the larger scheme of self-regulation; primarily atomic low-Σ outer disks may have star formation regulated by ultraviolet heating

  9. 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

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

    PubMed

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

    2003-12-11

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

  11. 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

  12. DFT charge transfer of hybrid molecular ferrocene/Si structures

    NASA Astrophysics Data System (ADS)

    Calborean, Adrian; Buimaga-Iarinca, Luiza; Graur, Florin

    2015-05-01

    The electrochemical behavior and electronic properties of redox-active ferrocenes grafted onto semiconductor Si(100) substrate were investigated theoretically by first-principles calculations. Organic molecules were attached via the formation of Si-C covalent bonds through two different linkers: vinyl (direct grafting), and N3(CH2)11 (indirect grafting). Redox energies and the electronic properties relating to different spacers in hybrid ferrocene Fc/Si and ferrocenium Fc+/Si structures were theoretically extracted and compared with experimental cyclic voltametry data. Electronic charge transfers are discussed through the alignment positions of the frontier orbitals of the molecule with respect to the Si substrate gap. Periodic boundary conditions were used to investigate the Si(100) as a slab surface and hybrid Fc/Si structures. The resulting projected density of states (PDOS) were compared with molecular results and discussed in the light of experimental data.

  13. 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.

  14. 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.

  15. Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging.

    PubMed

    Mirjalili, Vahid; Noyes, Keenan; Feig, Michael

    2014-02-01

    We used molecular dynamics (MD) simulations for structure refinement of Critical Assessment of Techniques for Protein Structure Prediction 10 (CASP10) targets. Refinement was achieved by selecting structures from the MD-based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described, and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations versus a single long simulation, the success of a quality assessment criterion, the application of scoring versus averaging, and the impact of a final refinement step are discussed in detail.

  16. PCR hot start using primers with the structure of molecular beacons (hairpin-like structure).

    PubMed

    Kaboev, O K; Luchkina, L A; Tret'iakov, A N; Bahrmand, A R

    2000-11-01

    A new technique of PCR hot start using oligonucleotide primers with a stem-loop structure is developed here. The molecular beacon oligonucleotide structure without any chromophore addition to the ends was used. The 3'-end sequence of the primers was complementary to the target and five or six nucleotides complementary to the 3'-end were added to the 5'-end. During preparation of the reaction mixture and initial heating, the oligonucleotide has a stem-loop structure and cannot serve as an effective primer for DNA polymerase. After heating to the annealing temperature it acquires a linear structure and primer extension can begin.

  17. 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.

  18. 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

  19. Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles.

    PubMed

    Mirjalili, Vahid; Feig, Michael

    2013-02-12

    A molecular dynamics (MD) simulation based protocol for structure refinement of template-based model predictions is described. The protocol involves the application of restraints, ensemble averaging of selected subsets, interpolation between initial and refined structures, and assessment of refinement success. It is found that sub-microsecond MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.

  20. 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.

  1. 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'…

  2. Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data.

    PubMed

    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.

  3. 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.

  4. 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

  5. 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. PMID:27642240

  6. 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.

  7. Molecular Dynamics of Shock Wave Interaction with Nanoscale Structured Materials

    NASA Astrophysics Data System (ADS)

    Al-Qananwah, Ahmad K.

    Typical theoretical treatments of shock wave interactions are based on a continuum approach, which cannot resolve the spatial variations in solids with nano-scale porous structure. Nano-structured materials have the potential to attenuate the strength of traveling shock waves because of their high surface-to-volume ratio. To investigate such interactions we have developed a molecular dynamics simulation model, based on Short Range Attractive interactions. A piston, modeled as a uni-directional repulsive force field translating at a prescribed velocity, impinges on a region of gas which is compressed to form a shock, which in turn is driven against an atomistic solid wall. Periodic boundary conditions are used in the directions orthogonal to the piston motion, and we have considered solids based on either embedded atom potentials (target structure) or tethered potential (rigid piston, holding wall). Velocity, temperature and stress fields are computed locally in both gas and solid regions, and displacements within the solid are interpreted in terms of its elastic constants. In this work we present results of the elastic behavior of solid structures subjected to shock wave impact and analysis of energy transport and absorption in porous materials. The results indicated that the presence of nano-porous material layers in front of a target wall reduced the stress magnitude detected inside and the energy deposited there by about 30 percent while, at the same time, its loading rate was decreased substantially.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Normal and Starburst Galaxies in Deep X-ray Surveys

    NASA Technical Reports Server (NTRS)

    Hornschemeier, Ann

    2006-01-01

    This talk will cover progress of the last several years in unraveling the nature of normal and starburst galaxies in deep X-ray surveys. This includes discussion of the normal galaxy X-ray Luminosity Function in deep field and cluster surveys and what it tells us about the binary populations in galaxies. The utility of broad band X-ray emission, especially as compared to other multiwavelength measurements of current/recent star formation, will be reviewed. These broad band X-ray measurements of star formation are based upon X-ray/Star Formation Rate correlations that span the currently available redshift range (0 < z < 1). I will also discuss new efforts underway to systematically characterize the X-ray emission from galaxies in group and cluster environments, including a new effort underway in the Coma cluster of galaxies. I will finish with discussion of the redshift frontier for studies of X-ray star formation, currently 2 approx.4, where the UV-selected Lyman Break galaxies are the best glimpse we have into X-ray emission from star formation in the early Universe. Lyman Break galaxies are of particular interest due to the overlap in basic properties with starburst galaxies in the more local Universe. Understanding the outflows in such starburst galaxies is of critical importance to constraining the "stellar" portion of cosmic feedback. The talk will close with a brief discussion of distant normal galaxy science with future X-ray observatories such as the upcoming Con-X/XEUS mission(s).

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. High-resolution 12.4 micron images of the starburst region in M82

    NASA Technical Reports Server (NTRS)

    Telesco, C. M.; Gezari, D. Y.

    1992-01-01

    We present 12.4 micron images, made with 1" resolution, of the intense star-forming region in the galaxy M82. Considerable small-scale structure is evident, including several bright clumps less than about 20 pc in size which may be embedded with giant star clusters more massive than 3 x 100,000 solar mass. No correlation is seen between the infrared emission and the bright radio/X-ray point sources which are thought to be very young supernova remnants. We propose that high values of the ratio of nonthermal and infrared emission near the nucleus, and of the ratio LIR/LCO at one of the starburst lobes, can be attributed to disruption of the central region by supernova activity. However, we argue that the midinfrared-emitting dust is heated by young stars and not, as recently proposed, by supernova shocks.

  18. The Seyfert-Starburst Connection in X-rays. 2; Results and Implications

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

    We present the results of X-ray imaging and spectroscopic analysis of a sample of Seyfert 2 galaxies that contain starbursts, based on their optical and UV characteristics. These composite galaxies exhibit extended, soft, thermal X-ray emission, which we attribute to their starburst components. Comparing their X-ray and far-infrared properties with ordinary Seyfert and starburst galaxies, we identify the spectral characteristics of their various intrinsic emission sources. The observed far-infrared emission of the composite galaxies may be associated almost exclusively with star formation, rather than the active nucleus. The ratio of the hard X-ray luminosity to the far-infrared and [O III] (lambda)5007 luminosity distinguishes most of these composite galaxies from "pure" Seyfert 2 galaxies, while their total observed hard X-ray luminosity distinguishes them from "pure" starbursts. The hard nuclear X-ray source is generally heavily absorbed (N(sub H) greater than 10(exp 23)/sq cm) in the composite galaxies. Based on these results, we suggest that the interstellar medium of the nuclear starburst is a significant source of absorption. The majority of the sample are located in groups or are interacting with other galaxies, which may trigger the starburst or allow rapid mass infall to the central black hole or both. We conclude that starbursts are energetically important in a significant fraction of active galaxies and that starbursts and active galactic nuclei may be part of a common evolutionary sequence.

  19. Multi-Wavelength Observations of Nearby Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Lee, Janice

    2015-08-01

    Do cycles of violent, intense, but short-lived bursts constitute a significant mode of global star formation in present-day galaxies? Such events can have a profound effect on galaxies, particularly those with shallow potential wells, and observational measures of their prevalence inform our understanding of a wide range of issues in galaxy evolution. I will highlight what we have learned about starbursts from multi-wavelength observations of galaxies in the local volume on both galactic and smaller scales, and explore how connections with the study of the deaths of massive stars may further our understanding of open issues in galaxy evolution.

  20. Viscous time lags between starburst and AGN activity

    NASA Astrophysics Data System (ADS)

    Blank, Marvin; Duschl, Wolfgang J.

    2016-10-01

    There is strong observational evidence indicating a time lag of order of some 100 Myr between the onset of starburst and AGN activity in galaxies. Dynamical time lags have been invoked to explain this. We extend this approach by introducing a viscous time lag the gas additionally needs to flow through the AGN's accretion disc before it reaches the central black hole. Our calculations reproduce the observed time lags and are in accordance with the observed correlation between black hole mass and stellar velocity dispersion.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    SciTech Connect

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

    2011-12-31

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

  3. 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.

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

    PubMed

    Mehere, Prajwalini; Han, Qian; Lemkul, Justin A; Vavricka, Christopher J; Robinson, Howard; Bevan, David R; Li, Jianyong

    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 α-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 Å 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Iron affects the structure of cell membrane molecular models.

    PubMed

    Suwalsky, M; Martínez, F; Cárdenas, H; Grzyb, J; Strzałka, K

    2005-03-01

    The effects of Fe(3+) and Fe(2+) on molecular models of biomembranes were investigated. These consisted of bilayers of dimyristoylphosphatidylcholine (DMPC) and of dimyristoylphosphatidylethanolamine (DMPE), classes of phospholipids located in the outer and inner moieties of cell membranes, respectively. X-ray studies showed that very low concentrations of Fe(3+) affected DMPC organization and 10(-3)M induced a total loss of its multilamellar periodic stacking. Experiments carried out with Fe(2+) on DMPC showed weaker effects than those induced by Fe(3+) ions. Similar experiments were performed on DMPE bilayers. Fe(3+) from 10(-7)M up to 10(-4)M had practically no effect on DMPE structure. However, 10(-3)M Fe(3+) induced a deep perturbation of the multilamellar structure of DMPE. However, 10(-3)M Fe(2+) had no effect on DMPE organization practically. Differential scanning calorimetry measurements also revealed different effects of Fe(3+) and Fe(2+) on the phase transition and other thermal properties of the examined lipids. In conclusion, the results obtained indicate that iron ions interact with phospholipid bilayers perturbing their structures. These findings are consistent with the observation that iron ions change cell membrane fluidity and, therefore, affect its functions. PMID:15752465

  10. Towards a molecular description of intermediate filament structure and assembly

    SciTech Connect

    Parry, David A.D.; Strelkov, Sergei V.; Burkhard, Peter; Aebi, Ueli; Herrmann, Harald . E-mail: h.herrmann@dkfz.de

    2007-06-10

    Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central {alpha}-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling.

  11. 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.

  12. 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.

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    Aims: 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. Methods: 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 Hα line. These masses agree excellently with the photometric masses. The mass (gas+stars) range is ~109-1011.5ℳ⊙. As a selection criterion for starburst galaxies, we use, the birthrate parameter, b = SFR/ ⟨ SFR ⟩, requiring that b ≥ 3. For postburst galaxies, we use, the equivalent width of Hδ in absorption with the criterion EWHδ,abs ≥ 6 Å. 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 ~10 Myr, while almost no starbursts are found at ages >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 >3%) is bimodal with a break at logℳ(ℳ⊙) ~ 10.6, above which the ages are doubled. The starburst and postburst luminosity

  15. Studies of the correlation of electrode kinetics with molecular structure

    NASA Astrophysics Data System (ADS)

    Weaver, M. J.

    1983-06-01

    The overall objective is to develop our understanding of the connections between the kinetics and mechanisms of heterogeneous electron-transfer reactions at metal-electrolyte interfaces and the molecular structure of the reactant and the interfacial region. We have chiefly focussed attention on transition-metal redox couples, especially Co(III)/(II), Cr(III)/(II), and Ru(III)/(II) containing adsorbing inorganic and organic ligands at a number of electrocatalytic solid surfaces, especially silver, platinum, and gold, as well as at mercury electrodes. By combining electrochemical kinetic and reactant adsorption thermodynamic measurements, along with in situ vibrational spectroscopic studies using Surface-Enhanced Raman Scattering (SERS), the various catalytic influences exerted by the metal interface upon the energetics of electrode reactions have been probed in detail.

  16. Molecular structures and crystal packings of 2-styrylquinoxaline derivatives

    NASA Astrophysics Data System (ADS)

    Kuz'mina, L. G.; Sitin, A. G.; Gulakova, E. N.; Fedorova, O. A.; Lermontova, E. Kh.; Churakov, A. V.

    2012-01-01

    The crystal and molecular structures of 2-styrylquinoxaline derivatives with different substituents in the styryl fragment are determined. The degree of planarity of the molecules studied varies in a very wide range, from 1.7° to 33.5°. In the ethylene fragment, the double bond is essentially localized. The bicycle-pedal disordering of the ethylene fragment is found in the crystals of the methoxy and oxyacetyl derivatives of 2-styrylquinoxaline. None of the packings contains packing motifs favorable for the photocycloaddition (PCA) reaction with single crystal retention. The crystal packings of these compounds and that of 2-(4-methylstyryl)quinoxaline are characterized by a stacking motif of the head-to-head type, which eliminates the possibility of PCA taking place with single crystal retention but is suitable for this reaction in polycrystalline films. The crystal packing of 2-(3,4-dimethoxystyryl)quinoxaline does not contain elements with stacking interactions.

  17. 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.

  18. 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.

  19. The E-state as the basis for molecular structure space definition and structure similarity

    PubMed

    Hall; Kier

    2000-05-01

    The electrotopological state (E-state) is presented as a representation of molecular structure useful for definition of a space for chemical structures. This E-state representation provides the basis for chemical database management. The E-state formalism is presented along with its extension to the atom-type E-state. An approach to database organization, using polychlorobiphenyls (PCBs) as examples, reveals the descriptive power of the E-state paradigm. A well-organized chemical database, as described here, may be searched to find structures similar to a target structure with the expectation that such structures may exhibit properties similar to the target. Searches using the atom-type E-state indices are demonstrated with two example drug molecules.

  20. 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.

  1. A NICMOS search for obscured supernovae in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Maiolino, Roberto

    2003-07-01

    Recent near-IR monitoring campaigns were successful in detecting obscured supernovae {SNe} in starburst galaxies. The inferred SN rate is much higher than that obtained in previous optical campaigns, but it is still significanly lower than expected by the high level star formation of these systems. One possible explanation for the shortage of SNe is that most of them occur in the nuclear region, where the limited angular resolution of groundbased observations prevents their detection. We propose NICMOS SNAP observations of a sample of starburst galaxies already observed once by NICMOS, with the goal of exploiting its sensitivity and angular resolution to detect nuclear obscured SNe which might have been missed by groundbased surveys. These observation will allow to assess the real SN rate in starbust galaxies and deliver a sample of SN occurring in the extreme environment of galactic nuclei. We expect to detect more than 55 SNe {if the whole sample is observed}. If the number of SNe detected in the program is much lower than expected it would prompt for a revision of our understanding of the relation between the star formation rate and the SN rate.

  2. 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.

  3. 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

    2016-11-01

    We present a study of the complete ultraviolet to submillimetre spectral energy distributions (SEDs) of 12 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 active galactic nuclei (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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. Fast electronic structure methods for strongly correlated molecular systems

    NASA Astrophysics Data System (ADS)

    Head-Gordon, Martin; Beran, Gregory J. O.; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given.

  10. 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.

  11. 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

  12. Molecular structure and absolute configuration of the diterpene lactone, praelolide.

    PubMed

    Dai, J B; Wan, Z L; Rao, Z H; Liang, D C; Fang, Z; Luo, Y K; Long, K H

    1985-11-01

    Praelolide is a new compound which was isolated out from the gorgonian, Menella praelonga (Ridley), collected from the South Sea of China at Zhanjiang, Guangdong. The molecular formula is C28H35O12Cl. The research result by X-ray diffraction method on the crystal structure is presented. The compound is orthorhombic with space group P2(1)2(1)2, cell dimensions a = 16.936, b = 16.709, c = 10.333 A, and Z = 4. The structure has been solved by direct method and refined to R = 0.055 for 2257 unique observable reflexions by least-squares. The molecule is composed of the major conformational isomer in which the three main rings (a six-membered ring, an eight-membered ring, a six-membered ring) take separately the form of chair-chairboat-chair, a five-membered actone ring, a C1 substitution, 4 acetate groups, and a three-membered epoxide ring. The absolute configuration of the molecule has also been determined by statistics (R factor ratio R = 1.012) and Bijvoet pairs observation. For 30 pairs of the greatest anomalous contributions the residuals are R'(+) = 0.057 for the first enantiomorph and R'(-) = 0.005 for the second one, so the latter should unambiguously correspond to the absolute configuration of the molecule.

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

    SciTech Connect

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

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

  14. Molecular and Supramolecular Structural Studies on Human Tropoelastin Sequences

    PubMed Central

    Ostuni, Angela; Bochicchio, Brigida; Armentano, Maria F.; Bisaccia, Faustino; Tamburro, Antonio M.

    2007-01-01

    One of the unusual properties of elastin is its ability to coacervate, which has been proposed to play an important role in the alignment of monomeric elastin for cross-linking into the polymeric elastin matrix. The temperature at which this transition takes place depends on several factors including protein concentration, ionic strength, and pH. Previously, polypeptide sequences encoded by different exons of the human tropoelastin gene have been analyzed for their ability to coacervate and to self-assemble. Few of them were indeed able to coacervate and only one, that encoded by exon 30 (EX30), gave amyloid fibers. In this article, we report on two chemically synthesized peptides—a decapeptide and an octadecapeptide—whose sequences are contained in the longer EX30 peptide and on a polypeptide (EX1–7) of 125 amino-acid residues corresponding to the sequence coded by the exons 1–7 and on a polypeptide (EX2–7) of 99 amino-acid residues encoded by exons 2–7 of human tropoelastin obtained by recombinant DNA techniques. Molecular and supramolecular structural characterization of these peptides showed that a minimum sequence of ∼20 amino acids is needed to form amyloid fibers in the exon 30-derived peptides. The N-terminal region of mature tropoelastin (EX2–7) gives rise to a coacervate and forms elastinlike fibers, whereas the polypeptide sequence containing the signal peptide (EX1–7) forms mainly amyloid fibers. Circular dichroism spectra show that β-structure is ubiquitous in all the sequences studied, suggesting that the presence of a β-structure is a necessary, although not sufficient, requirement for the appearance of amyloid fibers. PMID:17693470

  15. 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

  16. Starburst-Driven Winds May Have Created Giant "Lobe" in Galactic Center

    NASA Astrophysics Data System (ADS)

    2004-06-01

    An astronomer using the National Science Foundation's Robert C. Byrd Green Bank Telescope (GBT) has discovered that two prominent features rising out of the center of the Milky Way Galaxy are actually the distant edges of the same superstructure. This object, which has the appearance of a "lobe," may have been formed during an epoch of furious star formation. Lobe Galactic center radio image with lobe feature shown in outline. CREDIT: NRAO/AUI/NSF Yusef-Zadeh, et.al. (Click for Image w/o lines) Astronomer Casey Law of Northwestern University presented his results at the Denver, Colorado, meeting of the American Astronomical Society. "The center of our Galaxy is an incredibly dynamic place and morphologically very difficult to untangle" said Law. "Among the many features we see there, including supernova remnants, hot star-forming regions, and massive molecular clouds, are two very prominent columns of radio-emitting material that seem to erupt out of the plane of the Galaxy. The nature and origin of these features have been the subjects of much speculation, but with the new data from the Green Bank Telescope we're finally able to discern that they are in fact part of the same superstructure." Much of what we know about the center of our Galaxy has come from studies conducted on radio telescopes. The center of the Milky Way is, in fact, hidden from view to optical telescopes due to intervening clouds of dust and gas. Radio waves, however, are able to pass through the obscuring material and reveal details about the core of our Galaxy. Astronomers now know that this area of the Milky Way -- approximately 26,000 light-years from Earth -- is a densely packed region brimming with hot , young stars, supernova remnants, and more esoteric features -- like long radio-emitting filaments. At the center of it all is a remarkably radio-bright region known as Sagittarius A* (pronounced A-star), which is known to contain a supermassive black hole. Deciphering what all these

  17. Light-operated machines based on threaded molecular structures.

    PubMed

    Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

  18. 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

  19. Correlation of molecular structure with fluorescence spectra in rare earth chelates. I.

    NASA Technical Reports Server (NTRS)

    Bjorklund, S.; Degnan, J.; Filipescu, N.; Mcavoy, N.

    1968-01-01

    Rare earth chelates fluorescence spectra correlation with molecular structure, analyzing emission spectrum internal Stark splitting of tetramethylammonium tetrakis /dibenzoylmethido/europate microcrystals

  20. 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.

  1. 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

  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. 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

  4. 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

  5. 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.

  6. 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

  7. Molecular advances in understanding social insect population structure.

    PubMed

    Crozier, R H; Oldroyd, B P; Tay, W T; Kaufmann, B E; Johnson, R N; Carew, M E; Jennings, K M

    1997-08-01

    Social insects present many phenomena seen in all organisms but in more extreme forms and with larger sample sizes than those observable in most natural populations of vertebrates. Microsatellites are proving very much more informative than allozymes for the analysis of population biological problems, and prolifically polymorphic markers are fairly readily developed. In addition, the male-haploid genetic system of many social insects facilitates genetic analysis. The ability to amplify DNA from sperm stored in a female's sperm storage device enables the determination of mating types long after the death of the short-lived males, in addition to information on the degree of mixing of sperm from different males. Mitochondrial (mt) DNA sequences are also proving important, not only in phylogenetic studies but also in molecular population genetics, as a tracer of female movements. Mitochondrial markers have definitively shown the movement of females between colonies, challenging models giving exclusive primacy to kin selection as the explanation for multiqueen colonies, in Australian meat ants, Iridomyrmex purpureus, and the aridzone queenless ant Rhytidoponera sp. 12. Microsatellite and mtDNA variation are being studied in Camponotus consobrinus sugar ants, showing an unexpected diversity of complexity in colony structure, and microsatellites have shown that transfer of ants between nests of the weaver ant Polyrhachis doddi must be slight, despite an apparent lack of hostility.

  8. 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.

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  12. 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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  15. 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

  16. 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.

  17. Super Star Cluster Nebula in the Starburst Galaxy NGC 660

    NASA Astrophysics Data System (ADS)

    Naiman, J. P.; Turner, J. L.; Tsai, C.-W.; Beck, S. C.; Ho, P. T. P.

    2004-12-01

    We have mapped the starburst galaxy NGC 660 at 100mas resolution at K band (1.3 cm) with the NRAO Very Large Array. A peculiar galaxy at a distance of 13 Mpc, NGC 660 contains concentrated central star formation of power ˜ 2 x 1010 Lsun. Our 1.3 cm continuum image reveals a bright, compact source of less than 10 pc extent with a rising spectral index. We infer that this is optically thick free-free emission from a super star cluster nebula. The nebula is less than 10 pc in size, comparable in luminosity to the ``supernebula" in the dwarf galaxy, NGC 5253. We estimate that there are a few thousand O stars contained in this single young cluster. There are a number of other weaker continuum sources, either slightly smaller or more evolved clusters of similar size within the central 300 parsecs of the galaxy. This work is supported in part by the National Science Foundation.

  18. Markov Chain Monte-Carlo Models of Starburst Clusters

    NASA Astrophysics Data System (ADS)

    Melnick, Jorge

    2015-01-01

    There are a number of stochastic effects that must be considered when comparing models to observations of starburst clusters: the IMF is never fully populated; the stars can never be strictly coeval; stars rotate and their photometric properties depend on orientation; a significant fraction of massive stars are in interacting binaries; and the extinction varies from star to star. The probability distributions of each of these effects are not a priori known, but must be extracted from the observations. Markov Chain Monte-Carlo methods appear to provide the best statistical approach. Here I present an example of stochastic age effects upon the upper mass limit of the IMF of the Arches cluster as derived from near-IR photometry.

  19. The role of starburst amacrine cells in visual signal processing

    PubMed Central

    TAYLOR, W.R.; SMITH, R.G.

    2012-01-01

    Starburst amacrine cells (SBACs) within the adult mammalian retina provide the critical inhibition that underlies the receptive field properties of direction-selective ganglion cells (DSGCs). The SBACs generate direction-selective output of GABA that differentially inhibits the DSGCs. We review the biophysical mechanisms that produce directional GABA release from SBACs and test a network model that predicts the effects of reciprocal inhibition between adjacent SBACs. The results of the model simulations suggest that reciprocal inhibitory connections between closely spaced SBACs should be spatially selective, while connections between more widely spaced cells could be indiscriminate. SBACs were initially identified as cholinergic neurons and were subsequently shown to contain release both acetylcholine and GABA. While the role of the GABAergic transmission is well established, the role of the cholinergic transmission remains unclear. PMID:22310373

  20. Radio identifications of UGC galaxies - starbursts and monsters

    SciTech Connect

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

    1988-07-01

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

  1. Structurally-modified subphthalocyanines: molecular design towards realization of expected properties from the electronic structure and structural features of subphthalocyanine.

    PubMed

    Shimizu, Soji; Kobayashi, Nagao

    2014-07-01

    This feature article summarizes recent contributions of the authors in the synthesis of structurally-modified subphthalocyanines. The structural modification covers (1) modification of the conjugated system of subphthalocyanines to create novel conjugated systems comprising three pyrroles or pyrrole-like subunits, (2) core-modification by expansion of the inner pyrrolic five-membered ring to larger six- and seven-membered ring units, and (3) exterior-modification by annulation of functional units to subphthalocyanines. These modifications in the structure of subphthalocyanines have been performed with the aim of demonstrating unique properties originating from the bowl-shaped C3v-symmetric structure as well as the electronic structure delineated by the 14π-electron conjugated system on the curved molecular surface. The possible structural modifications surveyed in this feature article and their concomitant properties will provide important future guidelines to the design of subphthalocyanine-based functional molecules, considering the fact that subphthalocyanines have recently been attracting considerable attention as potential candidates in the field of optoelectronics and molecular electronics. PMID:24710280

  2. A NICMOS search for obscured supernovae in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Cresci, G.; Mannucci, F.; Della Valle, M.; Maiolino, R.

    2007-02-01

    The detection of obscured supernovae (SNe) in near-infrared monitoring campaigns of starburst galaxies has shown that a significant fraction of SNe is missed by optical surveys. However, the number of SNe detected in ground-based near-IR observations is still significantly lower than the number of SNe extrapolated from the FIR luminosity of the hosts. A possibility is that most SNe occur within the nuclear regions, where the limited angular resolution of ground-based observations prevents their detection. This issue prompted us to exploit the superior angular resolution of NICMOS-HST to search for obscured SNe within the first kpc from the nucleus of strong starbursting galaxies. A total of 17 galaxies were observed in SNAPSHOT mode. Based on their FIR luminosity, we did not expect to detect fewer than ~ 12 SNe. However, no confirmed SN event was found. From our data we derived an observed nuclear SN rate <0.5 SN/yr per galaxy. The shortage of SN detections can be explained by a combination of several effects. The most important are: i) the existence of a strong extinction, A_V⪆ 11; ii) most SNe occur within the first 0.5 arcsec (which corresponds in our sample to about 500 pc) where even NICMOS is unable to detect SN events. Based on observations made with the NASA/ESA Hubble Space Telescope associated with program 9726, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555, and on data obtained at the VLT through the ESO program 272.D-5043.

  3. The ULX Population in the Starburst Galaxy NGC 253

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Near-Infrared Integral Field Spectroscopy and Mid-Infrared Spectroscopy of the Starburst Galaxy M82

    NASA Astrophysics Data System (ADS)

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

    2001-05-01

    We present new infrared observations of the central regions of the starburst galaxy M82. The observations consist of near-infrared integral field spectroscopy in the H and K bands obtained with the MPE 3D instrument and of λ=2.4-45 μm spectroscopy from the Short Wavelength Spectrometer (SWS) onboard the Infrared Space Observatory. These measurements are used, together with data from the literature, to (1) reexamine the controversial issue of extinction, (2) determine the physical conditions of the interstellar medium (ISM) within the star-forming regions, and (3) characterize the composition of the stellar populations. Our results provide a set of constraints for detailed starburst modeling, which we present in a companion paper. We find that purely foreground extinction cannot reproduce the global relative intensities of H recombination lines from optical to radio wavelengths. A good fit is provided by a homogeneous mixture of dust and sources, and with a visual extinction of AV=52 mag. The SWS data provide evidence for deviations from commonly assumed extinction laws between 3 and 10 μm. The fine-structure lines of Ne, Ar, and S detected with SWS imply an electron density of ~300 cm-3, and abundance ratios Ne/H and Ar/H nearly solar and S/H about one-fourth solar. The excitation of the ionized gas indicates an average effective temperature for the OB stars of 37,400 K, with little spatial variation across the starburst regions. We find that a random distribution of closely packed gas clouds and ionizing clusters and an ionization parameter of ~10-2.3 represent well the star-forming regions on spatial scales ranging from a few tens to a few hundreds of parsecs. From detailed population synthesis and the mass-to-K-light ratio, we conclude that the near-infrared continuum emission across the starburst regions is dominated by red supergiants with average effective temperatures ranging from 3600 to 4500 K and roughly solar metallicity. Our data rule out significant

  9. Probing the molecular structure of interfacial films and crystals

    NASA Astrophysics Data System (ADS)

    Wang, Anfeng

    The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes

  10. 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.

  11. Laser pulse induced multiple exciton kinetics in molecular ring structures

    NASA Astrophysics Data System (ADS)

    Hou, Xiao; Wang, Luxia

    2016-11-01

    Multiple excitons can be formed upon strong optical excitation of molecular aggregates and complexes. Based on a theoretical approach on exciton-exciton annihilation dynamics in supramolecular systems (May et al., 2014), exciton interaction kinetics in ring aggregates of two-level molecules are investigated. Excited by the sub-picosecond laser pulse, multiple excitons keep stable in the molecular ring shaped as a regular polygon. If the symmetry is destroyed by changing the dipole of a single molecule, the excitation of different molecules becomes not identical, and the changed dipole-dipole interaction initiates subsequent energy redistribution. Depending on the molecular distance and the dipole configuration, the kinetics undergo different types of processes, but all get stable within some hundreds of femtoseconds. The study of exciton kinetics will be helpful for further investigations of the efficiency of optical devices based on molecular aggregates.

  12. 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.

  13. Evidence of Nuclear Disks from the Radial Distribution of CCSNe in Starburst Galaxies

    NASA Astrophysics Data System (ADS)

    Herrero-Illana, Rubén; Pérez-Torres, Miguel Ángel; Alberdi, Antxon

    Galaxy-galaxy interactions are expected to be responsible for triggering massive star formation and possibly accretion onto a supermassive black hole, by providing large amounts of dense molecular gas down to the central kiloparsec region. Several scenarios to drive the gas further down to the central ˜ 100 pc, have been proposed, including the formation of a nuclear disk around the black hole, where massive stars would produce supernovae. Here, we probe the radial distribution of supernovae and supernova remnants in the nuclear regions of the starburst galaxies M82, Arp 299-A, and Arp 220, by using high-angular resolution (≲ 0.'1) radio observations. We derived scale-length values for the putative nuclear disks, which range from ˜ 20-30 pc for Arp 299-A and Arp 220, up to ˜ 140 pc for M82. The radial distribution of SNe for the nuclear disks in Arp 299-A and Arp 220 is also consistent with a power-law surface density profile of exponent γ = 1, as expected from detailed hydrodynamical simulations of nuclear disks. This study is detailed in Herrero-Illana, Perez-Torres, and Alberdi [11].

  14. A chromogenic molecular capsule attributable to dipolar amide resonance structure.

    PubMed

    Park, Yeon Sil; Park, Juwan; Paek, Kyungsoo

    2015-04-01

    A new chromogenic, self-assembled molecular capsule G@22 is developed by introducing four (N,N-dimethyl-4-aminophenyl) azobenzyl moieties on the upper rim of a resorcin[4]arene-based amidoimino-cavitand. The tuning of conjugation between amido and (N,N-dimethyl-4-aminophenyl)azobenzyl groups by acid-base titration allows naked-eye detection of molecular capsule formation. PMID:25740710

  15. 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.

  16. 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.

  17. 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

  18. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

    PubMed

    Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F

    2008-02-01

    We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

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

    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

  7. 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.

  8. Molecular structure descriptors in the computer-aided design of biologically active compounds

    NASA Astrophysics Data System (ADS)

    Raevsky, Oleg A.

    1999-06-01

    The current state of description of molecular structure in computer-aided molecular design of biologically active compounds by means of descriptors is analysed. The information contents of descriptors increases in the following sequence: element-level descriptors-structural formulae descriptors-electronic structure descriptors-molecular shape descriptors-intermolecular interaction descriptors. Each subsequent class of descriptors normally covers information contained in the previous-level ones. It is emphasised that it is practically impossible to describe all the features of a molecular structure in terms of any single class of descriptors. It is recommended to optimise the number of descriptors used by means of appropriate statistical procedures and characteristics of structure-property models based on these descriptors. The bibliography includes 371 references.

  9. 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

  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. Supersonic turbulence and structure of interstellar molecular clouds.

    PubMed

    Boldyrev, Stanislav; Nordlund, Ake; Padoan, Paolo

    2002-07-15

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

  12. 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.

  13. 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

  14. The radial distribution of SNe in nuclear starbursts

    NASA Astrophysics Data System (ADS)

    Herrero-Illana, R.; Pérez-Torres, M. Á.; Alberdi, A.

    2012-10-01

    We have probed the radial distribution of supernovae and supernova remnants in the nuclear regions of the starburst galaxies M82, Arp 299-A, and Arp 220, by using high-angular resolution (≤ 0."1) radio observations. We derived scale-length values for the putative nuclear disks, which range from ~20-30 pc for Arp 299-A and Arp 220, up to ~140 pc for M82. The radial distribution of SNe for the nuclear disks in Arp 299-A and Arp 220 is also consistent with a power-law surface density profile of exponent γ = 1, as expected from detailed hydrodynamical simulations of nuclear disks. Our results give thus support to scenarios where a nuclear disk of size ~100 pc is formed in (U)LIRGs, and is sustained by gas pressure, in which case the accretion onto the black hole could be lowered due to supernova feedback. This study is detailed in Herrero-Illana et al. (2012). Database: ast

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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...

  3. Ultra-low-molecular-weight heparins: precise structural features impacting specific anticoagulant activities.

    PubMed

    Lima, Marcelo A; Viskov, Christian; Herman, Frederic; Gray, Angel L; de Farias, Eduardo H C; Cavalheiro, Renan P; Sassaki, Guilherme L; Hoppensteadt, Debra; Fareed, Jawed; Nader, Helena B

    2013-03-01

    Ultra-low-molecular-weight heparins (ULMWHs) with better efficacy and safety ratios are under development; however, there are few structural data available. The main structural features and molecular weight of ULMWHs were studied and compared to enoxaparin. Their monosaccharide composition and average molecular weights were determined and preparations studied by nuclear magnetic resonance spectroscopy, scanning ultraviolet spectroscopy, circular dichroism and gel permeation chromatography. In general, ULMWHs presented higher 3-O-sulphated glucosamine and unsaturated uronic acid residues, the latter being comparable with their higher degree of depolymerisation. The analysis showed that ULMWHs are structurally related to LMWHs; however, their monosaccharide/oligosaccharide compositions and average molecular weights differed considerably explaining their different anticoagulant activities. The results relate structural features to activity, assisting the development of new and improved therapeutic agents, based on depolymerised heparin, for the prophylaxis and treatment of thrombotic disorders.

  4. 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...

  5. 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...

  6. 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.

  7. 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.

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

    PubMed

    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

    Here we report the bias-evolution of the electrical double layer structure of an ionic liquid on highly ordered pyrolytic graphite measured by atomic force microscopy. 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, which improves our understanding of the mechanism of charge storage on a molecular level.

  9. Resolved photometry of young massive clusters in the starburst galaxy NGC 4214

    NASA Astrophysics Data System (ADS)

    Sollima, A.; Cignoni, M.; Gratton, R. G.; Tosi, M.; Bragaglia, A.; Lucatello, S.; Meurer, G.

    2014-01-01

    We present the results of deep high-resolution imaging performed with Advanced Camera for Surveys (ACS)/HRC@HST in the most active region of the nearby starburst galaxy NGC 4214. We resolved the stellar populations of five young massive clusters and their surrounding galactic field. The star formation history of this region is characterized by two main bursts occurred within the last 500 Myr, with the oldest episode spread out across an area larger than that covered by the most recent one. The ages derived for the analysed clusters cover a wide range within 6.4 < log t/yr < 8.1 in agreement with those predicted by recent analyses based on integrated photometry. The comparison between the mass of the young associations and that of the surrounding field population with similar ages indicates a high cluster formation efficiency (Γ ˜ 33 per cent) which decreases when old populations are considered. The mass function of the major assembly has been found to be slightly flatter than the Salpeter law with a hint of mass segregation. We found no clear signatures of multiple stellar populations in the two young (log t/yr < 6.8) associations where we were able to resolve their innermost region. The masses and sizes of three clusters indicate that at least one of them could evolve towards a globular cluster-like structure.

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

    NASA Astrophysics Data System (ADS)

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

    2001-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2001-02-01

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

  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. 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

  14. Crystal structural and diffusion property in titanium carbides: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Lv, Yanan; Gao, Weimin

    2016-09-01

    Titanium carbides were studied via molecular dynamics simulation to characterize TiCx structures with respect to the carbon diffusion properties in this study. The effect of carbon concentration on atomic structures of titanium carbides was investigated through discussing the structure variation and the radial distribution functions of carbon atoms in titanium carbides. The carbon diffusion in titanium carbides was also analyzed, focusing on the dependence on carbon concentration and carbide structure. Carbon diffusivity with different carbon concentrations was determined by molecular dynamics (MD) calculations and compared with the available experimental data. The simulation results showed an atomic exchange mechanism for carbon diffusion in titanium carbide.

  15. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    SciTech Connect

    Bibby, Jaclyn; Keegan, Ronan M.; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

    2013-11-01

    Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

  16. The Obscuring Starburst of NGC 6221 and Implications for the Hard X-Ray Background

    NASA Technical Reports Server (NTRS)

    Levenson, N. A.; CidFernandes, R., Jr.; Weaver, K. A.; Heckman, T. M.; Storchi-Bergmann, T.; White, Nicholas E. (Technical Monitor)

    2001-01-01

    We present NGC 6221 as a case study of "X-ray-loud composite galaxies," which appear similar to starbursts at optical wavelengths and resemble traditional active galactic nuclei in X-rays. The net optical spectrum of NGC 6221 is properly characterized as a starburst galaxy, but in X-rays, NGC 6221 is similar to Seyfert 1 galaxies, exhibiting a power-law continuum spectrum, a broad Fe K(alpha) line, and continuum variability on timescales of days and years. High-resolution images reveal that the detected active nucleus is relatively weak, not only at optical, but also at near-infrared wavelengths. An obscuring starburst, in which the interstellar gas and dust associated with the starburst conceal the active nucleus, accounts for these peculiar features. We demonstrate quantitatively that obscuration by column density N(sub H) = 10(exp 22)/sq cm combined with relatively weak intrinsic nuclear activity can produce an optical spectrum that is characteristic of the surrounding starburst alone. While optical surveys would not identify the active nuclei that make these galaxies significant X-ray sources, such galaxies may, in fact, be important contributors to the X-ray background.

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

    NASA Astrophysics Data System (ADS)

    Sparre, Martin; Springel, Volker

    2016-11-01

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

  18. 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.

  19. 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

  20. VAMMPIRE: a matched molecular pairs database for structure-based drug design and optimization.

    PubMed

    Weber, Julia; Achenbach, Janosch; Moser, Daniel; Proschak, Ewgenij

    2013-06-27

    Structure-based optimization to improve the affinity of a lead compound is an established approach in drug discovery. Knowledge-based databases holding molecular replacements can be supportive in the optimization process. We introduce a strategy to relate the substitution effect within matched molecular pairs (MMPs) to the atom environment within the cocrystallized protein-ligand complex. Virtually Aligned Matched Molecular Pairs Including Receptor Environment (VAMMPIRE) database and the supplementary web interface ( http://vammpire.pharmchem.uni-frankfurt.de ) provide valuable information for structure-based lead optimization.

  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. 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.

  3. Gas-phase molecular structure and energetics of anionic silicates

    NASA Astrophysics Data System (ADS)

    Gomes, José R. B.; Cordeiro, M. Natália D. S.; Jorge, Miguel

    2008-09-01

    The gas-phase stabilities of linear, branched and cyclic silicates made of up to five silicon atoms were studied with density functional theory (DFT). The starting geometries for the DFT calculations at the B3LYP/6-311+G(2d,2p) level of theory were obtained from classical molecular dynamics simulations. We have observed that geometric parameters and charges are mainly affected by the degree of deprotonation. Charges on Si atoms are also influenced by their degree of substitution. The enthalpy of deprotonation of the neutral species was found to decrease with the size of the molecule, while the average deprotonation enthalpy of highly charged compounds increased with molecular size. Furthermore, the formation of rings in highly charged silicates is enthalpically preferred to chain growth. These observations result from two competing effects: the easier distribution of negative charge in silicates with low charge density and the strong intramolecular repulsions present in silicates with high charge density. As a consequence, highly charged silicates in the gas phase tend to be as small and as highly condensed as possible, which is in line with experimental observations from solution NMR.

  4. Exponential repulsion improves structural predictability of molecular docking.

    PubMed

    Bazgier, Václav; Berka, Karel; Otyepka, Michal; Banáš, Pavel

    2016-10-30

    Molecular docking is a powerful tool for theoretical prediction of the preferred conformation and orientation of small molecules within protein active sites. The obtained poses can be used for estimation of binding energies, which indicate the inhibition effect of designed inhibitors, and therefore might be used for in silico drug design. However, the evaluation of ligand binding affinity critically depends on successful prediction of the native binding mode. Contemporary docking methods are often based on scoring functions derived from molecular mechanical potentials. In such potentials, nonbonded interactions are typically represented by electrostatic interactions between atom-centered partial charges and standard 6-12 Lennard-Jones potential. Here, we present implementation and testing of a scoring function based on more physically justified exponential repulsion instead of the standard Lennard-Jones potential. We found that this scoring function significantly improved prediction of the native binding modes in proteins bearing narrow active sites such as serine proteases and kinases. © 2016 Wiley Periodicals, Inc. PMID:27620738

  5. Molecular structure of β-amyloid fibrils in Alzheimer’s disease brain tissue

    PubMed Central

    Lu, Jun-Xia; Qiang, Wei; Yau, Wai-Ming; Schwieters, Charles D.; Meredith, Stephen C.; Tycko, Robert

    2013-01-01

    In vitro, β-amyloid (Aβ) peptides form polymorphic fibrils, with molecular structures that depend on growth conditions, plus various oligomeric and protofibrillar aggregates. Detailed structural information about Aβ assemblies in the human brain has been lacking. Here, we investigate structures of brain-derived Aβ fibrils, using seeded fibril growth from brain extract and data from solid state nuclear magnetic resonance and electron microscopy. Experiments on tissue from two Alzheimer’s disease (AD) patients with distinct clinical histories indicate a single predominant 40-residue Aβ (Aβ40) fibril structure in each patient, but different structures in the two patients. A molecular structural model developed for Aβ40 fibrils from one patient reveals features that distinguish in vivo from in vitro fibrils. The data suggest that fibrils in the brain may spread from a single nucleation site, that structural variations may correlate with variations in AD, and that structure-specific amyloid imaging agents may be an important future goal. PMID:24034249

  6. Molecular Modeling of Mechanosensory Ion Channel Structural and Functional Features

    PubMed Central

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-01-01

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex. PMID:20877470

  7. Molecular modeling of mechanosensory ion channel structural and functional features.

    PubMed

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-09-16

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  8. Structure-function relationships of shared-stem and conventional molecular beacons.

    PubMed

    Tsourkas, Andrew; Behlke, Mark A; Bao, Gang

    2002-10-01

    Molecular beacons are oligonucleotide probes capable of forming a stem-loop hairpin structure with a reporter dye at one end and a quencher at the other end. Conventional molecular beacons are designed with a target-binding domain flanked by two complementary short arm sequences that are independent of the target sequence. Here we report the design of shared-stem molecular beacons with one arm participating in both stem formation when the beacon is closed and target hybridization when it is open. We performed a systematic study to compare the behavior of conventional and shared-stem molecular beacons by conducting thermodynamic and kinetic analyses. Shared-stem molecular beacons form more stable duplexes with target molecules than conventional molecular beacons; however, conventional molecular beacons may discriminate between targets with a higher specificity. For both conventional and shared-stem molecular beacons, increasing stem length enhanced the ability to differentiate between wild-type and mutant targets over a wider range of temperatures. Interestingly, probe-target hybridization kinetics were similar for both classes of molecular beacons and were influenced primarily by the length and sequence of the stem. These findings should enable better design of molecular beacons for various applications.

  9. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    SciTech Connect

    Marcia, Marco Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-11-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

  10. 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.

  11. 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.

  12. 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.

  13. Structural Basis for Molecular Recognition at Serotonin Receptors

    PubMed Central

    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, Edward X.; Melcher, Karsten; Zhang, Chenghai; Bai, Fang; Yang, Huaiyu; Yang, Linlin; Jiang, Hualiang; Roth, Bryan L.; Cherezov, Vadim; Stevens, Raymond C.; Xu, H. Eric

    2013-01-01

    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 anti-migraine 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 to the accompanying 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

  14. Molecular Structure of Frizzled, a Drosophila Tissue Polarity Gene

    PubMed Central

    Adler, P. N.; Vinson, C.; Park, W. J.; Conover, S.; Klein, L.

    1990-01-01

    The function of the frizzled (fz) locus is required to coordinate the cytoskeletons of pupal epidermal cells so that a parallel array of cuticular hairs and bristles is produced. We report here the molecular cloning and characterization of the fz locus. The locus is very large. Mutations that inactivate the gene are spread over 100 kb of genomic DNA. The major mRNA product of the gene is a 4-kb RNA that is encoded by 5 exons spread over more than 90 kb of genomic DNA. Conceptual translation of this mRNA indicates that it encodes an integral membrane protein that is likely to contain both extracellular and cytoplasmic domains. PMID:2174014

  15. 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.

  16. The structural, functional, and molecular organization of the brainstem.

    PubMed

    Nieuwenhuys, Rudolf

    2011-01-01

    According to His (1891, 1893) the brainstem consists of two longitudinal zones, the dorsal alar plate (sensory in nature) and the ventral basal plate (motor in nature). Johnston and Herrick indicated that both plates can be subdivided into separate somatic and visceral zones, distinguishing somatosensory and viscerosensory zones within the alar plate, and visceromotor and somatomotor zones within the basal plate. To test the validity of this "four-functional-zones" concept, I developed a topological procedure, surveying the spatial relationships of the various cell masses in the brainstem in a single figure. Brainstems of 16 different anamniote species were analyzed, and revealed that the brainstems are clearly divisible into four morphological zones, which correspond largely with the functional zones of Johnston and Herrick. Exceptions include (1) the magnocellular vestibular nucleus situated in the viscerosensory zone; (2) the basal plate containing a number of evidently non-motor centers (superior and inferior olives). Nevertheless the "functional zonal model" has explanatory value. Thus, it is possible to interpret certain brain specializations related to particular behavioral profiles, as "local hypertrophies" of one or two functional columns. Recent developmental molecular studies on brains of birds and mammals confirmed the presence of longitudinal zones, and also showed molecularly defined transverse bands or neuromeres throughout development. The intersecting boundaries of the longitudinal zones and the transverse bands appeared to delimit radially arranged histogenetic domains. Because neuromeres have been observed in embryonic and larval stages of numerous anamniote species, it may be hypothesized that the brainstems of all vertebrates share a basic organizational plan, in which intersecting longitudinal and transverse zones form fundamental histogenetic and genoarchitectonic units. PMID:21738499

  17. The Structural, Functional, and Molecular Organization of the Brainstem

    PubMed Central

    Nieuwenhuys, Rudolf

    2011-01-01

    According to His (1891, 1893) the brainstem consists of two longitudinal zones, the dorsal alar plate (sensory in nature) and the ventral basal plate (motor in nature). Johnston and Herrick indicated that both plates can be subdivided into separate somatic and visceral zones, distinguishing somatosensory and viscerosensory zones within the alar plate, and visceromotor and somatomotor zones within the basal plate. To test the validity of this “four-functional-zones” concept, I developed a topological procedure, surveying the spatial relationships of the various cell masses in the brainstem in a single figure. Brainstems of 16 different anamniote species were analyzed, and revealed that the brainstems are clearly divisible into four morphological zones, which correspond largely with the functional zones of Johnston and Herrick. Exceptions include (1) the magnocellular vestibular nucleus situated in the viscerosensory zone; (2) the basal plate containing a number of evidently non-motor centers (superior and inferior olives). Nevertheless the “functional zonal model” has explanatory value. Thus, it is possible to interpret certain brain specializations related to particular behavioral profiles, as “local hypertrophies” of one or two functional columns. Recent developmental molecular studies on brains of birds and mammals confirmed the presence of longitudinal zones, and also showed molecularly defined transverse bands or neuromeres throughout development. The intersecting boundaries of the longitudinal zones and the transverse bands appeared to delimit radially arranged histogenetic domains. Because neuromeres have been observed in embryonic and larval stages of numerous anamniote species, it may be hypothesized that the brainstems of all vertebrates share a basic organizational plan, in which intersecting longitudinal and transverse zones form fundamental histogenetic and genoarchitectonic units. PMID:21738499

  18. First results from the Goddard High-Resolution Spectrograph - Ultraviolet spectra of a starburst knot in NGC 1068

    SciTech Connect

    Hutchings, J.B.; Bruhweiler, F.; Truong, K.Q.; Boggess, A.; Heap, S.R.; Ebbets, D.; Beaver, E.; Rosenblatt, E.; Perez, M. Catholic Univ. of America, Washington, DC NASA, Goddard Space Flight Center, Greenbelt, MD Ball Aerospace Systems Group, Boulder, CO California Univ., La Jolla NASA, Goddard Space Flight Center Computer Sciences Corp., Greenbelt, MD )

    1991-08-01

    This paper presents UV spectroscopy of a circumnuclear starburst knot in the Seyfert 2 galaxy NGC 1068, a close-by active galaxy which has some of the most luminous known starburst knots. The spectrum shows the presence of several thousand O and B stars which appear to have formed about 3 million years ago. 19 refs.

  19. First results from the Goddard High-Resolution Spectrograph - Ultraviolet spectra of a starburst knot in NGC 1068

    NASA Technical Reports Server (NTRS)

    Hutchings, J. B.; Bruhweiler, F.; Truong, K. Q.; Boggess, A.; Heap, S. R.; Ebbets, D.; Beaver, E.; Rosenblatt, E.; Perez, M.

    1991-01-01

    This paper presents UV spectroscopy of a circumnuclear starburst knot in the Seyfert 2 galaxy NGC 1068, a close-by active galaxy which has some of the most luminous known starburst knots. The spectrum shows the presence of several thousand O and B stars which appear to have formed about 3 million years ago.

  20. 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

  1. 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.

  2. A near infrared spectroscopic study of the interstellar gas in the starburst core of M82

    NASA Technical Reports Server (NTRS)

    Lester, Dan F.; Carr, John; Joy, Marshall; Gaffney, Niall

    1990-01-01

    Researchers used the McDonald Observatory Infrared Grating Spectrometer, to complete a program of spatially resolved spectroscopy of M82. The inner 300 pc of the starburst was observed with 4 inch (50 pc) resolution. Complete J, H and K band spectra with resolution 0.0035 micron (lambda/delta lambda=620 at K) were measured at the near-infrared nucleus of the galaxy. Measurements of selected spectral features including lines of FeII, HII and H2 were observed along the starburst ridge-line, so the relative distribution of the diagnostic features could be understood. This information was used to better define the extinction towards the starburst region, the excitation conditions in the gas, and to characterize the stellar populations there.

  3. 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.

  4. 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.

  5. 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

  6. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance. PMID:23701000

  7. 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

  8. Effects of nanoscale surface texture and lubricant molecular structure on boundary lubrication in liquid.

    PubMed

    Al-Azizi, Ala' A; Eryilmaz, Osman; Erdemir, Ali; Kim, Seong H

    2013-11-01

    Nanoconfinement effects of boundary lubricants can significantly affect the friction behavior of textured solid interfaces. These effects were studied with nanotextured diamond-like carbon (DLC) surfaces using a reciprocating ball-on-flat tribometer in liquid lubricants with different molecular structures: n-hexadecane and n-pentanol for linear molecular structure and poly(α-olefin) and heptamethylnonane for branched molecular structure. It is well-known that liquid lubricants with linear molecular structures can readily form a long-range ordered structure upon nanoconfinement between flat solid surfaces. This long-range ordering, often called solidification, causes high friction in the boundary lubrication regime. When the solid surface deforms elastically due to the contact pressure and this deformation depth is larger than the surface roughness, even rough surfaces can exhibit the nanoconfinement effects. However, the liquid entrapped in the depressed region of the nanotextured surface would not solidify, which effectively reduces the solidified lubricant area in the contact region and decreases friction. When liquid lubricants are branched, the nanoconfinement-induced solidification does not occur because the molecular structure is not suitable for the long-range ordering. Surface texture, therefore, has an insignificant effect on the boundary lubrication of branched molecules.

  9. Effects of nanoscale surface texture and lubricant molecular structure on boundary lubrication in liquid.

    PubMed

    Al-Azizi, Ala' A; Eryilmaz, Osman; Erdemir, Ali; Kim, Seong H

    2013-11-01

    Nanoconfinement effects of boundary lubricants can significantly affect the friction behavior of textured solid interfaces. These effects were studied with nanotextured diamond-like carbon (DLC) surfaces using a reciprocating ball-on-flat tribometer in liquid lubricants with different molecular structures: n-hexadecane and n-pentanol for linear molecular structure and poly(α-olefin) and heptamethylnonane for branched molecular structure. It is well-known that liquid lubricants with linear molecular structures can readily form a long-range ordered structure upon nanoconfinement between flat solid surfaces. This long-range ordering, often called solidification, causes high friction in the boundary lubrication regime. When the solid surface deforms elastically due to the contact pressure and this deformation depth is larger than the surface roughness, even rough surfaces can exhibit the nanoconfinement effects. However, the liquid entrapped in the depressed region of the nanotextured surface would not solidify, which effectively reduces the solidified lubricant area in the contact region and decreases friction. When liquid lubricants are branched, the nanoconfinement-induced solidification does not occur because the molecular structure is not suitable for the long-range ordering. Surface texture, therefore, has an insignificant effect on the boundary lubrication of branched molecules. PMID:24156745

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  11. 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.

  12. 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…

  13. 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…

  14. 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

  15. 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

  16. 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

  17. 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.

  18. Molecular and crystal structure of a self-assembling pyridinium cationic lipid

    NASA Astrophysics Data System (ADS)

    Balaban, Alexandru T.; Ilies, Marc A.; Eichhöfer, Andreas; Balaban, Teodor Silviu

    2010-12-01

    Molecular insights into cationic lipid assemblies are relatively hard to reveal due to intrinsic mobility of the structural elements, hydration of the polar head and counterion, etc. Using X-ray diffraction of 4,6-dimethyl-2-tetradecyl-1-(2-tetradecanoyloxyethyl)pyridinium hexafluorophosphate ( 1) single crystals we succeeded in visualizing the molecular assembly of this amphiphile, in particular its U-shape structure and the impact of various structural parameters, including the counterion. The two alkyl chains lie parallel in orthogonal planes, and that the pyridinium cationic rings appear closely to the hexafluorophosphate anions. The whole assembly has therefore nonpolar zones alternating with polar cationic-anionic channel-zones. The relevance of this molecular and crystal structure to the gene transfection ability of this cationic lipid is also discussed.

  19. 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.

  20. Molecular Structure of o-Benzyne from Microwave Measurements

    NASA Astrophysics Data System (ADS)

    Kukolich, Stephen G.; McCarthy, Michael C.; Thaddeus, Patrick

    The o-benzyne mol. has been known for many years to be an important, but short-lived, reaction intermediate in substitution reactions and more recently in cyclization reactions of enediynes. Although there has been widespread interest in this transient mol., previous exptl. structural data were very limited. In the present work, rotational transitions for o-benzyne were measured with a pulsed-beam, Fourier transform microwave spectrometer for all unique, singly substituted 13C and single-D isotopomers. The o-benzyne was efficiently produced by flowing a dil. mixt. of isotopically enriched benzene in neon through a pulsed-DC discharge beam source. The new data, combined with previous data for the normal isotopomer, provide a complete set of structural parameters for this mol. The rs substitution coordinates and the coordinates from a least-squares fit are reported and are in good agreement. When using the least-squares fit to obtain structural parameters, correction terms arising from harmonic terms in the vibrational averaging were subtracted from the measured rotational consts. to obtain a better representation of the planar equil. structure. Further improvements in the fits were obtained by applying small, mass-dependent adjustments to the atom coordinates. Structural parameters obtained from the fit to these modified rotational consts. are an acetylenic C1.tplbond.C2 bond length of 1.264(3) .ANG., and the other bond lengths C2-C3 = 1.390(3) .ANG., C3-C4 = 1.403(3) .ANG., C4-C5 = 1.404(3) .ANG., C3-H1 = 1.095(9) .ANG., and C4-H2 = 1.099(4) .ANG.. The C1.tplbond.C2 bond is only 0.057 .ANG. longer than the free acetylene bond. The other C-C bond lengths are within 0.01 .ANG. of those of benzene C-C bonds. New spectral data for the single-D isotopomers were used to obtain better values for the deuterium quadrupole coupling. Bond-axis deuterium quadrupole coupling consts. are eQqzz(D1) = 188(2) kHz, and eQqzz(D2) = 185(10) kHz, which agree well with the value for

  1. High energy (gamma)-ray emission from the starburst nucleus of NGC 253

    SciTech Connect

    Domingo-Santamaria, E; Torres, D F

    2005-06-15

    The high density medium that characterizes the central regions of starburst galaxies and its power to accelerate particles up to relativistic energies make these objects good candidates as {gamma}-rays sources. In this paper, a self-consistent model of the multifrequency emission of the starburst galaxy NGC 253, from radio to gamma-rays, is presented. The model is in agreement with all current measurements and provides predictions for the high energy behavior of the NGC 253 central region. Prospects for observations with the HESS array and GLAST satellite are especially discussed.

  2. Changes of the molecular structure in polyelectrolyte multilayers under stress.

    PubMed

    Früh, Johannes; Köhler, Ralf; Möhwald, Helmuth; Krastev, Rumen

    2010-10-01

    Polyelectrolyte multilayers (PEMs) produced by layer-by-layer (LbL) self-assembly find different applications. Often the PEMs are exposed to mechanical stress which they have to sustain. A correlation of the mechanical properties of PEM on macroscopic level with the ordering of polyelectrolyte molecules on molecular level is of interest. Our study is focused on the changes of orientation of the polyelectrolyte molecules when the PEM is under lateral mechanical stress. The PEM was prepared from pyrene (PY) labeled polystyrene sulfonate (PSS-PY) and poly(diallyldimethylammonium) chloride (PDDA) on sheets of polydimethylsiloxane (PDMS) rubber used as substrates. The LbL dipping technique was used for the formation of PEMs. A special stretching device was constructed which allows the fluorescence of the films under stress to be observed. The change in the fluorescence spectra which can be attributed to a PY ordering change from the PEM under stress of up to 10% was monitored. We observed that PEMs undergo a plastic deformation under external mechanical stretching. We conclude that under mechanical stress the polyelectrolyte molecules organized in polyelectrolyte multilayers experience an irreversible transition from the coiled to decoiled state. PMID:20809658

  3. 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

  4. Dyes and stains: from molecular structure to histological application.

    PubMed

    Veuthey, Tania; Herrera, Georgina; Dodero, Veronica I

    2014-01-01

    In the present review, the chemistry of dyes as well as the interaction mechanisms between tissue and dye has been detailed, and also some of the key factors affecting the selectivity of dyes by certain cellular structures have been mentioned. Moreover, due to the relevance that histological stains have acquired in biomedical research, some of the most common stains have been described, pointing out previous and current applications in basic and applied research.

  5. 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.

  6. Electron spectra and structure of atomic and molecular clusters

    SciTech Connect

    Dehmer, Patricia M.

    1980-01-01

    Changes in electronic structure that occur during the stepwise transition from gas phase monomers to large clusters which resemble the condensed phase were studied. This basic information on weakly bound clusters is critical to the understanding of such phenomena as nucleation, aerosol formation, catalysis, and gas-to-particle conversion, yet there exist almost no experimental data on neutral particle energy levels or binding energies as a function of cluster size. (GHT)

  7. 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.

  8. The many structural faces of calmodulin: a multitasking molecular jackknife.

    PubMed

    Kursula, Petri

    2014-10-01

    Calmodulin (CaM) is a highly conserved protein and a crucial calcium sensor in eukaryotes. CaM is a regulator of hundreds of diverse target proteins. A wealth of studies has been carried out on the structure of CaM, both in the unliganded form and in complexes with target proteins and peptides. The outcome of these studies points toward a high propensity to attain various conformational states, depending on the binding partner. The purpose of this review is to provide examples of different conformations of CaM trapped in the crystal state. In addition, comparisons are made to corresponding studies in solution. The different CaM conformations in crystal structures are also compared based on the positions of the metal ions bound to their EF hands, in terms of distances, angles, and pseudo-torsion angles. Possible caveats and artifacts in CaM crystal structures are discussed, as well as the possibilities of trapping biologically relevant CaM conformations in the crystal state.

  9. Molecular structure of leucine aminopeptidase at 2. 7- angstrom resolution

    SciTech Connect

    Burley, S.K. Brigham and Women's Hospital, Boston, MA ); David, P.R.; Lipscomb, W.N. ); Taylor, A. )

    1990-09-01

    The three-dimensional structure of bovine lens leucine aminopeptidase complexed with bestatin, a slow-binding inhibitor, has been solved to 3.0-{angstrom} resolution by the multiple isomorphous replacement method with phase combination and density modification. In addition, the structure of the isomorphous native enzyme has been refined at 2.7-{angstrom} resolution, and the current crystallographic R factor is 0.169 for a model that includes the two zinc ions and all 487 amino acid residues comprising the asymmetric unit. The enzyme is physiologically active as a hexamer, which has 32 symmetry and is triangular in shape with a triangle edge length of 115 {angstrom} and maximal thickness of 90 {angstrom}. The monomers are crystallographically equivalent and each is folded into two unequal {alpha}/{beta} domains connected by an {alpha}-helix to give a comma-like shape with approximate maximal dimensions of 90 x 55 x 55 {angstrom}{sup 3}. The secondary structural composition is 40% {alpha}-helix and 19% {beta}-strand. The active site also contains two positively charged residues, Lys-250 and Arg-336. The six active sites are themselves located in the interior of the hexamer, where they line a disk-shaped cavity of radius 15 {angstrom} and thickness 10 {angstrom}. Access to this cavity is provided by solvent channels that run along the twofold symmetry axes.

  10. 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

  11. 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.

  12. Advances in Rosetta structure prediction for difficult molecular-replacement problems

    SciTech Connect

    DiMaio, Frank

    2013-11-01

    Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed. Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail. In this paper, an overview of the use of Rosetta for these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described. Several variations to the method are introduced that significantly reduce the time needed to generate a model and the sampling required to improve the starting template. The improvements are benchmarked on a set of nine difficult cases and it is shown that this improved method obtains consistently better models in less running time. Finally, strategies for best using Rosetta to solve difficult molecular-replacement problems are presented and future directions for the role of structure-prediction methods in crystallography are discussed.

  13. 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.

  14. 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).

  15. Molecular structure of fulvic acids by electrospray with quadrupole time-of-flight mass spectrometry.

    PubMed

    Plancque, G; Amekraz, B; Moulin, V; Toulhoat, P; Moulin, C

    2001-01-01

    Characterisation of the molecular structure of aquatic fulvic acids (FA) has been performed using a quadrupole time-of-flight (Q-TOF) mass spectrometer equipped with an electrospray ionisation interface. Molecular masses centred around 450 Da and sinusoidal spectral distributions have been obtained for all fulvic acids. Tandem mass spectrometry (MS/MS) experiments showed losses of 18 Da (H(2)O) and 44 Da (CO(2)), and possible molecular structures were determined for the first time to our knowledge. A methodology is reported for evaluating the average elemental composition of FA from high-resolution mass spectra by processing post-acquisition data calculations using molecular size distributions and atomic compositions of ions. The results are found to be consistent with elemental analysis data.

  16. 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.

  17. Discovery of a Galaxy Cluster with a Violently Starbursting Core at z = 2.506

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Elbaz, David; Daddi, Emanuele; Finoguenov, Alexis; Liu, Daizhong; Schreiber, Corentin; Martín, Sergio; Strazzullo, Veronica; Valentino, Francesco; van der Burg, Remco; Zanella, Anita; Ciesla, Laure; Gobat, Raphael; Le Brun, Amandine; Pannella, Maurilio; Sargent, Mark; Shu, Xinwen; Tan, Qinghua; Cappelluti, Nico; Li, Yanxia

    2016-09-01

    We report the discovery of a remarkable concentration of massive galaxies with extended X-ray emission at z spec = 2.506, which contains 11 massive (M * ≳ 1011 M ⊙) galaxies in the central 80 kpc region (11.6σ overdensity). We have spectroscopically confirmed 17 member galaxies with 11 from CO and the remaining ones from Hα. The X-ray luminosity, stellar mass content, and velocity dispersion all point to a collapsed, cluster-sized dark matter halo with mass M 200c = 1013.9±0.2 M ⊙, making it the most distant X-ray-detected cluster known to date. Unlike other clusters discovered so far, this structure is dominated by star-forming galaxies (SFGs) in the core with only 2 out of the 11 massive galaxies classified as quiescent. The star formation rate (SFR) in the 80 kpc core reaches ˜3400 M ⊙ yr-1 with a gas depletion time of ˜200 Myr, suggesting that we caught this cluster in rapid build-up of a dense core. The high SFR is driven by both a high abundance of SFGs and a higher starburst fraction (˜25%, compared to 3%-5% in the field). The presence of both a collapsed, cluster-sized halo and a predominant population of massive SFGs suggests that this structure could represent an important transition phase between protoclusters and mature clusters. It provides evidence that the main phase of massive galaxy passivization will take place after galaxies accrete onto the cluster, providing new insights into massive cluster formation at early epochs. The large integrated stellar mass at such high redshift challenges our understanding of massive cluster formation.

  18. The Magnetized Galactic Wind and Synchrotron Halo of the Starburst Dwarf Galaxy IC 10

    NASA Astrophysics Data System (ADS)

    Chyży, Krzysztof T.; Drzazga, Robert T.; Beck, Rainer; Urbanik, Marek; Heesen, Volker; Bomans, Dominik J.

    2016-03-01

    We aim to explore whether strong magnetic fields can be effectively generated in low-mass dwarf galaxies and, if so, whether such fields can be affected by galactic outflows and spread out into the intergalactic medium (IGM). We performed a radio continuum polarimetry study of IC 10, the nearest starbursting dwarf galaxy, using a combination of multifrequency interferometric (VLA) and single-dish (Effelsberg) observations. VLA observations at 1.43 GHz reveal an extensive and almost spherical radio halo of IC 10 in total intensity, extending twice more than the infrared-emitting galactic disk. The halo is magnetized with a magnetic field strength of 7 μG in the outermost parts. Locally, the magnetic field reaches about 29 μ {{G}} in H ii complexes, becomes more ordered, and weakens to 22 μ {{G}} in the synchrotron superbubble and to 7-10 μG within H i holes. At the higher frequency of 4.86 GHz, we found a large-scale magnetic field structure of X-shaped morphology, similar to that observed in several edge-on spiral galaxies. The X-shaped magnetic structure can be caused by the galactic wind, advecting magnetic fields injected into the interstellar medium by stellar winds and supernova explosions. The radio continuum scale heights at 1.43 GHz indicate the bulk speed of cosmic-ray electrons outflowing from H ii complexes of about 60 km s-1, exceeding the escape velocity of 40 km s-1. Hence, the magnetized galactic wind in IC 10 inflates the extensive radio halo visible at 1.43 GHz and can seed the IGM with both random and ordered magnetic fields. These are signatures of intense material feedback onto the IGM, expected to be prevalent in the protogalaxies of the early universe.

  19. 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.

  20. CONNECTING LOCAL STRUCTURE TO INTERFACE FORMATION: A Molecular Scale van der Waals Theory of Nonuniform Liquids

    NASA Astrophysics Data System (ADS)

    Weeks, John D.

    2002-10-01

    This article reviews a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. The method optimally combines two standard approximations, molecular (mean) field theory to describe interface formation and linear response (or Gaussian fluctuation) theory to describe local structure. Accurate results have been found in many different applications in nonuniform simple fluids and these ideas may have important implications for the theory of hydrophobic interactions in water.

  1. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    PubMed Central

    Bibby, Jaclyn; Keegan, Ronan M.; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

    2013-01-01

    AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided. PMID:24189230

  2. Molecular determinants of staphylococcal biofilm dispersal and structuring

    PubMed Central

    Le, Katherine Y.; Dastgheyb, Sana; Ho, Trung V.; Otto, Michael

    2014-01-01

    Staphylococci are frequently implicated in human infections, and continue to pose a therapeutic dilemma due to their ability to form deeply seated microbial communities, known as biofilms, on the surfaces of implanted medical devices and host tissues. Biofilm development has been proposed to occur in three stages: (1) attachment, (2) proliferation/structuring, and (3) detachment/dispersal. Although research within the last several decades has implicated multiple molecules in the roles as effectors of staphylococcal biofilm proliferation/structuring and detachment/dispersal, to date, only phenol soluble modulins (PSMs) have been consistently demonstrated to serve in this role under both in vitro and in vivo settings. PSMs are regulated directly through a density-dependent manner by the accessory gene regulator (Agr) system. They disrupt the non-covalent forces holding the biofilm extracellular matrix together, which is necessary for the formation of channels, a process essential for the delivery of nutrients to deeper biofilm layers, and for dispersal/dissemination of clusters of biofilm to distal organs in acute infection. Given their relevance in both acute and chronic biofilm-associated infections, the Agr system and the psm genes hold promise as potential therapeutic targets. PMID:25505739

  3. Structured attachment of bacterial molecular motors for defined microflow induction

    NASA Astrophysics Data System (ADS)

    Woerdemann, Mike; Hörner, Florian; Denz, Cornelia

    2014-01-01

    Bacterial rotational motor complexes that propel flagellated bacteria possess unique properties like their size of a few nanometres and the ability of selfreproduction that have led to various exciting applications including biohybrid nano-machines. One mandatory prerequisite to utilize bacterial nano motors in fluid applications is the ability to transfer force and torque to the fluid, which usually can be achieved by attachment of the bacterial cell to adequate surfaces. Additionally, for optimal transfer of force or torque, precise control of the position down to the single cell level is of utmost importance. Based on a PIV (particle image velocimetry) evaluation of the induced flow of single bacteria,we propose and demonstrate attachment of arbitrary patterns of motile bacterial cells in a fast light-based two-step process for the first time to our knowledge. First, these cells are pre-structured by holographic optical tweezers and then attached to a homogeneous, polystyrene-coated surface. In contrast to the few approaches that have been implemented up to now and which rely on pre-structured surfaces, our scheme allows for precise control on a single bacterium level, is versatile, interactive and has low requirements with respect to the surface preparation.

  4. NMR studies of molecular structure in fruit cuticle polyesters.

    PubMed

    Fang, X; Qiu, F; Yan, B; Wang, H; Mort, A J; Stark, R E

    2001-07-01

    The cuticle of higher plants functions primarily as a protective barrier for the leaves and fruits, controlling microbial attack as well as the diffusion of water and chemicals from the outside environment. Its major chemical constituents are waxes (for waterproofing) and cutin (a structural support polymer). However, the insolubility of cutin has hampered investigations of its covalent structure and domain architecture, which are viewed as essential for the design of crop protection strategies and the development of improved synthetic waterproofing materials. Recently developed strategies designed to meet these investigative challenges include partial depolymerization using enzymatic or chemical reagents and spectroscopic examination of the intact polyesters in a solvent-swelled form. The soluble oligomers from degradative treatments of lime fruit cutin are composed primarily of the expected 10,16-dihydroxyhexadecanoic and 16-hydroxy-10-oxo-hexadecanoic acids; low-temperature HF treatments also reveal sugar units that are covalently attached to the hydroxyfatty acids. Parallel investigations of solvent-swollen cutin using 2D NMR spectroscopy assisted by magic-angle spinning yield well-resolved spectra that permit detailed comparisons to be made among chemical moieties present in the intact biopolymer, the soluble degradation products, and the unreacted solid residue. PMID:11423150

  5. Current and emerging opportunities for molecular simulations in structure-based drug design

    PubMed Central

    Michel, Julien

    2014-01-01

    An overview of the current capabilities and limitations of molecular simulation of biomolecular complexes in the context of computer-aided drug design is provided. Steady improvements in computer hardware coupled with more refined representations of energetics are leading to a new appreciation of the driving forces of molecular recognition. Molecular simulations are poised to more frequently guide the interpretation of biophysical measurements of biomolecular complexes. Ligand design strategies emerge from detailed analyses of computed structural ensembles. The feasibility of routine applications to ligand optimization problems hinges upon successful extensive large scale validation studies and the development of protocols to intelligently automate computations. PMID:24469595

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. Atomic spectral methods for molecular electronic structure calculations.

    PubMed

    Langhoff, P W; Boatz, J A; Hinde, R J; Sheehy, J A

    2004-11-15

    Theoretical methods are reported for ab initio calculations of the adiabatic (Born-Oppenheimer) electronic wave functions and potential energy surfaces of molecules and other atomic aggregates. An outer product of complete sets of atomic eigenstates familiar from perturbation-theoretical treatments of long-range interactions is employed as a representational basis without prior enforcement of aggregate wave function antisymmetry. The nature and attributes of this atomic spectral-product basis are indicated, completeness proofs for representation of antisymmetric states provided, convergence of Schrodinger eigenstates in the basis established, and strategies for computational implemention of the theory described. A diabaticlike Hamiltonian matrix representative is obtained, which is additive in atomic-energy and pairwise-atomic interaction-energy matrices, providing a basis for molecular calculations in terms of the (Coulombic) interactions of the atomic constituents. The spectral-product basis is shown to contain the totally antisymmetric irreducible representation of the symmetric group of aggregate electron coordinate permutations once and only once, but to also span other (non-Pauli) symmetric group representations known to contain unphysical discrete states and associated continua in which the physically significant Schrodinger eigenstates are generally embedded. These unphysical representations are avoided by isolating the physical block of the Hamiltonian matrix with a unitary transformation obtained from the metric matrix of the explicitly antisymmetrized spectral-product basis. A formal proof of convergence is given in the limit of spectral closure to wave functions and energy surfaces obtained employing conventional prior antisymmetrization, but determined without repeated calculations of Hamiltonian matrix elements as integrals over explicitly antisymmetric aggregate basis states. Computational implementations of the theory employ efficient recursive

  11. Theoretical studies of molecular spectroscopy at structured surfaces

    NASA Astrophysics Data System (ADS)

    Hider, Matthew Henry

    2001-07-01

    The fluorescence behavior of molecules at rough surfaces and in cavities forms the major part of this work. The molecule is modeled as a radiating point dipole and a spherical island represents the surface morphology. To accurately model this problem in the near surface region, nonlocal electrodynamic effects are taken into account within the hydrodynamic description of the surface electrons. This nonlocal description for the sphere is taken from the model of Fuchs and Claro, and the solution for the cavity is obtained by reformulating this nonlocal theory. The results for the molecular-sphere system show that the dispersion resonances for the nonlocal case are blue shifted in the frequency spectrum relative to the local case, while the magnitude of the frequency shifts are suppressed in the nonlocal case. The degree of this suppression is found to be more significant closer to the substrate, with a local to nonlocal ratio in magnitude being roughly 2:1 and 10:1 for distances of 11 a.u. and 3 ax (1a.u. = 0.529A), respectively. The results of the cavity case show an even more dramatic blue shift than the sphere case, with similar frequency shift suppression as the case of the sphere. Results for decay rate and for different dipole orientations are also presented. A simple transformation is obtained for the local case, which allows us to transform from the well-known local dipole-sphere solution to the dipole-cavity solution. This transform is shown to break down for the nonlocal case. Our results are compared with cavity results by another group, with comments and criticisms given. Finally, surfaced-enhanced Raman scattering of molecules at rough metal surfaces as a function of temperature is presented. Again the roughness is represented as a metal sphere, and the temperature effects on the surface plasmon are accounted for via a slightly modified Ujihara model. The enhancement ratio is found in general to vary inversely with temperature, with this effect being

  12. 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.

  13. Unraveling microalgal molecular interactions using evolutionary and structural bioinformatics.

    PubMed

    Vlachakis, Dimitrios; Pavlopoulou, Athanasia; Kazazi, Dorothea; Kossida, Sophia

    2013-10-10

    Microalgae are unicellular microorganisms indispensible for environmental stability and life on earth, because they produce approximately half of the atmospheric oxygen, with simultaneously feeding on the harmful greenhouse gas carbon dioxide. Using gene fusion analysis, a series of five fusion/fission events was identified, that provided the basis for critical insights to their evolutionary history. Moreover, the three-dimensional structures of both the fused and the component proteins were predicted, allowing us to envisage putative protein-protein interactions that are invaluable for the efficient usage, handling and exploitation of microalgae. Collectively, our proposed approach on the five fusion/fission alga protein events contributes towards the expansion of the microalgae knowledgebase, bridging protein evolution of the ancient microalgal species and the rapidly evolving, modern, bioinformatics field.

  14. 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

  15. Molecular Structure and Reactivity in the Pyrolysis of Aldehydes

    NASA Astrophysics Data System (ADS)

    Sias, Eric; Cole, Sarah; Sowards, John; Warner, Brian; Wright, Emily; McCunn, Laura R.

    2016-06-01

    The effect of alkyl chain structure on pyrolysis mechanisms has been investigated in a series of aldehydes. Isovaleraldehyde, CH_3CH(CH_3)CH_2CHO, and pivaldehyde, (CH_3)_3CCHO, were subject to thermal decomposition in a resistively heated SiC tubular reactor at 800-1200 °C. Matrix-isolation FTIR spectroscopy was used to identify pyrolysis products. Carbon monoxide and isobutene were major products from each of the aldehydes, which is consistent with what is known from previous studies of unbranched alkyl-chain aldehydes. Other products observed include vinyl alcohol, propene, acetylene, and ethylene, revealing complexities to be considered in the pyrolysis of large, branched-chain aldehydes.

  16. Molecular Structure and Chirality Detection by Fourier Transform Microwave Spectroscopy.

    PubMed

    Lobsiger, Simon; Perez, Cristobal; Evangelisti, Luca; Lehmann, Kevin K; Pate, Brooks H

    2015-01-01

    We describe a three-wave mixing experiment using time-separated microwave pulses to detect the enantiomer-specific emission signal of the chiral molecule using Fourier transform microwave (FTMW) spectroscopy. A chirped-pulse FTMW spectrometer operating in the 2-8 GHz frequency range is used to determine the heavy-atom substitution structure of solketal (2,2-dimethyl-1,3-dioxolan-4-yl-methanol) through analysis of the singly substituted (13)C and (18)O isotopologue rotational spectra in natural abundance. A second set of microwave horn antennas is added to the instrument design to permit three-wave mixing experiments where an enantiomer-specific phase of the signal is observed. Using samples of R-, S-, and racemic solketal, the properties of the three-wave mixing experiment are presented, including the measurement of the corresponding nutation curves to demonstrate the optimal pulse sequence.

  17. 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

  18. THE ANATOMY OF AN EXTREME STARBURST WITHIN 1.3 Gyr OF THE BIG BANG REVEALED BY ALMA

    SciTech Connect

    Carilli, C. L.; Riechers, D.; Walter, F.; Maiolino, R.; Lentati, L.; Wagg, J.; McMahon, R.; Wolfe, A.

    2013-02-15

    We present further analysis of the [C II] 158 {mu}m fine structure line and thermal dust continuum emission from the archetype extreme starburst/active galactic nucleus (AGN) group of galaxies in the early universe, BRI 1202-0725 at z = 4.7, using the Atacama Large Millimeter Array. The group has long been noted for having a closely separated (26 kpc in projection) FIR-hyperluminous quasar host galaxy and an optically obscured submillimeter galaxy (SMG). A short ALMA test observation reveals a rich laboratory for the study of the myriad processes involved in clustered massive galaxy formation in the early universe. Strong [C II] emission from the SMG and the quasar have been reported earlier by Wagg et al. based on these observations. In this paper, we examine in more detail the imaging results from the ALMA observations, including velocity channel images, position-velocity plots, and line moment images. We present detections of [C II] emission from two Ly{alpha}-selected galaxies in the group, demonstrating the relative ease with which ALMA can detect the [C II] emission from lower star formation rate galaxies at high redshift. Imaging of the [C II] emission shows a clear velocity gradient across the SMG, possibly indicating rotation or a more complex dynamical system on a scale {approx}10 kpc. There is evidence in the quasar spectrum and images for a possible outflow toward the southwest, as well as more extended emission (a {sup b}ridge{sup )}, between the quasar and the SMG, although the latter could simply be emission from Ly{alpha}-1 blending with that of the quasar at the limited spatial resolution of the current observations. These results provide an unprecedented view of a major merger of gas-rich galaxies driving extreme starbursts and AGN accretion during the formation of massive galaxies and supermassive black holes within 1.3 Gyr of the big bang.

  19. Searching molecular structure databases with tandem mass spectra using CSI:FingerID.

    PubMed

    Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

    2015-10-13

    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.

  20. 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

  1. 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.

  2. 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

  3. Super star clusters in Haro 11: properties of a very young starburst and evidence for a near-infrared flux excess

    NASA Astrophysics Data System (ADS)

    Adamo, A.; Östlin, G.; Zackrisson, E.; Hayes, M.; Cumming, R. J.; Micheva, G.

    2010-09-01

    We have used multiband imaging to investigate the nature of an extreme starburst environment in the nearby Lyman break galaxy analogue Haro 11 (ESO350-IG038) by means of its stellar cluster population. The central starburst region has been observed in eight different high-resolution Hubble Space Telescope (HST) wavebands, sampling the stellar and gas components from UV to near-infrared. Photometric imaging of the galaxy was also carried out at 2.16μm by NaCo AO instrument at the ESO Very Large Telescope. We constructed integrated spectral energy distributions (SEDs) for about 200 star clusters located in the active star-forming regions and compared them with single stellar population models (suitable for physical properties of very young cluster population) in order to derive ages, masses and extinctions of the star clusters. The cluster age distribution we recover confirms that the present starburst has lasted for 40Myr, and shows a peak of cluster formation only 3.5 Myr old. With such an extremely young cluster population, Haro 11 represents a unique opportunity to investigate the youngest phase of the cluster formation process and evolution in starburst systems. We looked for possible relations between cluster ages, extinctions and masses. Extinction tends to diminish as a function of the cluster age, but the spread is large and reaches the highest dispersion for clusters in partial embedded phases (<5Myr). A fraction of low-mass (below 104 Msolar), very young (1-3Myr) clusters is missing, either because they are embedded in the parental molecular cloud and heavily extinguished, or because of blending with neighbouring clusters. The range of the cluster masses is wide; we observe that more than 30 per cent of the clusters have masses above 105 Msolar, qualifying them as super star clusters. Almost half of the cluster sample is affected by flux excesses at wavelengths >8000Å which cannot be explained by simple stellar evolutionary models. Fitting SED models

  4. Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

    PubMed

    Hartman, Joshua D; Beran, Gregory J O

    2014-11-11

    First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations. PMID:26584373

  5. MolLoc: a web tool for the local structural alignment of molecular surfaces.

    PubMed

    Angaran, Stefano; Bock, Mary Ellen; Garutti, Claudio; Guerra, Concettina

    2009-07-01

    MolLoc stands for Molecular Local surface comparison, and is a web server for the structural comparison of molecular surfaces. Given two structures in PDB format, the user can compare their binding sites, cavities or any arbitrary residue selection. Moreover, the web server allows the comparison of a query structure with a list of structures. Each comparison produces a structural alignment that maximizes the extension of the superimposition of the surfaces, and returns the pairs of atoms with similar physicochemical properties that are close in space after the superimposition. Based on this subset of atoms sharing similar physicochemical properties a new rototranslation is derived that best superimposes them. MolLoc approach is both local and surface-oriented, and therefore it can be particularly useful when testing if molecules with different sequences and folds share any local surface similarity. The MolLoc web server is available at http://bcb.dei.unipd.it/MolLoc.

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

    PubMed Central

    Tycko, Robert

    2016-01-01

    Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made on characterization of the molecular structures of Aβ aggregates. Full molecular structural models that are based primarily on data from solid state nuclear magnetic resonance measurements have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates. PMID:27481836

  7. 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

  8. Molecular structure and functional morphology of echinoderm collagen fibrils.

    PubMed

    Trotter, J A; Thurmond, F A; Koob, T J

    1994-03-01

    The collagenous tissues of echinoderms, which have the unique capacity to rapidly and reversibly alter their mechanical properties, resemble the collagenous tissues of other phyla in consisting of collagen fibrils in a nonfibrillar matrix. Knowledge of the composition and structure of their collagen fibrils and interfibrillar matrix is thus important for an understanding of the physiology of these tissues. In this report it is shown that the collagen molecules from the fibrils of the spine ligament of a sea-urchin and the deep dermis of a sea-cucumber are the same length as those from vertebrate fibrils and that they assemble into fibrils with the same repeat period and gap/overlap ratio as do those of vertebrate fibrils. The distributions of charged residues in echinoderm and vertebrate molecules are somewhat different, giving rise to segment-long-spacing crystallites and fibrils with different banding patterns. Compared to the vertebrate pattern, the banding pattern of echinoderm fibrils is characterized by greatly increased stain intensity in the c3 band and greatly reduced stain intensity in the a3 and b2 bands. The fibrils are spindle-shaped, possessing no constant-diameter region throughout their length. The shape of the fibrils is mechanically advantageous for their reinforcing role in a discontinuous fiber-composite material.

  9. Can we predict lattice energy from molecular structure?

    PubMed

    Ouvrard, Carole; Mitchell, John B O

    2003-10-01

    By using simply the numbers of occurrences of different atom types as descriptors, a conceptually transparent and remarkably accurate model for the prediction of the enthalpies of sublimation of organic compounds has been generated. The atom types are defined on the basis of atomic number, hybridization state and bonded environment. Models of this kind were applied firstly to aliphatic hydrocarbons, secondly to both aliphatic and aromatic hydrocarbons, thirdly to a wide range of non-hydrogen-bonding molecules, and finally to a set of 226 organic compounds including 70 containing hydrogen-bond donors and acceptors. The final model gives squared correlation coefficients of 0.925 for the 226 compounds in the training set and 0.937 for an independent test set of 35 compounds. The success of such a simple model implies that the enthalpy of sublimation can be predicted accurately without knowledge of the crystal packing. This hypothesis is in turn consistent with the idea that, rather than being determined by the particular features of the lowest-energy packing, the lattice energy is similar for a number of hypothetical alternative crystal structures of a molecule.

  10. 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

  11. Computational nanochemistry study of the molecular structure and properties of ethambutol.

    PubMed

    Salgado-Morán, Guillermo; Ruiz-Nieto, Samuel; Gerli-Candia, Lorena; Flores-Holguín, Norma; Favila-Pérez, Alejandra; Glossman-Mitnik, Daniel

    2013-09-01

    The M06 family of density functionals was employed to calculate the molecular structure and properties of the ethambutol molecule. Besides determination of molecular structures, UV-vis spectra were computed using TD-DFT in the presence of a solvent and the results compared with available experimental data. The chemical reactivity descriptors were calculated through conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to Fukui function indices. A comparison between the descriptors calculated through vertical energy values and those arising from Koopmans' theorem approximation were performed in order to check the validity of the latter procedure.

  12. 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.

  13. Starburst triarylamine based dyes for efficient dye-sensitized solar cells.

    PubMed

    Ning, Zhijun; Zhang, Qiong; Wu, Wenjun; Pei, Hongcui; Liu, Bo; Tian, He

    2008-05-16

    We report here on the synthesis and photophysical/electrochemical properties of a series of novel starburst triarylamine-based organic dyes (S1, S2, S3, and S4) as well as their application in dye-sensitized nanocrystalline TiO2 solar cells (DSSCs). For the four designed dyes, the starburst triarylamine group and the cyanoacetic acid take the role of electron donor and electron acceptor, respectively. It was found that the introduction of starburst triarylamine group to form the D-D-pi-A configuration brought about superior performance over the simple D-pi-A configuration, in terms of bathochromically extended absorption spectra, enhanced molar extinction coefficients and better thermo-stability. Moreover, the HOMO and LUMO energy levels tuning can be conveniently accomplished by alternating the donor moiety, which was confirmed by electrochemical measurements and theoretical calculations. The DSSCs based on the dye S4 showed the best photovoltaic performance: a maximum monochromatic incident photon-to-current conversion efficiency (IPCE) of 85%, a short-circuit photocurrent density (J(sc)) of 13.8 mA cm(-2), an open-circuit photovoltage (V(oc)) of 0.63 V, and a fill factor (ff) of 0.69, corresponding to an overall conversion efficiency of 6.02% under 100 mW cm(-2) irradiation. This work suggests that the dyes based on starburst triphenylamine donor are promising candidates for improvement of the performance of the DSSCs.

  14. Far-infrared continuum emission from the nucleus, starburst, and extended spiral arms of NGC 1068

    SciTech Connect

    Lester, D.F.; Joy, M.; Harvey, P.M.; Ellis, H.B. Jr.; Parmar, P.S.

    1987-10-01

    Far-infrared slit scans across NGC 1068 are used to better define the contribution of the active nucleus, starburst disk, and extended spiral arms in the luminous output of this bright Seyfert 2 galaxy. The decomposition of the emission from the bright, inner 3 kpc of this galaxy suggests that at 50 microns, about half the emission is from star formation in a starburst disk and half from the compact, centrally heated circumnuclear cloud. The 100-micron profile of the starburst disk is asymmetric with respect to the nucleus. This appears to be the result of an extraordinary star-forming complex about a kiloparsec away from the center. With the application of maximum entropy deconvolution to the scans, evidence is found for 100-micron emission from the extended spiral arms of the galaxy. The far-infrared emission from the starburst region is distinguished from that of the extended spiral arms. In terms of both total luminosity and surface brightness, the extended spiral arms of NGC 1068 are at the bright end of the range of far-infrared emission from quiescent, noninteracting spirals. 17 references.

  15. Far-infrared continuum emission from the nucleus, starburst, and extended spiral arms of NGC 1068

    NASA Technical Reports Server (NTRS)

    Lester, D. F.; Joy, M.; Harvey, P. M.; Ellis, H. B., Jr.; Parmar, P. S.

    1987-01-01

    Far-infrared slit scans across NGC 1068 are used to better define the contribution of the active nucleus, starburst disk, and extended spiral arms in the luminous output of this bright Seyfert 2 galaxy. The decomposition of the emission from the bright, inner 3 kpc of this galaxy suggests that at 50 microns, about half the emission is from star formation in a starburst disk and half from the compact, centrally heated circumnuclear cloud. The 100-micron profile of the starburst disk is asymmetric with respect to the nucleus. This appears to be the result of an extraordinary star-forming complex about a kiloparsec away from the center. With the application of maximum entropy deconvolution to the scans, evidence is found for 100-micron emission from the extended spiral arms of the galaxy. The far-infrared emission from the starburst region is distinguished from that of the extended spiral arms. In terms of both total luminosity and surface brightness, the extended spiral arms of NGC 1068 are at the bright end of the range of far-infrared emission from quiescent, noninteracting spirals.

  16. Cosmic-ray induced gamma-ray emission from the starburst galaxy NGC 253

    SciTech Connect

    Wang, Xilu; Fields, Brian D.

    2014-05-09

    Cosmic rays in galaxies interact with the interstellar medium and give us a direct view of nuclear and particle interactions in the cosmos. For example, cosmic-ray proton interactions with interstellar hydrogen produce gamma rays via PcrPism→π{sup 0}→γγ. For a 'normal' star-forming galaxy like the Milky Way, most cosmic rays escape the Galaxy before such collisions, but in starburst galaxies with dense gas and huge star formation rate, most cosmic rays do suffer these interactions [1,2]. We construct a 'thick-target' model for starburst galaxies, in which cosmic rays are accelerated by supernovae, and escape is neglected. This model gives an upper limit to the gamma-ray emission. Only two free parameters are involved in the model: cosmic-ray proton acceleration energy rate from supernova and the proton injection spectral index. The pionic gamma-radiation is calculated from 10 MeV to 10 TeV for the starburst galaxy NGC 253, and compared to Fermi and HESS data. Our model fits NGC 253 well, suggesting that cosmic rays in this starburst are in the thick target limit, and that this galaxy is a gamma-ray calorimeter.

  17. A connection between star formation activity and cosmic rays in the starburst galaxy M82.

    PubMed

    2009-12-10

    Although Galactic cosmic rays (protons and nuclei) are widely believed to be mainly accelerated by the winds and supernovae of massive stars, definitive evidence of this origin remains elusive nearly a century after their discovery. The active regions of starburst galaxies have exceptionally high rates of star formation, and their large size-more than 50 times the diameter of similar Galactic regions-uniquely enables reliable calorimetric measurements of their potentially high cosmic-ray density. The cosmic rays produced in the formation, life and death of massive stars in these regions are expected to produce diffuse gamma-ray emission through interactions with interstellar gas and radiation. M82, the prototype small starburst galaxy, is predicted to be the brightest starburst galaxy in terms of gamma-ray emission. Here we report the detection of >700-GeV gamma-rays from M82. From these data we determine a cosmic-ray density of 250 eV cm(-3) in the starburst core, which is about 500 times the average Galactic density. This links cosmic-ray acceleration to star formation activity, and suggests that supernovae and massive-star winds are the dominant accelerators.

  18. A connection between star formation activity and cosmic rays in the starburst galaxy M82

    NASA Astrophysics Data System (ADS)

    VERITAS Collaboration; Acciari, V. A.; Aliu, E.; Arlen, T.; Aune, T.; Bautista, M.; Beilicke, M.; Benbow, W.; Boltuch, D.; Bradbury, S. M.; Buckley, J. H.; Bugaev, V.; Byrum, K.; Cannon, A.; Celik, O.; Cesarini, A.; Chow, Y. C.; Ciupik, L.; Cogan, P.; Colin, P.; Cui, W.; Dickherber, R.; Duke, C.; Fegan, S. J.; Finley, J. P.; Finnegan, G.; Fortin, P.; Fortson, L.; Furniss, A.; Galante, N.; Gall, D.; Gibbs, K.; Gillanders, G. H.; Godambe, S.; Grube, J.; Guenette, R.; Gyuk, G.; Hanna, D.; Holder, J.; Horan, D.; Hui, C. M.; Humensky, T. B.; Imran, A.; Kaaret, P.; Karlsson, N.; Kertzman, M.; Kieda, D.; Kildea, J.; Konopelko, A.; Krawczynski, H.; Krennrich, F.; Lang, M. J.; Lebohec, S.; Maier, G.; McArthur, S.; McCann, A.; McCutcheon, M.; Millis, J.; Moriarty, P.; Mukherjee, R.; Nagai, T.; Ong, R. A.; Otte, A. N.; Pandel, D.; Perkins, J. S.; Pizlo, F.; Pohl, M.; Quinn, J.; Ragan, K.; Reyes, L. C.; Reynolds, P. T.; Roache, E.; Rose, H. J.; Schroedter, M.; Sembroski, G. H.; Smith, A. W.; Steele, D.; Swordy, S. P.; Theiling, M.; Thibadeau, S.; Varlotta, A.; Vassiliev, V. V.; Vincent, S.; Wagner, R. G.; Wakely, S. P.; Ward, J. E.; Weekes, T. C.; Weinstein, A.; Weisgarber, T.; Williams, D. A.; Wissel, S.; Wood, M.; Zitzer, B.

    2009-12-01

    Although Galactic cosmic rays (protons and nuclei) are widely believed to be mainly accelerated by the winds and supernovae of massive stars, definitive evidence of this origin remains elusive nearly a century after their discovery. The active regions of starburst galaxies have exceptionally high rates of star formation, and their large size-more than 50 times the diameter of similar Galactic regions-uniquely enables reliable calorimetric measurements of their potentially high cosmic-ray density. The cosmic rays produced in the formation, life and death of massive stars in these regions are expected to produce diffuse γ-ray emission through interactions with interstellar gas and radiation. M82, the prototype small starburst galaxy, is predicted to be the brightest starburst galaxy in terms of γ-ray emission. Here we report the detection of >700-GeV γ-rays from M82. From these data we determine a cosmic-ray density of 250eVcm-3 in the starburst core, which is about 500 times the average Galactic density. This links cosmic-ray acceleration to star formation activity, and suggests that supernovae and massive-star winds are the dominant accelerators.

  19. Cosmic-ray induced gamma-ray emission from the starburst galaxy NGC 253

    NASA Astrophysics Data System (ADS)

    Wang, Xilu; Fields, Brian D.

    2014-05-01

    Cosmic rays in galaxies interact with the interstellar medium and give us a direct view of nuclear and particle interactions in the cosmos. For example, cosmic-ray proton interactions with interstellar hydrogen produce gamma rays via PcrPism→π0→γγ. For a "normal" star-forming galaxy like the Milky Way, most cosmic rays escape the Galaxy before such collisions, but in starburst galaxies with dense gas and huge star formation rate, most cosmic rays do suffer these interactions [1,2]. We construct a "thick-target" model for starburst galaxies, in which cosmic rays are accelerated by supernovae, and escape is neglected. This model gives an upper limit to the gamma-ray emission. Only two free parameters are involved in the model: cosmic-ray proton acceleration energy rate from supernova and the proton injection spectral index. The pionic gamma-radiation is calculated from 10 MeV to 10 TeV for the starburst galaxy NGC 253, and compared to Fermi and HESS data. Our model fits NGC 253 well, suggesting that cosmic rays in this starburst are in the thick target limit, and that this galaxy is a gamma-ray calorimeter.

  20. 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.

  1. Supramolecular structure formation of molecular copper(II)methylsalicylate complexes with nicotinamide or methylnicotinamide - Crystal structure and spectral properties

    NASA Astrophysics Data System (ADS)

    Puchoňová, Miroslava; Repická, Zuzana; Moncol, Jan; Růžičková, Zdeňka; Mazúr, Milan; Valigura, Dušan

    2015-07-01

    As the systematic investigation of salicylatocopper complexes with nicotinamide derivatives the preparation, characterization and X-ray structure determination of four new molecular copper(II) complexes with x-methylsalicylate anion (x-Mesal-) and nicotinamide (nia) or N-methylnicotinamide (mna) are reported. The molecular complexes [Cu(5-Mesal)2(nia)2] (1), [Cu(3-Mesal)2(nia)2] (2) build up 2-D supramolecular structures of different character. The ladder-type supramolecular structure of (1) is formed by the head-to-head H-bonds of neighbouring carboxamide groups, while the supramolecular structure of (2) is formed by Nsbnd H⋯O H-bonds of carboxamide groups into 1-D chain that are by the additional Hsbnd H⋯O H-bonds of Nsbnd H carboxamide and the carboxylate group oxygen atoms linked to 2-D layers. The centrosymmetrical crystal molecular structure of [Cu(4-Mesal)2(mna)2(H2O)2]ṡ2EtOH (3) or [Cu(5-Mesal)2(mna)2(H2O)2]ṡ2MeOH (4) are forming 1-D supramolecular chains that involve the methylcarboxamide Nsbnd H group, the crystalosolvate alcohol Osbnd H group, the coordinated water molecule Osbnd H bond and oxygen atom of neighbouring complex molecule. The coordination polyhedron symmetry corresponds with the isotropic character of EPR spectra of (1) and (2) while the EPR spectrum of (4) is of axial symmetry.

  2. 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

  3. Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Rankin, David W H

    2007-07-01

    A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).

  4. Six polycyclic pyrimidoazepine derivatives: syntheses, molecular structures and supramolecular assembly.

    PubMed

    Acosta Quintero, Lina M; Palma, Alirio; Cobo, Justo; Glidewell, Christopher

    2016-04-01

    A versatile synthetic method has been developed for the formation of variously substituted polycyclic pyrimidoazepine derivatives, formed by nucleophilic substitution reactions on the corresponding chloro-substituted compounds; the reactions can be promoted either by conventional heating in basic solutions or by microwave heating in solvent-free systems. Thus, (6RS)-6,11-dimethyl-3,5,6,11-tetrahydro-4H-benzo[b]pyrimido[5,4-f]azepin-4-one, C14H15N3O, (I), was isolated from a solution containing (6RS)-4-chloro-8-hydroxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepine and benzene-1,2-diamine; (6RS)-4-butoxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-8-ol, C18H23N3O2, (II), was formed by reaction of the corresponding 6-chloro compound with butanol, and (RS)-4-dimethylamino-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-8-ol, C16H20N4O, (III), was formed by reaction of the chloro analogue with alkaline dimethylformamide. (6RS)-N-Benzyl-8-methoxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-4-amine, C22H24N4O, (IV), (6RS)-N-benzyl-6-methyl-1,2,6,7-tetrahydropyrimido[5',4':6,7]azepino[3,2,1-hi]indol-8-amine, C22H22N4, (V), and (7RS)-N-benzyl-7-methyl-2,3,7,8-tetrahydro-1H-pyrimido[5',4':6,7]azepino[3,2,1-ij]quinolin-9-amine, C23H24N4, (VI), were all formed by reaction of the corresponding chloro compounds with benzylamine under microwave irradiation. In each of compounds (I)-(IV) and (VI), the azepine ring adopts a conformation close to the boat form, with the C-methyl group in a quasi-equatorial site, whereas the corresponding ring in (V) adopts a conformation intermediate between the twist-boat and twist-chair forms, with the C-methyl group in a quasi-axial site. No two of the structures of (I)-(VI) exhibit the same range of intermolecular hydrogen bonds: different types of sheet are formed in each of (I), (II), (V) and (VI), and different types of chain in each of (III) and (IV). PMID:27045186

  5. 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.

  6. 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

  7. STAR FORMATION RATES FOR STARBURST GALAXIES FROM ULTRAVIOLET, INFRARED, AND RADIO LUMINOSITIES

    SciTech Connect

    Sargsyan, Lusine A.; Weedman, Daniel W. E-mail: dweedman@isc.astro.cornell.edu

    2009-08-20

    We present a comparison of star formation rates (SFR) determined from mid-infrared 7.7 {mu}m polycyclic aromatic hydrocarbon (PAH) luminosity [SFR(PAH)], from 1.4 GHz radio luminosity [SFR(radio)], and from far-ultraviolet luminosity [SFR(UV)] for a sample of 287 starburst galaxies with z < 0.5 having Spitzer IRS observations. The previously adopted relation log [SFR(PAH)] = log [{nu}L {sub {nu}}(7.7 {mu}m)] - 42.57 {+-} 0.2, for SFR in M{sub sun} yr{sup -1} and {nu}L {sub {nu}}(7.7 {mu}m) the luminosity at the peak of the 7.7 {mu}m PAH feature in erg s{sup -1}, is found to agree with SFR(radio). Comparing with SFR(UV) determined independently from ultraviolet observations of the same sources with the Galaxy Evolution Explorer mission (not corrected for dust extinction), the median log [SFR(PAH)/SFR(UV)] = 1.67, indicating that only 2% of the ultraviolet continuum typically escapes extinction by dust within a starburst. This ratio SFR(PAH)/SFR(UV) depends on infrared luminosity, with the form log [SFR(PAH)/SFR(UV)] = (0.53 {+-} 0.05)log [{nu}L{sub {nu}}(7.7 {mu}m)] - 21.5 {+-} 0.18, indicating that more luminous starbursts are also dustier. Using our adopted relation between {nu}L{sub {nu}}(7.7 {mu}m) and L {sub ir}, this becomes log [SFR(PAH)/SFR(UV)]= (0.53 {+-} 0.05)log L{sub ir} - 4.11 {+-} 0.18, for L{sub ir} in L{sub sun}. Only blue compact dwarf galaxies show comparable or greater SFR(UV) compared to SFR(PAH). We also find that the ratio SFR(PAH)/SFR(UV) is similar to that in infrared-selected starbursts for a sample of Markarian starburst galaxies originally selected using optical classification, which implies that there is no significant selection effect in SFR(PAH)/SFR(UV) using starburst galaxies discovered by Spitzer. These results indicate that SFRs determined with ultraviolet luminosities require dust corrections by a factor of {approx}10 for typical local starbursts but this factor increases to >700 for the most luminous starbursts at z {approx} 2

  8. Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

    PubMed Central

    Heffernan, Natalie; Brunton, Nigel P.; FitzGerald, Richard J.; Smyth, Thomas J.

    2015-01-01

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds. PMID:25603345

  9. Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

    PubMed

    Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

    2015-01-16

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  10. Using Molecular Replacement Phasing to Study the Structure and Function of RNA.

    PubMed

    Marcia, Marco

    2016-01-01

    In recent years a wide variety of RNA molecules regulating fundamental cellular processes has been discovered. Therefore, RNA structure determination is experiencing a boost and many more RNA structures are likely to be determined in the years to come. The broader availability of experimentally determined RNA structures implies that molecular replacement (MR) will be used more and more frequently as a method for phasing future crystallographic structures. In this report we describe various aspects relative to RNA structure determination by MR. First, we describe how to select and create MR search models for nucleic acids. Second, we describe how to perform MR searches on RNA using available crystallographic software. Finally, we describe how to refine and interpret the successful MR solutions. These protocols are applicable to determine novel RNA structures as well as to establish structural-functional relationships on existing RNA structures.

  11. THE LESSER ROLE OF STARBURSTS IN STAR FORMATION AT z = 2

    SciTech Connect

    Rodighiero, G.; Baronchelli, I.; Feltre, A.; Franceschini, A.; Daddi, E.; Aussel, H.; Elbaz, D.; Renzini, A.; Popesso, P.; Lutz, D.; Berta, S.; Foerster Schreiber, N. M.; Genzel, R.; Andreani, P.; Cava, A.; Fontana, A.; Grazian, A.; Gruppioni, C.; Ilbert, O.

    2011-10-01

    Two main modes of star formation are know to control the growth of galaxies: a relatively steady one in disk-like galaxies, defining a tight star formation rate (SFR)-stellar mass sequence, and a starburst mode in outliers to such a sequence which is generally interpreted as driven by merging. Such starburst galaxies are rare but have much higher SFRs, and it is of interest to establish the relative importance of these two modes. PACS/Herschel observations over the whole COSMOS and GOODS-South fields, in conjunction with previous optical/near-IR data, have allowed us to accurately quantify for the first time the relative contribution of the two modes to the global SFR density in the redshift interval 1.5 < z < 2.5, i.e., at the cosmic peak of the star formation activity. The logarithmic distributions of galaxy SFRs at fixed stellar mass are well described by Gaussians, with starburst galaxies representing only a relatively minor deviation that becomes apparent for SFRs more than four times higher than on the main sequence. Such starburst galaxies represent only 2% of mass-selected star-forming galaxies and account for only 10% of the cosmic SFR density at z {approx} 2. Only when limited to SFR > 1000 M{sub sun} yr{sup -1}, off-sequence sources significantly contribute to the SFR density (46% {+-} 20%). We conclude that merger-driven starbursts play a relatively minor role in the formation of stars in galaxies, whereas they may represent a critical phase toward the quenching of star formation and morphological transformation in galaxies.

  12. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    PubMed

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  13. The Vertex Version of Weighted Wiener Number for Bicyclic Molecular Structures.

    PubMed

    Gao, Wei; Wang, Weifan

    2015-01-01

    Graphs are used to model chemical compounds and drugs. In the graphs, each vertex represents an atom of molecule and edges between the corresponding vertices are used to represent covalent bounds between atoms. We call such a graph, which is derived from a chemical compound, a molecular graph. Evidence shows that the vertex-weighted Wiener number, which is defined over this molecular graph, is strongly correlated to both the melting point and boiling point of the compounds. In this paper, we report the extremal vertex-weighted Wiener number of bicyclic molecular graph in terms of molecular structural analysis and graph transformations. The promising prospects of the application for the chemical and pharmacy engineering are illustrated by theoretical results achieved in this paper. PMID:26640513

  14. The Vertex Version of Weighted Wiener Number for Bicyclic Molecular Structures

    PubMed Central

    Gao, Wei; Wang, Weifan

    2015-01-01

    Graphs are used to model chemical compounds and drugs. In the graphs, each vertex represents an atom of molecule and edges between the corresponding vertices are used to represent covalent bounds between atoms. We call such a graph, which is derived from a chemical compound, a molecular graph. Evidence shows that the vertex-weighted Wiener number, which is defined over this molecular graph, is strongly correlated to both the melting point and boiling point of the compounds. In this paper, we report the extremal vertex-weighted Wiener number of bicyclic molecular graph in terms of molecular structural analysis and graph transformations. The promising prospects of the application for the chemical and pharmacy engineering are illustrated by theoretical results achieved in this paper. PMID:26640513

  15. Molecular structure and dynamical properties of niosome bilayers with and without cholesterol incorporation: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Ritwiset, Aksornnarong; Krongsuk, Sriprajak; Johns, Jeffrey Roy

    2016-09-01

    Niosomes are non-ionic surfactant vesicles having a bilayer structure formed by self-assembly of hydrated surfactants, usually with cholesterol incorporation. Stability and mechanical properties of niosomes strongly depend on type of non-ionic surfactants and compositions used. In this study we present the structural and dynamical properties of niosome bilayers composed of sorbitan monostearate (Span60) with 0% and 50% cholesterol compositions which are investigated by using molecular dynamics simulations. The simulations reveal that niosome bilayer without cholesterol prefer to form in the gel phase with a higher order structure, while in the presence of cholesterol the bilayer exhibits more fluidity having a less ordered structure. The niosome bilayer with 50% cholesterol inclusion shows an increase of area per lipid (∼11%) and thickness (∼39%) compared with the niosome bilayer without cholesterol. The Span60 tailgroup orientation of the niosome bilayers without cholesterol exhibits more tilt (34.5o ± 0.5) than that of the bilayer with 50% cholesterol (15.4o ± 0.8). Additionally, our results show that the addition of cholesterol to the bilayer causes the higher in lateral and transverse diffusion, as well as an increase in the hydrogen bond number between Span60 and water. Such characteristics not only enhance the niosome stability but also increase the fluidity, which are necessary for the niosomal drug delivery.

  16. Molecular dynamics simulations of soliton-like structures in a dusty plasma medium

    SciTech Connect

    Tiwari, Sanat Kumar Das, Amita; Sen, Abhijit; Kaw, Predhiman

    2015-03-15

    The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.

  17. ATOMIC AND MOLECULAR PHYSICS: Triatomic wake effect and the determination of the molecular structure of HD2+ from the Coulomb explosion

    NASA Astrophysics Data System (ADS)

    Zhu, Zhou-Sen; Miao, Jing-Wei; Liao, Xue-Hua; Miao, Lei; Yuan, Xue-Dong; Shi, Mian-Gong

    2009-11-01

    A new theoretical model of the triatomic molecular wake effect is proposed and applied to molecular ions D3+ and HD2+ while passing through a solid. The wake effects resulting from the reactions of the two similar ions with thin carbon foil are also investigated by using the Coulomb explosion technique. The experimental results are in good agreement with theoretical estimates and the molecular structure of HD2+ is determined by using the model.

  18. All the X-ray binaries in the Universe: X-ray Emission from Normal and Starburst Galaxies Near and Far

    NASA Astrophysics Data System (ADS)

    Hornschemeier, Ann; Basu-Zych, Antara; Lehmer, Bret

    2015-08-01

    There has recently been quite a bit of excitement on the role of X-ray emission from galaxies in early heating of the IGM, demonstrating that understanding of X-ray emission from normal and starburst galaxies may have significant impact on structure formation in the Universe. The X-ray output from X-ray binaries and hot gas are both important and may rival the ionizing output of AGN at z>5, particularly for Hydrogen reionization. Here we present our research on constraining the X-ray SED of galaxies across cosmic time via several complementary approaches. In the very local universe (d <~ 30 Mpc including the Local Group) we are using NuSTAR to understand the accretion states and total output of black hole and neutron star binaries using the important lever arm of 0.5-30 keV emission. At intermediate distances (10-100 Mpc), we are comparing the X-ray output of galaxies with star formation histories and population synthesis model predictions using both Chandra and XMM data. In the slightly more distant universe (z~0.1-0.2) we can find rare analogs to primordial starbursts via wide-field optical/UV surveys that may be studied with Chandra. We will finish with a discussion of starburst galaxies emitting X-rays at z>4, which thanks to the extremely deep Chandra Deep Field-South 7 Ms survey, are better constrained than ever before. We discuss survey strategy and how the various pieces of the puzzle fit together regarding the X-ray output of galaxies and their X-ray binary populations over cosmic time. We discuss implications for next-generation missions and instruments, including those with wide-field survey capabilities and high throughput, especially the Athena mission.

  19. Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

    NASA Astrophysics Data System (ADS)

    Kluber, Alexander; Hayre, Robert; Cox, Daniel

    2012-02-01

    Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

  20. CO mapping of the Orion molecular cloud: The influence of star formation on cloud structure

    NASA Technical Reports Server (NTRS)

    Schloerb, F. P.; Snell, R. L.; Goldsmith, P. F.; Morgan, J. A.

    1986-01-01

    Regions of massive star formation have long been believed to have a profound influence on the structure of their surrounding molecular clouds. The ways in which massive star formation has altered the structure and kinematics of the Orion Molecular Cloud are discussed. The data to be discussed consists of a large scale map of the CO J=1-0 emission from approximately 3 square degrees of OMC-1. During 1985, the Five College Radio Astronomy Observatory 14M antenna was used to map a 2 deg x 1 deg region centered on alpha(1950) = 5(h)33(m)00(s) delta(1950) = -5 deg 30 min. The region mapped in 1985 covers the well known HII regions M42, M43, and NGC1977, and the CO map contains abundant evidence of the interaction between these regions and the molecular cloud. Indeed, the global structure of the cloud appears to have been strongly influenced by the continuous formation of massive stars within the cloud. Individual instances of some of these features are discussed. There appear to be two classes of features which are indicative of this interaction: CO bright rims and CO holes. During 1986, we have undertaken further mapping of OMC-1 to the south of the region covered by the 1985 map. This portion of the cloud contains significant regions of star formation, but O star formation has not occured and large HII regions have not developed to alter the appearance of the cloud. A detailed map of this region is thus an opportunity to view the structure of the molecular cloud before it has been altered by massive star formation. Preliminary analysis of data obtained in this region suggests that the structure and kinematics of the southern portion of the Orion cloud are indeed dramatically different from those of the region previously mapped. Comparison of the two regions thus supports models of the development of structure in molecular clouds through interaction with the HII regions formed within them.

  1. Low-resolution molecular structures of isolated functional units from arthropodan and molluscan hemocyanin.

    PubMed Central

    Grossmann, J G; Ali, S A; Abbasi, A; Zaidi, Z H; Stoeva, S; Voelter, W; Hasnain, S S

    2000-01-01

    Synchrotron x-ray scattering measurements were performed on dilute solutions of the purified hemocyanin subunit (Bsin1) from scorpion (Buthus sindicus) and the N-terminal functional unit (Rta) from a marine snail (Rapana thomasiana). The model-independent approach based on spherical harmonics was applied to calculate the molecular envelopes directly from the scattering profiles. Their molecular shapes in solution could be restored at 2-nm resolution. We show that these units represent stable, globular building blocks of the two hemocyanin families and emphasize their conformational differences on a subunit level. Because no crystallographic or electron microscopy data are available for isolated functional units, this study provides for the first time structural information for isolated, monomeric functional subunits from both hemocyanin families. This has been made possible through the use of low protein concentrations (< or = 1 mg/ml). The observed structural differences may offer advantages in building very different overall molecular architectures of hemocyanin by the two phyla. PMID:10653810

  2. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    PubMed Central

    Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-01-01

    Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts. PMID:24189228

  3. Molecular clouds and the large-scale structure of the galaxy

    NASA Technical Reports Server (NTRS)

    Thaddeus, Patrick; Stacy, J. Gregory

    1990-01-01

    The application of molecular radio astronomy to the study of the large-scale structure of the Galaxy is reviewed and the distribution and characteristic properties of the Galactic population of Giant Molecular Clouds (GMCs), derived primarily from analysis of the Columbia CO survey, and their relation to tracers of Population 1 and major spiral features are described. The properties of the local molecular interstellar gas are summarized. The CO observing programs currently underway with the Center for Astrophysics 1.2 m radio telescope are described, with an emphasis on projects relevant to future comparison with high-energy gamma-ray observations. Several areas are discussed in which high-energy gamma-ray observations by the EGRET (Energetic Gamma-Ray Experiment Telescope) experiment aboard the Gamma Ray Observatory will directly complement radio studies of the Milky Way, with the prospect of significant progress on fundamental issues related to the structure and content of the Galaxy.

  4. Ab initio molecular dynamics: Relationship between structural phases and the sound velocity in dense hydrogen

    NASA Astrophysics Data System (ADS)

    Guerrero, Carlo L.; Cuesta-Lopez, Santiago; Perlado, Jose M.

    2014-10-01

    The phase diagram and the possible stable structures of molecular solid hydrogen are intriguing physical phenomena that still remain to be fully unveiled. Particularly, its transition to metallic hydrogen at high pressures is currently a hot topic of discussion. This letter reports a simulation method that links the ab initio, quantum molecular dynamic and mechanical properties calculations to study the relation between the structural phase transitions and sound velocity in solid molecular hydrogen. The pressure range studied is from 0.1 GPa to 180 GPa, at 15 K temperature, thereby our aim is to simulate the conditions of manufacture, handling and early stages of compression of the target fuel used in confinement inertial fusion. Phase I degeneration below 1 GPa is discussed.

  5. SHAKEN, NOT STIRRED: THE DISRUPTED DISK OF THE STARBURST GALAXY NGC 253

    SciTech Connect

    Davidge, T. J.

    2010-12-10

    Near-infrared images obtained with WIRCam on the Canada-France-Hawaii Telescope are used to investigate the recent history of the nearby Sculptor Group spiral NGC 253, which is one of the nearest starburst galaxies. Bright asymptotic giant branch (AGB) stars are traced out to projected distances of {approx}22-26 kpc ({approx}13-15 disk scale lengths) along the major axis. The distribution of stars in the disk is lopsided, in the sense that the projected density of AGB stars in the northeast portion of the disk between 10 and 20 kpc from the galaxy center is {approx}0.5 dex higher than on the opposite side of the galaxy. A large population of red supergiants is also found in the northeast portion of the disk and, with the exception of the central 2 kpc, this area appears to have been the site of the highest levels of star-forming activity in the galaxy during the past {approx}0.1 Gyr. It is argued that such high levels of localized star formation may have produced a fountain that ejected material from the disk, and the extraplanar H I detected by Boomsma et al. may be one manifestation of such activity. Diffuse stellar structures are found in the periphery of the disk, and the most prominent of these is to the south and east of the galaxy. Bright AGB stars, including cool C stars that are identified based on their J - K colors, are detected out to 15 kpc above the disk plane, and these are part of a diffusely distributed, flattened extraplanar component. Comparisons between observed and model luminosity functions suggest that the extraplanar regions contain stars that formed throughout much of the age of the universe. Additional evidence of a diffuse, extraplanar stellar component that contains moderately young stars comes from archival Galaxy Evolution Explorer images. It is suggested that the disk of NGC 253 was disrupted by a tidal encounter with a now defunct companion. This encounter introduced asymmetries that remain to this day, and the projected distribution

  6. Molecular structures and protonation state of 2-Mercaptopyridine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Eckert, S.; Miedema, P. S.; Quevedo, W.; O'Cinneide, B.; Fondell, M.; Beye, M.; Pietzsch, A.; Ross, M.; Khalil, M.; Föhlisch, A.

    2016-03-01

    The speciation of 2-Mercaptopyridine in aqueous solution has been investigated with nitrogen 1s Near Edge X-ray Absorption Fine Structure spectroscopy and time dependent Density Functional Theory. The prevalence of distinct species as a function of the solvent basicity is established. No indications of dimerization towards high concentrations are found. The determination of different molecular structures of 2-Mercaptopyridine in aqueous solution is put into the context of proton-transfer in keto-enol and thione-thiol tautomerisms.

  7. Conformation of the umifenovir cation in the molecular and crystal structures of four carboxylic acid salts

    NASA Astrophysics Data System (ADS)

    Orola, Liana; Sarcevica, Inese; Kons, Artis; Actins, Andris; Veidis, Mikelis V.

    2014-01-01

    The umifenovir salts of maleic, salicylic, glutaric, and gentisic acid as well as the chloroform solvate of the salicylate were prepared. Single crystals of the five compounds were obtained and their molecular and crystal structures determined by X-ray diffraction. In each structure the conformation of phenyl ring with respect to the indole group of the umifenovir moiety is different. The water solubility and melting points of the studied umifenovir salts have been determined.

  8. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    ERIC Educational Resources Information Center

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

    2010-01-01

    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  9. Improved isolation protocol to detect high molecular weight polysaccharide structures of Campylobacter jejuni.

    PubMed

    Kovács, Judit K; Felső, Péter; Emődy, Levente; Schneider, György; Kocsis, Béla

    2014-12-01

    Simple detection of high molecular weight, LPS-like structures of Campylobacter jejuni is still an unsolved problem. A phenol-free extraction method for the detection of HMW polysaccharide was developed without the need for Western blot. This method provides a reliable technique for large-scale screening and comparative characterization study of different isolates.

  10. Development and Assessment of a Molecular Structure and Properties Learning Progression

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Underwood, Sonia M.; Hilley, Caleb Z.; Klymkowsky, Michael W.

    2012-01-01

    Previously, we found that: (i) many students were unable to construct representations of simple molecular structures; (ii) a majority of students fail to make the important connection between these representations and macroscopic properties of the material; and (iii) they were unable to decode the information contained in such representations.…

  11. Well-ordered monolayers of alkali-doped coronene and picene: Molecular arrangements and electronic structures

    SciTech Connect

    Yano, M.; Endo, M.; Hasegawa, Y.; Okada, R.; Yamada, Y. Sasaki, M.

    2014-07-21

    Adsorptions of alkali metals (such as K and Li) on monolayers of coronene and picene realize the formation of ordered phases, which serve as well-defined model systems for metal-intercalated aromatic superconductors. Upon alkali-doping of the monolayers of coronene and picene, scanning tunneling microscopy and X-ray absorption spectroscopy revealed the rearrangement of the entire molecular layer. The K-induced reconstruction of both monolayers resulted in the formation of a structure with a herringbone-like arrangement of molecules, suggesting the intercalation of alkali metals between molecular planes. Upon reconstruction, a shift in both the vacuum level and core levels of coronene was observed as a result of a charge transfer from alkali metals to coronene. In addition, a new density of states near the Fermi level was formed in both the doped coronene and the doped picene monolayers. This characteristic electronic feature of the ordered monolayer has been also reported in the multilayer picene films, ensuring that the present monolayer can model the properties of the metal-intercalated aromatic hydrocarbons. It is suggested that the electronic structure near the Fermi level is sensitive to the molecular arrangement, and that both the strict control and determinations of the molecular structure in the doped phase should be important for the determination of the electronic structure of these materials.

  12. Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

    ERIC Educational Resources Information Center

    Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

    2011-01-01

    We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

  13. Molecular Docking of Enzyme Inhibitors: A Computational Tool for Structure-Based Drug Design

    ERIC Educational Resources Information Center

    Rudnitskaya, Aleksandra; Torok, Bela; Torok, Marianna

    2010-01-01

    Molecular docking is a frequently used method in structure-based rational drug design. It is used for evaluating the complex formation of small ligands with large biomolecules, predicting the strength of the bonding forces and finding the best geometrical arrangements. The major goal of this advanced undergraduate biochemistry laboratory exercise…

  14. Correlates across the Structural, Functional, and Molecular Phenotypes of Fragile X Syndrome

    ERIC Educational Resources Information Center

    Beckel-Mitchener, Andrea; Greenough, William T.

    2004-01-01

    Fragile X syndrome (FXS) is characterized by a pattern of morphological, functional, and molecular characteristics with, in at least some cases, apparent relationships among phenotypic features at different levels. Gross morphology differences in the sizes of some human brain regions are accompanied by fine structural alterations in the shapes and…

  15. The History of Molecular Structure Determination Viewed through the Nobel Prizes.

    ERIC Educational Resources Information Center

    Jensen, William P.; Palenik, Gus J.; Suh, Il-Hwan

    2003-01-01

    Discusses the importance of complex molecular structures. Emphasizes their individual significance through examination of the Nobel Prizes of the 20th century. Highlights prizes awarded to Conrad Rontgen, Francis H.C. Crick, James D. Watson, Maurice H.F. Wilkins, and others. (SOE)

  16. Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations

    NASA Astrophysics Data System (ADS)

    Marques, Helder M.; Egan, Timothy J.; de Villiers, Katherine A.

    The use of empirical force field methods for modeling important systems in bioinorganic chemistry, including the cobalt corrins (derivatives of vitamin B12) and the iron porphyrins, is described. Particular attention is given to the use of molecular dynamics and simulated annealing calculations in exploring the solution structures of corrin, and those of likely complexes between the ferriprotoporphyrin-IX and the arylmethanol antimalarials.

  17. GPU-accelerated analysis and visualization of large