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Sample records for 3d crustal structure

  1. A 3-D crustal velocity structure across the Variscides of southwest Ireland

    NASA Astrophysics Data System (ADS)

    Landes, M.; Readman, P. W.; O'Reilly, B. M.; Shannon, P. M.

    2003-04-01

    In the VARNET-96 experiment three seismic refraction profiles were acquired to examine the crustal structure in the south-west of Ireland. The shotpoint geometry allowed for both in-line and off-line fan shot recordings on the three profiles. Results of 3-D inversion modelling illustrate that there is pervasive lateral heterogeneity of the sedimentary and crustal velocity structure south of the Shannon Estuary. Palaeozoic strata at the south coast are about 5-6 km thick associated with the sedimentary infill of the Munster and South Munster Basins. To the north, shallow upper crust in the vicinity of the Killarney-Mallow Fault Zone is followed by a 3-4 km thick sedimentary succession in the Dingle-Shannon Basin. A zone of high-velocity upper crust (6.4-6.6 km/s) beneath the South Munster Basin correlates with a gravity high between the Kenmare-Killarney and the Leinster Granite gravity lows. Other high-velocity zones beneath Dingle Bay and the Kenmare River region may be associated with the deep traces of the Killarney-Mallow Fault Zone and the Cork-Kenmare Line. The 3-D velocity model was taken as a basis for the computation of PmP reflected arrivals from the crust-mantle boundary. The Moho depth varies from 28-29 km at the south coast to 32-33 km beneath the Dingle-Shannon Basin. Pervasive Variscan deformation appears to be confined to the sedimentary and upper crustal structure thus supporting a thin-skinned tectonic model for Variscan deformation. Deep-crustal variations only occur where they can be correlated with major tectonic features such as the Caledonian Iapetus Suture near the Shannon Estuary. The shallowing of the Moho towards the coast may result from Mesozoic crustal extension in the adjacent offshore sedimentary basins.

  2. 3D Crustal Structure and 3D-b-value in AbuDabbab Seismogenic Source, Northern Red Sea.

    NASA Astrophysics Data System (ADS)

    Al-Arifi, Nassir; El Kherpy, Sami; Koulakov, Ivan

    2014-05-01

    Abu Dabbab seismogenic source region is of unique seismic activity located on the Egyptian Red Sea coast. It's known as earthquake Cannons where the earthquakes are accompanied by a sound of distinct rumbling similar to the sound of a distant quarry blast which is heard by humans for several generations. Seismic activity of Abu Dabbab becomes very well determined after establishing of the Egyptian National Seismic Network 1997. Joint earthquake tomography inversion of local and regional data has been performed in order to image the crustal heterogeneity and the origin of the cannons earthquakes. Most previous studies suggested that this activity is of magmatic origin. We found the seismicity forms an arc shaped cluster that surrounds an aseismic block. This aseismic block has high velocities and a low Vp/Vs ratio. The origin of this seismic activity is probably due an active fault below the non-deformed block of Precambrian Igneous rock reaching a depth of ~10 km. Spatial mapping of the frequency magnitude distribution of the earthquakes and 3D-b-value indicate a strong variation moreover high b-value (1.4) at depth downward the rigid block. The Combined interpretation of the seismic imaging and 3D b-value in addition to the seismological and the geophysical observations revealed the tectonic origin of the earthquake activity in this area which is related strongly to the evolution of the crust in the Red Sea and its tectonic activity. KEYWARD:Three dimensional Crustal Structure - Seismic activity -Three-D b-value- Red Sea tectonics- Tectonic activity

  3. Complex Crustal Structure Beneath Western Turkey Revealed by 3D Seismic Full Waveform Inversion (FWI)

    NASA Astrophysics Data System (ADS)

    Cubuk-Sabuncu, Yesim; Taymaz, Tuncay; Fichtner, Andreas

    2016-04-01

    We present a 3D radially anisotropic velocity model of the crust and uppermost mantle structure beneath the Sea of Marmara and surroundings based on the full waveform inversion method. The intense seismic activity and crustal deformation are observed in the Northwest Turkey due to transition tectonics between the strike-slip North Anatolian Fault (NAF) and the extensional Aegean region. We have selected and simulated complete waveforms of 62 earthquakes (Mw > 4.0) occurred during 2007-2015, and recorded at (Δ < 10°) distances. Three component earthquake data is obtained from broadband seismic stations of Kandilli Observatory and Earthquake Research Center (KOERI, Turkey), Hellenic Unified Seismic Network (HUSN, Greece) and Earthquake Research Center of Turkey (AFAD-DAD). The spectral-element solver of the wave equation, SES3D algorithm, is used to simulate seismic wave propagation in 3D spherical coordinates (Fichtner, 2009). The Large Scale Seismic Inversion Framework (LASIF) workflow tool is also used to perform full seismic waveform inversion (Krischer et al., 2015). The initial 3D Earth model is implemented from the multi-scale seismic tomography study of Fichtner et al. (2013). Discrepancies between the observed and simulated synthetic waveforms are determined using the time-frequency misfits which allows a separation between phase and amplitude information (Fichtner et al., 2008). The conjugate gradient optimization method is used to iteratively update the initial Earth model when minimizing the misfit. The inversion is terminated after 19 iterations since no further advances are observed in updated models. Our analysis revealed shear wave velocity variations of the shallow and deeper crustal structure beneath western Turkey down to depths of ~35-40 km. Low shear wave velocity anomalies are observed in the upper and mid crustal depths beneath major fault zones located in the study region. Low velocity zones also tend to mark the outline of young volcanic

  4. A 3-D crustal velocity structure across the southeastern Carpathians of Romania

    NASA Astrophysics Data System (ADS)

    Landes, M.; Hauser, F.; Ritter, J. R. R.; Fielitz, W.; Popa, M.

    2003-04-01

    The Vrancea zone in the southeastern Carpathians is one of the most active seismic regions in Europe. In order to study the crustal and upper-mantle structure in this region, two seismic refraction experiments were carried out in 1999 and 2001. The 1999 campaign comprised a 320 km long N-S profile and a 80 km long transverse profile. All shots were recorded simultaneously on both profiles. The profile conducted in 2001 extended in E-W direction from the Hungarian border across the Vrancea zone to the Black Sea. A first ever 3-D crustal velocity model of the south-eastern Carpathians within a 115 x 235 km wide region around the Vrancea zone is presented. This model was generated by application of a 3-D refraction and reflection tomography algorithm (Hole 1992, 1995). In order to enhance the model resolution, first arrival data from local earthquakes were also included. The results indicate a high-velocity structure above the Vrancea zone extending from shallow levels to depths of about 11 km. A possible relation to the Trotus and Capidava-Ovidiu faults, which converge to the north of it, is deemed unlikely. However,the existence of the outstanding high velocities may be explained by crystalline basement thrust onto the sub-Carpathian nappes. The high-velocity region is surrounded by the lower velocity Focsani and Brasov basins. The sedimentary succession beneath the southern part of the model area extends to 18 km depth, while in the north sediment thickness varies between 10 and 15 km. Further results of the interface modelling of prominent reflections show that the mid-crustal and Moho interfaces shallow northwards from 30 km to 22 km and from 42 km to 38 km, respectively.

  5. Joint inversion of 3D crustal structure with ambient noise and earthquake body wave travel time

    NASA Astrophysics Data System (ADS)

    Li, Z.; Ni, S.; Chong, J.; Wang, X.

    2012-12-01

    Surface wave tomography based on the noise correlation function of seismic ambient noise has been widely used in studies of crustal and mantle structure . However, the periods of surface wave dispersions in the ambient noise tomography are typically less than 40 s, which limits its resolution on the lower crust. Travel times of earthquake body waves, such as Sg and SmS, could provide additional constraints to the crustal structure, especially to the lower crust due to the ray paths of SmS traveling through the lower crust twice. Here, we proposed a joint inversion method for 3D crustal structure with ambient noise and earthquake body wave travel time data, with the goal of providing better constraints and resolutions on the whole crust. We constructed the linear equations for joint inversion of crustal S velocity structure with the surface wave dispersion and body wave travel time data, and solved the equations with LSQR algorithm. Different weighting and damping factors, together with smoothing constraints, are adopted for surface wave dispersion and body wave travel time data to fit both dataset simultaneously. Synthetics experiments showed that the joint inversion could resolve the crust structure better than sole tomography of ambient noise or body wave travel time. We conducted the joint inversion around the Yangtze block in the eastern China. Rayleigh wave dispersions are extracted from the seismic ambient noise tomography by Zheng et al (2011) in this area. The body waves (e.g., Sg, SmS, Sn) are coherent to be identified and their travel times are measured with accuracy from high quality waveforms of some recent local earthquakes in this area. In order to minimize the travel time uncertainties, the focal depth and epicenter of these local earthquakes were resolved by depth phases and temporary aftershock observations. The result from joint inversion suggests that the crustal velocity structure, especially the lower crust, was well improved, which not only

  6. 3-D Crustal Velocity Structure Across the Vrancea Zone in Romania, Derived From Seismic Data

    NASA Astrophysics Data System (ADS)

    Landes, M.; Hauser, F.; Popa, M.

    2002-12-01

    The Vrancea zone in the south-eastern Carpathians is one of the most active seismic zones in Europe. In order to study the crustal and upper-mantle structure in this region, two seismic refraction/wide-angle reflection experiments were carried out in 1999 and 2001. The 1999 campaign comprised a 320 km long N-S profile and a 80 km long transverse profile (E-W). All shots were recorded simultaneously on both profiles. The profile conducted in 2001 extended in E-W direction from the Hungarian border across the Vrancea zone to the Black Sea. We present an application of a 3-D refraction and reflection tomography algorithm (Hole 1992, 1995), elaborating the crustal velocity and interface structure within a 115 x 235 km wide region around the Vrancea zone. In order to enhance the model resolution, first arrival data from local earthquakes of the CALIXTO-99 teleseismic project were also included. The results indicate a high-velocity structure beneath the northern part of the Vrancea zone extending from shallow levels to depths of about 11 km. This structure may be related to the Trotus and Capidava-Ovidiu faults, which converge to the north of it. The high-velocity region is surrounded by the lower velocity Focsani and Brasov basins. The sedimentary succession beneath the southern part of the model extends to 18 km depth, while in the north sediment thickness varies between 10 and 15 km. Further results of the interface modelling of prominent reflections show that the mid-crustal and Moho interfaces shallow northwards from 30 km to 22 km and from 42 km to 38 km, respectively. This correlates well with previous results of Hauser et al. (2001).

  7. The crustal and mantle velocity structure in central Asia from 3D traveltime tomography

    NASA Astrophysics Data System (ADS)

    Sun, Y.; Martin, R. V.; Toksoz, M. N.; Pei, S.

    2010-12-01

    The lithospheric structure in central Asia features large blocks such as the Indian plate, the Afghan block, the Turan plate, and the Tarim block. This geologically and tectonically complicated area is also one of the most seismically active regions in the world. We developed P- and S- wave velocity structures of the central Asia in the crust using the traveltime data from Kyrgyzstan, Tajikistan, Kazakhstan, and Uzbek. We chose the events and stations between 32N65E and 45N85E and focused on the areas of Pamir and western Tianshan. In this data set, there are more than 6000 P and S arrivals received at 80 stations from about 300 events. The double difference tomography is applied to relocate events and to invert for seismic structures simultaneously. Our results provide accurate locations of earthquakes and high resolution crustal structure in this region. To extend the model deeper into the mantle through the upper mantle transition zone, ISC/EHB data for P and PP phases are combined with the ABCE data. To counteract the “smearing effect,” the crust and upper mantle velocity structure, derived from regional travel-times, is used. An adaptive grid method based on ray density is used in the inversion. A P-wave velocity model extending down to a depth of 2000 km is obtained. regional-teleseismic tomography provides a high-resolution, 3-D P-wave velocity model for the crust, upper mantle, and the transition zone. The crustal models correlate well with geologic and tectonic features. The upper mantle tomograms show the images of Tian Shan. The slab geometry is quite complex, reflecting the history of the changes in the plate motions and collision processes. Vp/Vs tomography was also determined in the study region, and an attenuation tomography was obtained as well.

  8. 3D Crustal and Lithospheric Structures in the Southeastern Mediterranean and Northeastern Egypt

    NASA Astrophysics Data System (ADS)

    Saleh, Salah

    2013-12-01

    Crustal and lithospheric thicknesses of the southeastern Mediterranean Basin region were determined using 3D Bouguer and elevation data analysis. The model is based on the assumption of local isostatic equilibrium. The calculated regional and residual Bouguer anomaly maps were employed for highlighting both deep and shallow structures. Generally, the regional field in the area under study is considered to be mainly influenced by the density contrast between the crust and upper mantle. Use of the gravity and topographic data with earthquake focal depths has improved both the geometry and the density distribution in the 3-D calculated profiles. The oceanic-continental boundary, the basement relief, Moho depth and lithosphere-asthenosphere boundary maps were estimated. The results point to the occurrence of thick continental crust areas with a thickness of approximately 32 km in northern Egypt. Below the coastal regions, the thickness of crust decreases abruptly (transition zone). An inverse correlation between sediment and crustal thicknesses shows up from the study. Furthermore, our density model reveals the existence of a continental crustal zone below the Eratosthenes Seamount block. Nevertheless, the crustal type beneath the Levantine basin is typically oceanic; this is covered by sedimentary sequences more than 14 km thick. The modeled Moho map shows a depth of 28-30 km below Cyprus and a depth of 26-28 km beneath the south Florence Rise in the northern west. However, the Moho lies at a constant shallow depth of 22-24 km below the Levantine Basin, which indicates thinning of the crust beneath this region. The Moho map reveals also a maximum depth of about 33-35 km beneath both the northern Egypt and northern Sinai, both of which are of the continental crust. The resulting mantle density anomalies suggest important variations of the lithosphere-asthenosphere boundary (LAB) topography, indicating prominent lithospheric mantle thinning beneath south Cyprus (LAB ~90

  9. Simultaneous inversion for 3D crustal and anisotropic lithospheric structure and regional hypocenters beneath Germany

    NASA Astrophysics Data System (ADS)

    Muench, Thomas; Koch, Manfred; Schlittenhardt, Jörg

    2010-05-01

    There is now ample evidence from both refraction seismic studies, done already a quarter century ago and from more recent local earthquake traveltime analysis of some of the authors above that large sections of the upper mantle underneath Europe and Germany, in particular, are anisotropic. Employing a modified version of the method of simultaneous inversion for structure and hypocenters (SSH) of the first author, including a priori known upper mantle anisotropy, the investigations of Song et al. [2001] and Song et al. [2004] by means of a 1D time-term analysis and a full 2D Pn anisotropic inversion of regional traveltime data are extended here to a full 3D SSH-inversion underneath Germany. Regional traveltimes from local events occurring between 1975 - 2003 are used which, after application of several selection criteria, results in ~1300 events with a total of ~30000 P- and S-phases for the SSH inversion. Because many of the recorded events appear to suffer from relatively poor hypocentral depth locations a full SSH analysis becomes an intricate undertaking. To alleviate the problem the SSH procedure is carried out in several incremental steps of increasing complexity. First of all improved vertically inhomogeneous velocity (1D) models are derived assuming an isotropic as well as an anisotropic upper mantle. In addition of a slightly better model fit for the anisotropic than for the isotropic model, the latter gives also a somewhat lower Pn-velocity of ~7.90 km/s, compared with ~8.0 km/s for the former. This indicates that inclusion of upper mantle anisotropy into the model is required to obtain physically reasonable Pn-velocities. The results for the P-velocity in the lower crustal layer of the model are less clear, as there appears to be some trade-off in the velocity of that layer and that of the upper mantle. During the course of this part of the study the 3D models have been increasingly refined, starting with a lateral discretization into 15 x 15 blocs

  10. Gravity verification of 3-D crustal structure (CRUST2) for the Eastern Mediterranean

    NASA Astrophysics Data System (ADS)

    Rybakov, M.

    2009-12-01

    CRUST2 - a global 3-D tomography model of the seismic velocity and density structure of the Earth's crust and uppermost mantle (Bassin, C., Laske, G. and Masters, G., The Current Limits of Resolution for Surface Wave Tomography in North America, EOS Trans AGU, 81, F897, 2000) is now public domain data set available from http:// mahi. ucsd.edu/ Gabi/rem.dir/crust/crust2.html.The data are extremely important for various purposes e. g. the seismic monitoring of nuclear explosions etc. Therefore the validity and quality of the CRUST2 should be verified by using the external data such as gravity observations. By extracting the data for the Eastern Mediterranean region (20-40 East and 26-40 North) the set of deep surfaces and densities maps for each layer (2 x 2 degree cell ~250*250km for study region) was compiled. It should be noted that the crust separation was made into three layers (upper, middle and lower crust) instead of usual separation for granite and basalt sub crust. The maps were compared with the existing structural compilations of Cornel University (Seber et al., 2001), Rybakov and Segev, 2004, Segev et al., 2006. The main subjects of comparison were the top of the crystalline basement and Moho surface. That shows the CRUST2.0 model is at a small enough scale to resolve significant lateral variations in crustal properties. Gravity effect of the CRUST2.0 model was calculated using 3-D forward modeling program from three rectangular grids which define the distribution of mass: the top surface (e. g. sea bottom), the bottom surface (e. g. base of soft sediments) and the density of the soft sediments. Calculated gravity was compared with observed gravity data and one can see good coincidence of the subglobal scale gravity pattern. There is no need to mention that regional scale anomalies can’t be seen in the calculated gravity. At whole the 3-D CRUST2 model provides uniform valuable data (e.g. mantle density etc), which can not be obtained by any other way

  11. The 3D crustal structure of Northeastern Tibetan area from seismic tomography

    NASA Astrophysics Data System (ADS)

    Sun, Anhui

    2015-04-01

    The Northeastern Tibetan region is located in the border area of three sub-plates in China, i.e. the Tibetan plateau, North China block and Xinjiang block. Effected simultaneously by the extrusion driven by the India-Eurasia plat collision and the blockage of the Ordos basin, this area has complex geology, strong tectonics activities and suffered from several large historic earthquakes, such as the Haiyuan earthquake (M8.6) in 1920, the Gulang earthquake (M8.0) in 1927. To enhance our understanding of the crustal structure and the interaction between different tectonic blocks of this region, we conduct a three-dimensional (3D) tomographic study by using the arrival time date recorded by regional seismic network. We used 101101 P and 103313 S wave arrival times from 11650 local earthquakes during 1970 to 2013 recorded by 154 permanent seismic stations of the local Seismic Network, installed over five provinces in China, i.e. Gansu, Ningxia, Qinghai, Shanxi, Neimenggu. We first established a 1D primary crustal model from LITHO1.0, an updated crust and lithospheric model of the Earth by weighted averaging. To better performer ray tracing, our inversion involved three discontinuities (including the Moho) with depth variation over the mantle derived from LITHO1.0. Detailed three-dimensional seismic velocity (Vp and Vs) structures of the crust of the Northeastern Tibetan are determined with a horizontal resolution of about 35 km and a depth resolution of 6-20 km. The Poisson's ratio (σ) structure was also estimated after obtained Vp and Vs structures. We detected low-velocity anomalies in the lower crust and relative high-velocity anomalies in the upper crust beneath the Longmenshan faults zone, which are in good agreement with the results of most previous geophysical studies. Our results revealed clear different velocity variation beneath both sides of different tectonic blocks. In addition, we found the correlation between our tomographic result and previous

  12. High-resolution 3D seismic model of the crustal and uppermost mantle structure in Poland

    NASA Astrophysics Data System (ADS)

    Grad, Marek; Polkowski, Marcin; Ostaficzuk, Stanisław R.

    2016-01-01

    in the Moho depth, from 30-35 km in the Paleozoic Platform to 42-52 km in the Precambrian craton. The new model confirms the Moho depth derived from previous compilations. In the TESZ the lower crust has a very high seismic velocity (> 7.0 km/s) which correlates to the high P-wave velocity (about 8.4 km/s) in the uppermost mantle beneath the Polish Basin. The Cratonic area is generally characterized by high P-wave velocities (> 8.2 km/s), while the Phanerozoic area is characterized by velocities of ~ 8.0 km/s. In the TESZ very high velocities of 8.3-8.4 km/s are observed, and the southwestern limitation of this area coincides with a high velocity lower crust, and could be continued to the NW toward the Elbe line. The influence of the structure for teleseismic tomography time residuals of seismic waves traveling through the 3D seismic model was analyzed. Lithological candidates for the crust and uppermost mantle of the EEC and WEP were suggested by comparison to laboratory data. The presented 3D seismic model may make more reliable studies on global dynamics, and geotectonic correlations, particularly for sedimentary basins in the Polish Lowlands, the napped flysch sediment series in the Carpathians, the basement shape, the southwestern edge of the EEC, a high-velocity lower crust and the high-velocity uppermost mantle in the TESZ. Finally, the new 3D velocity model of the crust shows a heterogeneous structure and offers a starting point for the numerical modeling of deeper structures by allowing for a correction of the crustal effects in studies of the mantle heterogeneities.

  13. The upper crustal 3-D resistivity structure of the Kristineberg area, Skellefte district, northern Sweden revealed by magnetotelluric data

    NASA Astrophysics Data System (ADS)

    Hübert, Juliane; Juanatey, María de los Ángeles García; Malehmir, Alireza; Tryggvason, Ari; Pedersen, Laust B.

    2013-02-01

    A 3-D model of the crustal electrical resistivity was constructed from the inversion of magnetotelluric data in the Kristineberg area, Skellefte district, the location of one of Sweden's most successful mining activities. Forward modelling of vertical magnetic transfer data supports our model which was derived from the magnetotelluric impedance only. The dominant features in the 3-D model are the strong conductors at various depth levels and resistive bodies of variable thickness occurring in the shallower subsurface. The deepest conductor, previously associated with the Skellefte crustal conductivity anomaly, is imaged in the southern part of the area as a north-dipping feature starting at ˜4 km depth. Several shallow conductors are attributed to graphite in the black shales defining the contact between the metasedimentary rocks and the underlying metavolcanic rocks. Furthermore, an elongated intermediate depth conductor is possibly associated with alteration zones in the metavolcanic rocks that host the ore occurrences. The most prominent crustal resistors occur in the southern and northern part of the area, where their lateral extent on the surface coincides with the late-orogenic Revsund type intrusions. To the east, a resistive feature can be correlated to the early-orogenic Viterliden intrusion. The 3-D model is compared with two previous 2-D inversion models along two perpendicular profiles. The main electrical features are confirmed with the new model and previous uncertainties regarding 3-D effects, caused by off-profile conductors, can be better assessed in 3-D, although the resolution is lower due to a coarser model discretization. The comparison with seismic sections along two north-south profiles reveals structural correspondence between electrical features, zones of different reflectivity and geological units.

  14. 3D Crustal structure of Longmenshan and its surroundings revealed by receiver function data

    NASA Astrophysics Data System (ADS)

    Sun, Ya; Liu, jianxin

    2015-04-01

    Due to the convergence of India-Eurasia plates and the obstruction from the Sichuan Basin, Longmenshan (LMS) has suffered the steepest uplifting in the eastern Tibetan Plateau. However, the mechanisms of surface uplift are still controversial. In this paper, we estimate the crustal structure and deformation under LMS and its surroundings by analyzing a large amount of receiver functions data recorded by regional seismic networks of the China Earthquake Administration. A comprehensive splitting measurement technique is used to calculate the seismic anisotropy from azimuthal variations of receiver functions in this paper. Our results show that most of the seismic stations located near LMS exhibit significant seismic anisotropy with the splitting time of 0.22-0.94s and a fast polarization direction of NW-SE. Both the splitting time and fast polarization are comparable to those estimated from SKS/SKKS data, indicating that half of the SKS/SKKS splitting time may be caused by the lower crustal deformation. It also indicates that the deformation patterns of the crust and upper mantle may be vertically coherent, but incoherent between the upper crust and lower crust based on comparison of GPS data. In addition, both the Moho depth and Vp/Vs ratio are estimated using the H-κ stacking method. The results show a distinct difference between the west of LMS and the Sichuan Basin. Stations on the west of LMS have high Vp/Vs values (1.74-1.86) and very thick crust (>55 km), while a relatively low Vp/Vs (~1.70) and shallow Moho depth (<45 km) for the stations on the east of LMS. All of these observations sustain a scenario in which, the lower crustal materials flow and accumulate in the southeastern Songpan-Ganzi and LMS region. Combined with the observation of low effective elastic thickness and a thin lithosphere, we suggest that this lower crustal material may partly extrude along a subvertical trajectory into the weak mantle lithosphere as a result of the continuous

  15. Crustal and Uppermost Mantle Structure of the Atlas Mountains of Morocco Revealed from 3-D Inversion of Magnetotelluric Data

    NASA Astrophysics Data System (ADS)

    Kiyan, D.; Jones, A. G.; Fullea, J.; Ledo, J.; Siniscalchi, A.; Romano, G.

    2013-12-01

    The overarching objectives of the second phase of the PICASSO (Program to Investigate Convective Alboran Sea System Overturn) project and the concomitant TopoMed (Plate re-organization in the western Mediterranean: Lithospheric causes and topographic consequences - an ESF EUROSCORES TOPO-EUROPE project) project are (i) to provide new electrical conductivity constraints on the crustal and lithospheric structures of the Atlas Mountains, and (ii) to test the hypotheses for explaining the observation of a 'missing' mantle root inferred from surface heat flow, gravity and geoid anomalies, elevation and seismic data modeling (i.e. Zeyen et al., 2005; Teixell et al., 2005; Fullea et al., 2010). We present the results from three-dimensional (3-D) MT inversion of data from two MT profiles employing the parallel version of Modular system for Electromagnetic inversion (ModEM; Egbert & Kelbert, 2012) code. For the profile in eastern Morocco, passing through Midelt, a distinct conductivity difference between the Middle-High Atlas (conductive) and Anti Atlas (resistive) correlates with the South Atlas Front fault, the depth extent of which appears to be limited to the uppermost mantle (approximately 55 km). In all inverse solutions, the crust and the upper mantle show a resistive signature (750 Ωm - 1,000 Ωm) beneath the Anti Atlas to a depth of 100 km, which is the part of stable West African Craton. Our results are at variance with the proposed thin lithosphere beneath the Middle-High Atlas as we see no evidence for a shallow asthenosphere. Our second profile lies in western Morocco traversing through Marrakech. For the first time, the electrical resistivity distribution in the crust and in the upper mantle of Western High Atlas has been studied. Our 3-D resistivity model shows that conductive (1-20 Ωm) western High Atlas is confined by two resistive basins (>1,000 Ωm), Souss basin to the south and Houz basin to the north. At the southern boundary of the western High Atlas

  16. 3-D crustal structure of the western United States: application of Rayleigh-wave ellipticity extracted from noise cross-correlations

    NASA Astrophysics Data System (ADS)

    Lin, Fan-Chi; Tsai, Victor C.; Schmandt, Brandon

    2014-08-01

    We present a new 3-D seismic model of the western United States crust derived from a joint inversion of Rayleigh-wave phase velocity and ellipticity measurements using periods from 8 to 100 s. Improved constraints on upper-crustal structure result from use of short-period Rayleigh-wave ellipticity, or Rayleigh-wave H/V (horizontal to vertical) amplitude ratios, measurements determined using multicomponent ambient noise cross-correlations. To retain the amplitude ratio information between vertical and horizontal components, for each station, we perform daily noise pre-processing (temporal normalization and spectrum whitening) simultaneously for all three components. For each station pair, amplitude measurements between cross-correlations of different components (radial-radial, radial-vertical, vertical-radial and vertical-vertical) are then used to determine the Rayleigh-wave H/V ratios at the two station locations. We use all EarthScope/USArray Tranportable Array data available between 2007 January and 2011 June to determine the Rayleigh-wave H/V ratios and their uncertainties at all station locations and construct new Rayleigh-wave H/V ratio maps in the western United States between periods of 8 and 24 s. Combined with previous longer period earthquake Rayleigh-wave H/V ratio measurements and Rayleigh-wave phase velocity measurements from both ambient noise and earthquakes, we invert for a new 3-D crustal and upper-mantle model in the western United States. Correlation between the inverted model and known geological features at all depths suggests good resolution in five crustal layers. Use of short-period Rayleigh-wave H/V ratio measurements based on noise cross-correlation enables resolution of distinct near surface features such as the Columbia River Basalt flows, which overlie a thick sedimentary basin.

  17. 3D Tomographic Imaging of the Crustal Velocity Structure beneath the Marmara Sea using Air-gun and Earthquake Data

    NASA Astrophysics Data System (ADS)

    Tarancioglu, Adil; Kocaoglu, Argun H.; Ozalaybey, Serdar

    2014-05-01

    The objective of this study is to investigate the local seismicity and obtain a detailed three-dimensional crustal velocity structure beneath the Marmara Sea in an area surrounding the North Anatolian Fault Zone (NAFZ) by tomographic inversion using both controlled-source (air-gun) and earthquake data. The tomographic inversion is carried out by using the local earthquake tomography code SIMUL2000. Two sets of seismological data, collected in 2006 (EOSMARMARA experiment) and 2001 (SEISMARMARA experiment), are re-processed and used in this study. A total of 441 high quality earthquakes and 452 air-gun shots recorded by a total of 53 Ocean Bottom Seismometers (OBS) are selected for the simultaneous inversion for velocity and hypocentral parameters. The OBS location and time-drift errors are identified from air-gun shot records by a grid search method and required corrections are made on the travel time data. The initial (reference) velocity model and earthquake locations required for the three dimensional tomographic inversion are derived from the one-dimensional velocity model obtained by using the VELEST algorithm in which a subset of earthquakes are selected such that phase readings were made by at least five stations and maximum azimuthal gap was 180o. The inversion results are checked for initial model dependence and the effect of damping factor. The reliability of the results is also evaluated in terms of derivative-weighted-sum, resolution-diagonal-elements values and checkerboard tests. The hypocenter locations of the local earthquakes have been remarkably improved by the three-dimensional velocity model obtained from the tomographic inversion. The three-dimensional velocity model shows that the Tekirdag, Central and Cinarcik Basins are characterized generally by lower Vp (3.0 - 3.5 km/s) values and most of the earthquakes across these regions are located at the depths of 10 to 17 km, about 5 km deeper than those obtained from the one-dimensional reference

  18. Exploring Geothermal Energy Potential in Ireland through 3-D Geophysical-Petrological Modelling of Surface Heat-Flow and Crustal and Upper-Mantle Structure

    NASA Astrophysics Data System (ADS)

    Fullea, J.; Muller, M. R.; Jones, A. G.

    2012-04-01

    Little is known of Ireland's deep, low-enthalpy geothermal resources and the potential for space heating and/or electricity generation based on geothermal energy to displace Ireland's significant reliance on carbon-based fuels. IRETHERM (www.iretherm.ie) is a four-and-a-half year, all-island, academic-government-industry collaborative project, initiated in 2011, with the overarching objective of developing a strategic and holistic understanding of Ireland's geothermal energy potential through integrated modelling of new and existing geophysical and geological data. One of the challenges in searching for deep geothermal resources in the relatively unexplored setting of Ireland lies in identifying those areas most likely to support significantly elevated temperatures at depth. Available borehole data, although sparse and clustered around areas of mineral and hydrocarbon interest, suggest a marked regional increase in surface heat-flow across Ireland, from ~40 mW/m2 in the south to >80 mW/m2 in the north. The origins of both the observed regional heat-flow trend and local temperature anomalies have not been investigated and are not currently understood. Although variations in the structure of the crust and lithosphere have been revealed by a number of active-source seismic and teleseismic experiments, their effects on surface heat-flow have not been modelled. Bulk 3-D variation in crustal heat-production across Ireland, which may contribute significantly to the observed regional and local temperature variations, has also not been determined. We investigate the origins of Ireland's regional heat-flow trend and regional and local temperature variations using the software package LitMod. This software combines petrological and geophysical modelling of the lithosphere and sub-lithospheric upper mantle within an internally consistent thermodynamic-geophysical framework, where all relevant properties are functions of temperature, pressure and chemical composition. The major

  19. Constraints on Crustal Shear Wave Velocity Structure beneath Central Tibet from 3-D Multi-scale Finite-frequency Rayleigh Wave Travel-time Tomography

    NASA Astrophysics Data System (ADS)

    Jheng, Y.; Hung, S.; Zhou, Y.; Chang, Y.

    2012-12-01

    Surface wave travel-time tomography has been widely used as a powerful strategy to image shear wave velocity structure of the Earth's crust and upper mantle, providing comparable information other than body wave tomography. Traditionally, lateral variations of dispersive phase velocities are first obtained at multiple frequencies and then used to invert for shear wave velocity with 1-D depth-dependent sensitivity kernels. However, this approach runs short on considering the directional- and depth-dependence of scattering while surface wave propagating through laterally heterogeneous Earth. To refrain from these shortcomings, we here provide a fully 3-D finite-frequency method based on the Born scattering theory formulated with surface wave mode summation, and apply it to regional fundamental Rayleigh wave travel-time tomography in central Tibet. Our data were collected from Project Hi-CLIMB, which deployed an N-S trending linear array of over 100 broadband seismic stations with a large aperture of 800 km and very dense spacing of ~3-8 km across the Lhasa and Qiangtang terranes during 2004-2005. We follow a standard procedure of ambient noise cross correlation to extract empirical Green's functions of fundamental Rayleigh waves at 10-33 s between station pairs. A multi-taper method is employed to measure the phase differences as a function of period between observed and synthetic Rayleigh waves as well as the corresponding sensitivity kernels for the measured phase delays to 3-D shear wave velocity perturbations in a spherically-symmetric model suitable for central Tibet. A wavelet-based, multi-scale parameterization is invoked in the tomographic inversion to deal with the intrinsically multi-scale nature of unevenly distributed data and resolve the structure with data-adaptive spectral and spatial resolutions. The preliminary result shows that to the north of the Banggong-Nujiang suture (BNS), the crustal shear wave velocity beneath the Qiangtang terrane is

  20. Simultaneous inversion for 3D crustal and lithospheric structure and regional hypocenters beneath Germany in the presence of an anisotropic upper mantle

    NASA Astrophysics Data System (ADS)

    Koch, M.; Muench, T.

    2010-12-01

    There is now ample evidence from both refraction seismic studies and from more recent local earthquake travel-time analysis of some of the authors that large sections of the upper mantle underneath Europe and Germany, in particular, are anisotropic. Employing a modified version of the method of simultaneous inversion for structure and hypocenters (SSH) of the first author, including a priori known upper mantle anisotropy, a full 3D SSH-inversion underneath Germany is carried out. Regional travel times from local events occurring between 1975 - 2003 are used which, after application of several selection criteria, results in ~1300 events with a total of ~30000 P- and S-phases for the SSH inversion. The SSH procedure is carried out in several incremental steps. First of all improved 1D seismic velocity models are derived assuming an isotropic as well as an anisotropic upper mantle. In addition of a slightly better model fit for the anisotropic than for the isotropic model, the latter gives also a somewhat lower Pn-velocity of ~7.90 km/s, compared with ~8.0 km/s for the former. This indicates that inclusion of upper mantle anisotropy into the SSH model is required to obtain physically reasonable Pn-velocities. The results for the P-velocity in the lower crust are less clear, because of some trade-off with the upper mantle layer. Increasingly refined 3D seismic models are then computed, starting with a lateral discretization into 15 x 15 blocs (=40 x 40 km per bloc) and finally going up to 35 × 35 blocs, (=16 x 16 km). For each of the models, inversion solutions for the isotropic, as well as the anisotropic case are examined. The quality of the solution is estimated by means of various tests for resolution, covariance and other trade-off characteristics of the data- and the model-space. Significant improvements for both the isotropic and anisotropic upper mantle cases are obtained for full 3D SSH inversion models. Similar to the 1D Pn-velocity models there are

  1. Investigation of the deep crustal structure and magmatic activity at the NW Hellenic Volcanic Arc with 3-D aeromagnetic inversion and seimotectonic analysis.

    NASA Astrophysics Data System (ADS)

    Efstathiou, Angeliki; Tzanis, Andreas; Chailas, Stylianos; Stamatakis, Michael

    2013-04-01

    We report the results of a joint analysis of geophysical (aeromagnetic) and seismotectonic data, applied to the investigation of the deep structure, magmatic activity and geothermal potential of the north-western stretches of the Hellenic Volcanic Arc (HVA). The HVA is usually considered to be a single arcuate entity stretching from Sousaki (near Corinth) at the NW, to Nisyros Island at the SE. However, different types of and their ages indicate the presence of two different volcanic groups. Our study focuses on the northern part of the west (older) volcanic group and includes the Crommyonian (Sousaki) volcanic field at the west end of Megaris peninsula (east margin on the contemporary Corinth Rift), the Aegina and Methana volcanic complex at the Saronic Gulf, where typical Quaternary calc-alkaline volcanics predominate, and the Argolid peninsula to the south and south-west. In addition to the rocks associated with Quaternary volcanism, the study area includes a series of Mesozoic ultramafic (ophiolitic) outcrops at the Megaris peninsula, to the north and north-east of the Crommyonian volcanic field, as well as throughout the Argolid. A major deep structural and tectonic feature of the study area, and one with profound influence on crustal deformation and the evolution of rapidly deforming extensional structures like the Corinth Rift and the Saronic Gulf, is the local geometry and dynamics of the African oceanic crust subducting beneath the Aegean plate. Locally, the subducting slab has a NNW strike and ENE plunge, with the dip angle changing rapidly (steepening) approx. beneath the Argolid. The aeromagnetic data was extracted from the recently (re)compiled aeromagnetic map of Greece (Chailas et al, 2010) and was inverted with the UBC-GIF magnetic inversion suite (Li and Oldenburg, 1996). The inversion included rigorous geological constraints introduced by means of numerous in-situ magnetic susceptibility measurements. The inversion has imaged several isolated

  2. Anisotropic 3-D Crustal Velocity Structure of Idaho/ Oregon from a Joint Inversion of Group and Phase Velocities of Love and Rayleigh Waves from Ambient Seismic Noise: Results from the IDOR Project

    NASA Astrophysics Data System (ADS)

    Bremner, P. M.; Panning, M. P.; Russo, R.; Mocanu, V. I.; Stanciu, A. C.; Torpey, M. E.; Hongsresawat, S.; VanDecar, J. C.

    2015-12-01

    We present new 3-D radially anisotropic and isotropic crustal velocity models beneath central Idaho and eastern Oregon. We produced the velocity models from Love and horizontal component Rayleigh wave group and phase velocity measurements on the IDaho/ORegon (IDOR) Passive seismic network, 86 broadband seismic stations, dataset using ambient noise tomography and the methods of Gallego et. al (2010) and Lin et. al (2008). We calculated inter-station group/phase velocities in narrow frequency bands from travel-time measurements of the rotated stacked horizontal component cross-correlations (bandpass filtered between 2 and 30 seconds), which we used to invert for velocity structure beneath the network. We derived group and phase velocity maps for each frequency band using the damped least-squares inversion method of Tarantola (2005), and then jointly inverted for velocity with depth. Moho depths are prescribed in the joint inversions based on receiver functions, also from the IDOR seismic data, and provides a starting crustal velocity model. Goals of our work include refining models of crustal structure in the accreted Blue Mountain terranes in the western study area; determining the depth extent of the Salmon River Suture/West Idaho Shear Zone (WISZ), which crosses north-south through the middle of the network; determining the architecture of the Idaho batholith, an extensive largely crustal-derived pluton; and examining the nature of the autochthonous (?) North American crust and lithosphere beneath and east of the batholith.

  3. Complex 3D crustal model of Asia region

    NASA Astrophysics Data System (ADS)

    Baranov, A. A.

    2009-04-01

    The Southern and Central Asia is tectonically complex region with great collision between Asian and Indian plates and its evolution is strongly related to the active subduction along the Pacific border. Previous global crustal model (CRUST 2.0.) for Asia region have resolution 2x2 degree. Model AsCRUST-08 (Baranov et al., 2008) of Central and Southern Asia with resolution of 1x1 degree was sufficiently improved in several regions and we built integrated model of the crust for Asia region. Also we add several regions in North Eurasia as Mongolia, Kazahstan and others. For such regions as Red and Dead sea, Northern China, Southern India we built regional maps with more detailed resolution. It was used data of deep seismic reflection, refraction and receiver functions studies from published papers. The existing data were verified and crosschecked. As the first result, we demonstrate a new Moho map for the region. The complex crustal model consists of three layers: upper, middle and lower crust. Besides depth to the boundaries, we provide average P-wave velocities in the upper, middle and lower parts of the crystalline crust. Limits for Vp velocities are: for upper crust 5.5-6.2 km/s, for middle 6.0-6.6 km/s, for lower crust 6.6-7.5km/s. Also we recalculated seismic P velocity data to density in crustal layers using rheology properties and geology data. Conclusions: Moho map and the velocity structure of the crust are much more heterogeneous than in previous maps CRUST 2.0. (Bassin et al., 2000), and CRUST 5.1. (Mooney et al., 1998). Our model offers a starting point for numerical modeling of deep structures by allowing correction for crustal effects beforehand and to resolve trade-off with mantle heterogeneities. This model will be used as a starting point in the gravity modeling of the lithosphere and mantle structure. [1] A. Baranov et al., First steps towards a new crustal model of South and Central Asia , Geophysical Research Abstracts, Vol. 10, EGU2008-A-05313

  4. 3-D Crustal Velocity Structure of Central Idaho/ Eastern Oregon from Joint Inversion of Rayleigh Wave Group and Phase Velocities Derived from Ambient Seismic Noise: Newest Results from the IDOR Project

    NASA Astrophysics Data System (ADS)

    Bremner, P. M.; Panning, M. P.; Russo, R. M.; Mocanu, V. I.; Stanciu, A. C.; Torpey, M. E.; Hongsresawat, S.; VanDecar, J. C.

    2014-12-01

    We present the latest 3-D isotropic crustal velocity model beneath central Idaho and eastern Oregon. We produced the velocity model from vertical component Rayleigh wave group and phase velocity measurements on data from the IDaho/ORegon (IDOR) Passive seismic network, 86 broadband seismic stations, using ambient noise tomography and the methods of Gallego et. al (2010) and Lin et. al (2008). We calculated inter-station group/phase velocities in narrow frequency bands from travel-time measurements of the stacked cross-correlations (bandpass filtered between 2 and 30 seconds), which we used to invert for velocity structure beneath the network. Goals of our work include refining models of crustal structure in the accreted Blue Mountain terranes in the western study area; determining the depth extent of the Salmon River Suture/West Idaho Shear Zone (WISZ), which crosses north-south through the middle of the network; determining the architecture of the Idaho batholith, an extensive largely crustal-derived pluton; and examining the nature of the autochthonous (?) North American crust and lithosphere beneath and east of the batholith. We derived Rayleigh wave group and phase velocity maps for each frequency band using the damped least-squares inversion method of Tarantola (2005), and then jointly inverted for velocity with depth. Moho depths are prescribed in the joint inversions based on receiver functions, also from the IDOR seismic data, and provides a starting crustal velocity model. 3-D checkerboard resolution tests indicate lateral resolution of better than 40 km. Preliminary results show higher S wave velocities in the western study area, and lower velocities in the lower crust on the east side of the network, consistent with Basin-and-Range style extension there. A tabular velocity anomaly juxtaposing higher above lower seismic velocities dips shallow west in the midcrust on the west side of the network.

  5. 3D imaging of crustal structure under the Piedmont province in central Virginia, from reflection RVSP processing of aftershock recordings from the August 23, 2011 Virginia earthquake

    NASA Astrophysics Data System (ADS)

    Quiros, D. A.; Brown, L. D.; Cabolova, A.; Davenport, K. K.; Hole, J. A.; Mooney, W. D.

    2013-12-01

    Aftershocks from the magnitude Mw 5.8 August 23, 2011, central Virginia earthquake were recorded using an unusually dense array of seismometers in what has been termed an AIDA (Aftershock Imaging with Dense Arrays) deployment. Over 200 stations were deployed in the epicentral region of this event to a) more precisely determine hypocentral locations, b) more accurately define velocity structure in the aftershock zone, c) characterize propagation characteristics of the crust in the area, and d) image geologic structures in the hypocentral volume with reflection techniques using aftershocks as sources. The AIDA-Virginia experiment successfully recorded a large number of aftershocks from which local tomographic velocity estimates and accurate hypocentral locations were obtained. These results facilitated the use of aftershocks as sources for reflection imaging. In this study we demonstrate how earthquake sources recorded by surface arrays can be treated using the imaging techniques associated with Vertical Seismic Profiling (VSP), in particular a variant known as Reverse VSP (RVSP). The central VSP processing algorithms used for this study are VSP normal moveout (VSPnmo) and VSP-to-Common Reflection Point (CRP). Applying these techniques to individual aftershocks from the Virginia experiment results in 3D reflection images of structural complexity in the immediate vicinity of the aftershocks. The most prominent feature observed on these 3D images is a strong moderately east-dipping reflector at a depth of approximately 6 to 8 km that directly underlies, and is continuous beneath, the more steeply dipping aftershock zone. We interpret this reflector as part of a complex imbricate thrust sequence associated with Paleozoic convergence during the Appalachian orogeny. Its apparent continuity beneath the fault zone implied by the aftershock's hypocenters suggests that this inferred fault zone has little or no cumulative offset, supporting the speculation that this event

  6. Full-3D waveform tomography of Southern California crustal structure by using earthquake recordings and ambient noise Green's functions based on adjoint and scattering-integral methods

    NASA Astrophysics Data System (ADS)

    Lee, E.; Chen, P.; Jordan, T. H.; Maechling, P. J.; Denolle, M.; Beroza, G. C.

    2013-12-01

    We apply a unified methodology for seismic waveform analysis and inversions to Southern California. To automate the waveform selection processes, we developed a semi-automatic seismic waveform analysis algorithm for full-wave earthquake source parameters and tomographic inversions. The algorithm is based on continuous wavelet transforms, a topological watershed method, and a set of user-adjustable criteria to select usable waveform windows for full-wave inversions. The algorithm takes advantages of time-frequency representations of seismograms and is able to separate seismic phases in both time and frequency domains. The selected wave packet pairs between observed and synthetic waveforms are then used for extracting frequency-dependent phase and amplitude misfit measurements, which are used in our seismic source and structural inversions. Our full-wave waveform tomography uses the 3D SCEC Community Velocity Model Version 4.0 as initial model, a staggered-grid finite-difference code to simulate seismic wave propagations. The sensitivity (Fréchet) kernels are calculated based on the scattering integral and adjoint methods to iteratively improve the model. We use both earthquake recordings and ambient noise Green's functions, stacking of station-to-station correlations of ambient seismic noise, in our full-3D waveform tomographic inversions. To reduce errors of earthquake sources, the epicenters and source parameters of earthquakes used in our tomographic inversion are inverted by our full-wave CMT inversion method. Our current model shows many features that relate to the geological structures at shallow depth and contrasting velocity values across faults. The velocity perturbations could up to 45% with respect to the initial model in some regions and relate to some structures that do not exist in the initial model, such as southern Great Valley. The earthquake waveform misfits reduce over 70% and the ambient noise Green's function group velocity delay time variance

  7. Investigation of the deep crustal structure and magmatic activity at the NW Hellenic Volcanic Arc with 3-D aeromagnetic inversion and seimotectonic analysis.

    NASA Astrophysics Data System (ADS)

    Efstathiou, Angeliki; Tzanis, Andreas; Chailas, Stylianos; Stamatakis, Michael

    2013-04-01

    We report the results of a joint analysis of geophysical (aeromagnetic) and seismotectonic data, applied to the investigation of the deep structure, magmatic activity and geothermal potential of the north-western stretches of the Hellenic Volcanic Arc (HVA). The HVA is usually considered to be a single arcuate entity stretching from Sousaki (near Corinth) at the NW, to Nisyros Island at the SE. However, different types of and their ages indicate the presence of two different volcanic groups. Our study focuses on the northern part of the west (older) volcanic group and includes the Crommyonian (Sousaki) volcanic field at the west end of Megaris peninsula (east margin on the contemporary Corinth Rift), the Aegina and Methana volcanic complex at the Saronic Gulf, where typical Quaternary calc-alkaline volcanics predominate, and the Argolid peninsula to the south and south-west. In addition to the rocks associated with Quaternary volcanism, the study area includes a series of Mesozoic ultramafic (ophiolitic) outcrops at the Megaris peninsula, to the north and north-east of the Crommyonian volcanic field, as well as throughout the Argolid. A major deep structural and tectonic feature of the study area, and one with profound influence on crustal deformation and the evolution of rapidly deforming extensional structures like the Corinth Rift and the Saronic Gulf, is the local geometry and dynamics of the African oceanic crust subducting beneath the Aegean plate. Locally, the subducting slab has a NNW strike and ENE plunge, with the dip angle changing rapidly (steepening) approx. beneath the Argolid. The aeromagnetic data was extracted from the recently (re)compiled aeromagnetic map of Greece (Chailas et al, 2010) and was inverted with the UBC-GIF magnetic inversion suite (Li and Oldenburg, 1996). The inversion included rigorous geological constraints introduced by means of numerous in-situ magnetic susceptibility measurements. The inversion has imaged several isolated

  8. 3D-graphite structure

    SciTech Connect

    Belenkov, E. A. Ali-Pasha, V. A.

    2011-01-15

    The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.

  9. 3D crustal structure and long-period ground motions from a M9.0 megathrust earthquake in the Pacific Northwest region

    NASA Astrophysics Data System (ADS)

    Olsen, Kim B.; Stephenson, William J.; Geisselmeyer, Andreas

    2008-04-01

    We have developed a community velocity model for the Pacific Northwest region from northern California to southern Canada and carried out the first 3D simulation of a Mw 9.0 megathrust earthquake rupturing along the Cascadia subduction zone using a parallel supercomputer. A long-period (<0.5 Hz) source model was designed by mapping the inversion results for the December 26, 2004 Sumatra-Andaman earthquake (Han et al., Science 313(5787):658-662, 2006) onto the Cascadia subduction zone. Representative peak ground velocities for the metropolitan centers of the region include 42 cm/s in the Seattle area and 8-20 cm/s in the Tacoma, Olympia, Vancouver, and Portland areas. Combined with an extended duration of the shaking up to 5 min, these long-period ground motions may inflict significant damage on the built environment, in particular on the highrises in downtown Seattle.

  10. 3D crustal structure and long-period ground motions from a M9.0 megathrust earthquake in the Pacific Northwest region

    USGS Publications Warehouse

    Olsen, K.B.; Stephenson, W.J.; Geisselmeyer, A.

    2008-01-01

    We have developed a community velocity model for the Pacific Northwest region from northern California to southern Canada and carried out the first 3D simulation of a Mw 9.0 megathrust earthquake rupturing along the Cascadia subduction zone using a parallel supercomputer. A long-period (<0.5 Hz) source model was designed by mapping the inversion results for the December 26, 2004 Sumatra–Andaman earthquake (Han et al., Science 313(5787):658–662, 2006) onto the Cascadia subduction zone. Representative peak ground velocities for the metropolitan centers of the region include 42 cm/s in the Seattle area and 8–20 cm/s in the Tacoma, Olympia, Vancouver, and Portland areas. Combined with an extended duration of the shaking up to 5 min, these long-period ground motions may inflict significant damage on the built environment, in particular on the highrises in downtown Seattle.

  11. Crustal structure and fluid distribution beneath the southern part of the Hidaka collision zone revealed by 3-D electrical resistivity modeling

    NASA Astrophysics Data System (ADS)

    Ichihara, Hiroshi; Mogi, Toru; Tanimoto, Kengo; Yamaya, Yusuke; Hashimoto, Takeshi; Uyeshima, Makoto; Ogawa, Yasuo

    2016-04-01

    The Hidaka collision zone, where the Kurile and northeastern (NE) Japan arcs collide, provides a useful study area for elucidating the processes of arc-continent evolution and inland earthquakes. To produce an image of the collision structure and elucidate the mechanisms of anomalously deep inland earthquakes such as the 1970 Hidaka earthquake (M6.7), we conducted magnetotelluric observations and generated a three-dimensional resistivity distribution in the southern part of the Hidaka collision zone. The modeled resistivity was characterized by a high resistivity area in the upper crust of the Kurile arc corresponding to metamorphic rocks. The model also showed conductive zones beneath the center of the collision zone. The boundary between the resistive and conductive areas corresponds geometrically to the Hidaka main thrust, which is regarded as the arc-arc boundary. The correspondence supports the collision model that the upper-middle part of crust in the Kurile arc is obducting over the NE Japan arc. The conductive areas were interpreted as fluid-filled zones associated with collision processes and upwelling of dehydrated fluid from the subducting Pacific slab. The fluid flow possibly contributes to over-pressurized conduction that produces deep inland earthquakes. We also observed a significant conductive anomaly beneath the area of Horoman peridotite, which may be related to the uplift of mantle materials to the surface.

  12. Sydney-Gunnedah-Bowen Basin deep 3D structure

    NASA Astrophysics Data System (ADS)

    Danis, Cara

    2012-01-01

    Studies of the Sydney-Gunnedah-Bowen Basin (SGBB), one of the largest extensional rift sedimentary basins on the east coast of Australia, lack an understanding of the 3D upper crustal structure. Understanding of the subsurface structure is essential for many areas of resource exploration, development and management, as well as scientific research. Geological models provide a way to visualise and investigate the subsurface structure. The integrated regional scale gravity modelling approach, which uses boreholes and seismic data constraints, provides an understanding of the upper crustal structure and allows the development of a 3D geological model which can be used as the architectural framework for many different applications. This work presents a 3D geological model of the SGBB developed for application in high resolution thermal models. It is the culmination of geological surfaces derived from the interpolation of previous regional scale 2D gravity models and numerous borehole records. The model outlines the basement structure of the SGBB and provides information on depth to basement, depth to basal volcanics and thickness of overlying sediments. Through understanding the uncertainties, limitations, confidence and reliability of this model, the 3D geological model can provide the ideal framework for future research.

  13. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  14. Global 3-D Hybrid Simulations of Mars and the Effect of Crustal Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Brecht, S. H.; Ledvina, S. A.; Luhmann, J. G.

    2001-12-01

    Mars is not protected from the solar wind by a strong intrinsic magnetic field. Further, Mars is a very small planet. These two aspects of Mars mean that the solar wind interaction with the planet is both direct and kinetic in behavior. The large gyroradius of the incoming solar wind and the large gyroradius of the pick up ions make the solar wind interaction with Mars very unique. Over the years the authors using a 3-D kinetic hybrid particle code have studied this planet. Mars Global Surveyor has produced many exciting discoveries. Probably the most significant and unexpected was the presence of the crustal magnetic fields on the surface of the planet. The presence of these strong crustal fields suggests that the solar wind interaction with Mars will be altered. In fact, it suggests that the loss rate of pick up ions and the shape of the Martian magnetosphere will be substantially changed. Results will be presented from our latest 3-D hybrid particle code simulations of Mars where models for the crustal magnetic field have been inserted into the simulations. Particular emphasis will be placed on changes to the magnetic field topology and the change in the rate of pick up ions.

  15. Structured light field 3D imaging.

    PubMed

    Cai, Zewei; Liu, Xiaoli; Peng, Xiang; Yin, Yongkai; Li, Ameng; Wu, Jiachen; Gao, Bruce Z

    2016-09-01

    In this paper, we propose a method by means of light field imaging under structured illumination to deal with high dynamic range 3D imaging. Fringe patterns are projected onto a scene and modulated by the scene depth then a structured light field is detected using light field recording devices. The structured light field contains information about ray direction and phase-encoded depth, via which the scene depth can be estimated from different directions. The multidirectional depth estimation can achieve high dynamic 3D imaging effectively. We analyzed and derived the phase-depth mapping in the structured light field and then proposed a flexible ray-based calibration approach to determine the independent mapping coefficients for each ray. Experimental results demonstrated the validity of the proposed method to perform high-quality 3D imaging for highly and lowly reflective surfaces. PMID:27607639

  16. Seismic shaking scenarios in realistic 3D crustal model of Northern Italy

    NASA Astrophysics Data System (ADS)

    Molinari, I.; Morelli, A.; Basini, P.; Berbellini, A.

    2013-12-01

    Simulation of seismic wave propagation in realistic crustal structures is a fundamental tool to evaluate earthquake-generated ground shaking and assess seismic hazard. Current-generation numerical codes, and modern HPC infrastructures, allow for realistic simulations in complex 3D geologic structures. We apply such methodology to the Po Plain in Northern Italy -- a region with relatively rare earthquakes but having large property and industrial exposure, as it became clear during the two M~6 events of May 20-29, 2012. Historical seismicity is well known in this region, with maximum magnitudes estimates reaching M~7, and wave field amplitudes may be significantly amplified by the presence of the very thick sedimentary basin. Our goal is to produce estimates of expected ground shaking in Northern Italy through detailed deterministic simulations of ground motion due to expected earthquakes. We defined a three-dimensional model of the earth's crust using geo-statistical tools to merge the abundant information existing in the form of borehole data and seismic reflection profiles that had been shot in the '70s and the '80s for hydrocarbon exploration. Such information, that has been used by geologists to infer the deep structural setup, had never been merged to build a 3D model to be used for seismological simulations. We implement the model in SPECFEM3D_Cartesian and a hexahedral mesh with elements of ~2km, that allows us to simulate waves with minimum period of ~2 seconds. The model has then been optimized through comparison between simulated and recorded seismograms for the ~20 moderate-magnitude events (Mw > 4.5) that have been instrumentally recorded in the last 15 years. Realistic simulations in the frequency band of most common engineering relevance -- say, ~1 Hz -- at such a large scale would require an extremely detailed structural model, currently not available, and prohibitive computational resources. However, an interest is growing in longer period ground

  17. 3D crustal-scale heat-flow regimes at a developing active margin (Taranaki Basin, New Zealand)

    NASA Astrophysics Data System (ADS)

    Kroeger, K. F.; Funnell, R. H.; Nicol, A.; Fohrmann, M.; Bland, K. J.; King, P. R.

    2013-04-01

    The Taranaki Basin in the west of New Zealand's North Island has evolved from a rifted Mesozoic Gondwana margin to a basin straddling the Neogene convergent Australian-Pacific plate margin. However, given its proximity to the modern subduction front, Taranaki Basin is surprisingly cold when compared to other convergent margins. To investigate the effects of active margin evolution on the thermal regime of the Taranaki Basin we developed a 3D crustal-scale forward model using the petroleum industry-standard basin-modelling software Petromod™. The crustal structure inherited from Mesozoic Gondwana margin breakup and processes related to modern Hikurangi convergent margin initiation are identified to be the main controls on the thermal regime of the Taranaki Basin. Present-day surface heat flow across Taranaki on average is 59 mW/m2, but varies by as much as 30 mW/m2 due to the difference in crustal heat generation between mafic and felsic basement terranes alone. In addition, changes in mantle heat advection, tectonic subsidence, crustal thickening and basin inversion, together with related sedimentary processes result in variability of up to 10 mW/m2. Modelling suggests that increased heating of the upper crust due to additional mantle heat advection following the onset of subduction is an ongoing process and heating has only recently begun to reach the surface, explaining the relatively low surface heat flow. We propose that the depth of the subducted slab and related mantle convection processes control the thermal and structural regimes in the Taranaki Basin. The thermal effects of the subduction initiation process are modified and overprinted by the thickness, structure and composition of the lithosphere.

  18. 3D crustal and lithospheric model of the Arabia-Eurasia collision zone

    NASA Astrophysics Data System (ADS)

    Motavalli-Anbaran, Seyed-Hani; Zeyen, Hermann; Jamasb, Ali

    2016-05-01

    Three-dimensional joined inversion of topography, gravity and geoid data was carried out in the collision zone between the Eurasian and Arabian plates, comprising Central and Eastern Anatolia, the Black Sea Basin and the Caucasus region. The 3D algorithm, first introduced by Motavalli-Anbaran et al. (2013), is based on a Bayesian approach with Gaussian density functions in which the targeted area is divided into vertical columns, each comprised of four layers namely water (of known thickness i.e. bathymetry) if present, crust, lithospheric mantle, and asthenosphere. The inversion results are Moho depth, average crustal density and depth to the lithosphere-asthenosphere boundary, defined here as the 1350 °C isotherm. Existing seismic Moho depths were used as a priori information in order to constrain crustal thicknesses. Thickest crust (up to 50 km) was found underneath the Great Caucasus Mountains, thinnest crust (22-25 km) underneath the Black Sea Basin. The East-Anatolian plateau is underlain by relatively thick crust (up to 45 km), thinning to less than 40 km towards the Central Anatolian Plateau. Eastern Anatolia and the eastern part of Central Anatolia are underlain by strongly thinned lithosphere (up to 100 km). Thickest lithosphere (up to 200 km) underlies the Caspian Basin and the Russian Platform.

  19. Inferential modeling of 3D chromatin structure

    PubMed Central

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-01-01

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen. PMID:25690896

  20. 3D structure and nuclear targets

    NASA Astrophysics Data System (ADS)

    Dupré, Raphaël; Scopetta, Sergio

    2016-06-01

    Recent experimental and theoretical ideas are laying the ground for a new era in the knowledge of the parton structure of nuclei. We report on two promising directions beyond inclusive deep inelastic scattering experiments, aimed at, among other goals, unveiling the three-dimensional structure of the bound nucleon. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative content is parametrized in terms of generalized parton distributions. In this way the distribution of partons in the transverse plane will be obtained, providing a pictorial view of the realization of the European Muon Collaboration effect. In particular, we show how, through the generalized parton distribution framework, non-nucleonic degrees of freedom in nuclei can be unveiled. Analogously, the momentum space 3D structure can be accessed by studying transverse-momentum-dependent parton distributions in semi-inclusive deep inelastic scattering processes. The status of measurements is also summarized, in particular novel coincidence measurements at high-luminosity facilities, such as Jefferson Laboratory. Finally the prospects for the next years at future facilities, such as the 12GeV Jefferson Laboratory and the Electron Ion Collider, are presented.

  1. An elastic/viscoelastic finite element analysis method for crustal deformation using a 3-D island-scale high-fidelity model

    NASA Astrophysics Data System (ADS)

    Ichimura, Tsuyoshi; Agata, Ryoichiro; Hori, Takane; Hirahara, Kazuro; Hashimoto, Chihiro; Hori, Muneo; Fukahata, Yukitoshi

    2016-07-01

    As a result of the accumulation of high-resolution observation data, 3-D high-fidelity crustal structure data for large domains are becoming available. However, it has been difficult to use such data to perform elastic/viscoelastic crustal deformation analyses in large domains with quality assurance of the numerical simulation that guarantees convergence of the numerical solution with respect to the discretization size because the costs of analysis are significantly high. This paper proposes a method of constructing a high-fidelity crustal structure finite element (FE) model using high-fidelity crustal structure data and fast FE analysis to reduce the costs of analysis (based on automatic FE model generation for parallel computation, OpenMP/MPI hybrid parallel computation on distributed memory computers, a geometric multigrid, variable preconditioning and multiple precision arithmetic). Using the proposed methods, we construct 10 billion degree-of-freedom high-fidelity crustal structure FE models for the entire Japan, and conduct elastic/viscoelastic crustal deformation analysis using this model with enough high accuracy of the numerical simulation.

  2. Discovering Structural Regularity in 3D Geometry

    PubMed Central

    Pauly, Mark; Mitra, Niloy J.; Wallner, Johannes; Pottmann, Helmut; Guibas, Leonidas J.

    2010-01-01

    We introduce a computational framework for discovering regular or repeated geometric structures in 3D shapes. We describe and classify possible regular structures and present an effective algorithm for detecting such repeated geometric patterns in point- or mesh-based models. Our method assumes no prior knowledge of the geometry or spatial location of the individual elements that define the pattern. Structure discovery is made possible by a careful analysis of pairwise similarity transformations that reveals prominent lattice structures in a suitable model of transformation space. We introduce an optimization method for detecting such uniform grids specifically designed to deal with outliers and missing elements. This yields a robust algorithm that successfully discovers complex regular structures amidst clutter, noise, and missing geometry. The accuracy of the extracted generating transformations is further improved using a novel simultaneous registration method in the spatial domain. We demonstrate the effectiveness of our algorithm on a variety of examples and show applications to compression, model repair, and geometry synthesis. PMID:21170292

  3. A Simulation of crustal deformation around sourthwest Japan using 3D Finite Element Method

    NASA Astrophysics Data System (ADS)

    Oma, T.; Ito, T.; Sasajima, R.

    2015-12-01

    In southwest Japan, the Philippine Sea plate is subducting beneath the Amurian plate at the Nankai Trough. Megathrust earthquakes have been occurred with recurrence intervals of about 100-150 years. Previous studies have estimated co-seismic slip distribution at the 1944 Tokankai and the 1946 Nankai earthquakes and interplate plate coupling along the Nankai Trough. Many of previous studies employed a homogeneous elastic half space or elastic and viscoelastic layers structure. However, these assumptions as mentioned above are inadequate, since inhomogeneous structure is exceled in the real earth result from subducting plate. Therefore, in order to estimate the effect of inhomogeneous structure on the crustal deformation, we calculate crustal deformation due to Megathrust earthquake using 3-dimensional Finite Element Method (FEM). We use FEM software PyLith v2.1. In this study, we construct a finite element mesh with the region of 3000km(SW) × 2300km(NS) × 400km(depth) cover Japanese Islands, using Cubit 13.0. This mesh is considered topography, the Philippine Sea plate, the Pacific plate, Moho discontinuity, and curvature of the earth. In order to examine differences of surface displacement between inhomogeneous and homogeneous structures, we use co-seismic slip distribution of the 1944 and 1946 earthquakes estimated by Sagiya and Thatcher (1999). In result, surface elastic response under inhomogeneous structure becomes 30% larger than it's homogeneous structure at the Muroto cape. This difference indicates that co-seismic slip or plate coupling distribution estimated from Green's function under an assumption of homogeneous structure is overestimated. Then, we calculate viscoelastic response assuming Maxwell rheology model and viscosity as 1×1019. As a result, predicted horizontal velocity of viscoelastic response due to the events corresponds to 10 % of observed present deformation. It suggest that spatial pattern of plate coupling might be change when we

  4. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

    PubMed

    Sarver, Michael; Zirbel, Craig L; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B

    2008-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose

  5. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

    González-Torre, Iván; Losada, Juan Carlos; Falconer, Ruth; Hapca, Simona; Tarquis, Ana M.

    2015-04-01

    Soil structure may be defined as the spatial arrangement of soil particles, aggregates and pores. The geometry of each one of these elements, as well as their spatial arrangement, has a great influence on the transport of fluids and solutes through the soil. Fractal/Multifractal methods have been increasingly applied to quantify soil structure thanks to the advances in computer technology (Tarquis et al., 2003). There is no doubt that computed tomography (CT) has provided an alternative for observing intact soil structure. These CT techniques reduce the physical impact to sampling, providing three-dimensional (3D) information and allowing rapid scanning to study sample dynamics in near real-time (Houston et al., 2013a). However, several authors have dedicated attention to the appropriate pore-solid CT threshold (Elliot and Heck, 2007; Houston et al., 2013b) and the better method to estimate the multifractal parameters (Grau et al., 2006; Tarquis et al., 2009). The aim of the present study is to evaluate the effect of the algorithm applied in the multifractal method (box counting and box gliding) and the cube size on the calculation of generalized fractal dimensions (Dq) in grey images without applying any threshold. To this end, soil samples were extracted from different areas plowed with three tools (moldboard, chissel and plow). Soil samples for each of the tillage treatment were packed into polypropylene cylinders of 8 cm diameter and 10 cm high. These were imaged using an mSIMCT at 155keV and 25 mA. An aluminium filter (0.25 mm) was applied to reduce beam hardening and later several corrections where applied during reconstruction. References Elliot, T.R. and Heck, R.J. 2007. A comparison of 2D and 3D thresholding of CT imagery. Can. J. Soil Sci., 87(4), 405-412. Grau, J, Médez, V.; Tarquis, A.M., Saa, A. and Díaz, M.C.. 2006. Comparison of gliding box and box-counting methods in soil image analysis. Geoderma, 134, 349-359. González-Torres, Iván. Theory and

  6. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

    PubMed Central

    Sarver, Michael; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B.

    2010-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs

  7. 3-D structures of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Steffen, W.

    2016-07-01

    Recent advances in the 3-D reconstruction of planetary nebulae are reviewed. We include not only results for 3-D reconstructions, but also the current techniques in terms of general methods and software. In order to obtain more accurate reconstructions, we suggest to extend the widely used assumption of homologous nebula expansion to map spectroscopically measured velocity to position along the line of sight.

  8. STAR3D: a stack-based RNA 3D structural alignment tool

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  9. STAR3D: a stack-based RNA 3D structural alignment tool.

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  10. Magma Migration Through the Continental Crust - 3-D Seismic and Thermo-mechanical Constraints on Sites of Crustal Contamination

    NASA Astrophysics Data System (ADS)

    Wilson, M.; Wheeler, W.

    2002-12-01

    Current understanding of the processes and pathways by which magma travels from its mantle source, through the crust to the Earth's surface is limited by the lack of continuously exposed sections through "fossil" magmatic systems. We report results from a 50 x 30 km 3-D seismic reflection survey of part of the Voring rifted continental margin of Norway which provide the first detailed images of an entire crustal magmatic plumbing system, from a Moho-level magma chamber, through complexes of sills and dykes in the mid to upper crust, to lavas and vent fields extruded at the early Tertiary paleosurface. The Voring margin of Norway formed during a period of Late Cretaceous to early Tertiary (Eocene) continental break-up when Greenland rifted away from Eurasia, resulting in the opening the NE Atlantic Ocean. Rifting was accompanied by widespread magmatic activity, inferred to be related to the impingement of the Iceland mantle plume on the base of the continental lithosphere. Regionally, magma migration occurred in at least two pulses: 62-59 Ma (main initial phase) and 57-54 Ma (continental break-up phase). Wide-angle seismic experiments indicate the presence of a laccolith-like "high-velocity body" (HVB) in the lower crust beneath most of the outer Voring Basin with P-wave velocities (Vp 7.1-7.4 km/s) characteristic of basaltic igneous rocks, overlying typical mantle rocks with Vp of over 8 km/s. The HVB locally reaches 8 km thickness and at break-up (54 Ma) measured 300 km x 500 km - corresponding to a volume of 450,000 cubic km of basaltic magma. It is interpreted as a magmatic underplate formed over a period of several million years as rising basaltic magmas ponded at the Moho at their level of neutral buoyancy. A laterally extensive sill complex (1000 m thick) occurs at the interface between thinned crystalline basement and the overlying Mesozoic sedimentary sequence. This is interpreted as one of the main intra-crustal magma storage reservoirs and is the most

  11. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    PubMed

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

    2015-07-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  12. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

    PubMed Central

    Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

    2015-01-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  13. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

    Szalaj, Przemyslaw; Michalski, Paul J.; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-01-01

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892

  14. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

    Szalaj, Przemyslaw; Michalski, Paul J; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-07-01

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892

  15. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

    Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations. PMID:26172844

  16. AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures

    PubMed Central

    Zambrano, Rafael; Jamroz, Michal; Szczasiuk, Agata; Pujols, Jordi; Kmiecik, Sebastian; Ventura, Salvador

    2015-01-01

    Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. PMID:25883144

  17. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    PubMed Central

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  18. Crustal structure beneath Southwestern Mexico

    NASA Astrophysics Data System (ADS)

    Suhardja, S.; Grand, S.; Wilson, D.; Guzman Speziale, M.; Gomez Gonzalez, J.; Ni, J.; Dominguez Reyes, T.

    2007-12-01

    The MARS ( Mapping the Rivera Subduction zone ) project started in January 2006 deploying 50 broadband seismometers across southwestern Mexico for one and a half year duration. The stations were deployed in Jalisco, Michoacan and Colima states. The goal of the project is to understand the geometry of the Rivera and Cocos subducting plates and the effect of the subduction on the overriding plate. In this study, we employ the teleseismic receiver function technique to map out the lateral variation in Moho depth as well as the Vp/Vs ratio of the crust in this tectonically and magmatically active area. The ambiguity between the delay time of Ps and crustal Vp/Vs ratio is reduced by stacking later phases, the PpPs and PpSs + PsPs, for different values of Moho depth and Vp/Vs ratio (Zhu et al. ). An average crustal depth and crustal Vp/Vs ratio is obtained by finding the highest combination of parameters that give the largest amplitude stack. We find that the average Moho depth is 39 km but varies significantly from 25 to 45 km thick. The average crustal Vp/Vs ratio is 1.82 but is also variable ranging from 1.7 to 1.9. We will discuss correlations of crustal thickness and Vp/Vs ratio with crustal composition and magmatic activity.

  19. Crustal thickness from 3D MCS data collected over the fast-spreading East Pacific Rise at 9°50'N

    NASA Astrophysics Data System (ADS)

    Aghaei, O.; Nedimović, M. R.; Canales, J.; Carton, H. D.; Carbotte, S. M.; Mutter, J. C.

    2011-12-01

    higher degree of correlation with age than on the Pacific plate (5.6-6 km). The mean crustal thickness from 9°41' to 9°56' on the Cocos plate is 5.8 km and 5.7 km for the Pacific plate excluding the crustal thickness beneath the Lamont seamount. Assuming maximum picking error of 100 ms, the uncertainty in crustal thickness estimation is 360 m. Faulting contributes to crustal thickness variations on both plates. Our results also provide insight into the mantle upwelling pattern, which is actively debated for the study area, and give us new insight into the 3D structure of the Moho Transition Zone (MTZ).

  20. Constructing a 3D Crustal Model Across the Entire Contiguous US Using Broadband Rayleigh Wave Phase Velocity and Ellipticity Measurements

    NASA Astrophysics Data System (ADS)

    Lin, F. C.; Schmandt, B.

    2015-12-01

    Imaging the crust and lithosphere structure beneath North America is one of the primary targets for the NSF-funded EarthScope project. In this study, we apply the recently developed ambient noise and surface wave tomography methods to construct a detailed 3D crustal model across the entire contiguous US using USArray data between January 2007 and May 2015. By using both Rayleigh wave phase velocity and ellipticity measurements between 8 and 100 sec period, the shear velocity structure can be well resolved within the five crustal layers we modeled: three upper crust, one middle crust, and one lower crust. Clear correlations are observed between the resolved velocity anomalies and known geological features at all depths. In the uppermost crust, slow Vs anomalies are observed within major sedimentary environments such as the Williston Basin, Denver Basin, and Mississippi embayment, and fast Vs anomalies are observed in environments with deeply exhumed bedrock outcrops at the surface including the Laurentian Highlands, Ouachita-Ozark Interior Highlands, and Appalachian Highlands. In the deeper upper crust, slow anomalies are observed in deep sedimentary basins such as the Green River Basin, Appalachian Basin, Southern Oklahoma Aulacogen, and areas surrounding the Gulf of Mexico. Fast anomalies, on the other hand, are observed in the Colorado Plateau, within the Great Plains between the Front Ranges and Midcontinental Rift, and east of the Appalachian Mountains. At this depth, the Midcontinental Rift and Grenville Front clearly correlate well with various velocity structure boundaries. In the middle crust, slow anomalies are mostly observed in the tectonically active areas in the western US, but relatively slow anomalies are also observed southeast of the Precambrian Rift Margins. At this depth, fast anomalies are observed beneath various deep sedimentary basins such as the Southern Oklahoma Aulacogen, Appalachian Basin, and Central Valley. In the lower crust, a clear

  1. 3-D crustal velocity model for Lithuania and its application to local event studies

    NASA Astrophysics Data System (ADS)

    Budraitis, M.; Kozlovskaya, E.; Janutyte, I.; Motuza, G.

    2009-12-01

    PASSEQ 2006-2008 project (PASsive Seismic Experiment in TESZ) aimed at studying the lithosphere-asthenosphere system around the TransEuropean Suture Zone (TESZ)- the transition between old Proterozoic platform of north and east Europe and younger Phanerozoic platform in central and western Europe. The experiment was a seismic array research aiming to retrieve the structure of the crust and Earth's mantle down to the mantle transition zone, including mapping of upper mantle seismic velocity variations and discontinuities (Moho, lithosphere-asthenosphere boundary, mantle transition zone) using all available techniques. During the experiment 26 seismic stations (including four broadband stations) were installed in Lithuania and operated since June, 2006 till January, 2008. One of the main reasons of PASSEQ deployment in Lithuania is identification and characterisation of the local seismic activity. During the data acquisition period a number of local seismic events was identified and preliminary event location was made using LocSat and VELEST algorithms and 1-D velocity models. These standard procedures is not enough precise for Lithuania, however, because the thickness of the crust varies significantly in the region (from 45 to 55 km). Another problem was low quality of S-wave arrivals due to thick (up to 2 km) sediments in most part of Lithuania. In order to improve event location, we compiled a 3-D seismic velocity model of the crust down to a depth of 60 km. The model, consisting of four major layers (sediments, upper crust, middle crust, lower crust and uppermost mantle) was interpolated from 2-D velocity models along previous wide-angle reflection and refraction profiles into a regular grid. The quality of the approximation was analysed using comparison of travel times of P-waves recorded by controlled source experiments and calculated travel times through the 3-D velocity model. The model was converted into a density model using a special procedure, in which

  2. Computational modeling of RNA 3D structures and interactions.

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling. PMID:26689764

  3. The Precambrian crustal structure of East Africa

    NASA Astrophysics Data System (ADS)

    Tugume, Fred Alex

    In this thesis, the Precambrian crustal structure of East African is investigated along with the crustal structures of three Cenozoic rift basins located in the western branch of the East African Rift System (EARS). In the first part of the thesis, P-wave receiver functions are modeled using the H-k method to obtain new insights about the bulk composition and thickness of the crust for Precambrian terrains throughout East Africa. The average crustal thickness for all but one of the terrains is between 37 and 39 km. An exception is the Ubendian terrain, which has an average crustal thickness 42 km. In all terrains, the average Poisson's ratio is similar, ranging from 0.25 to 0.26, indicating a bulk crustal composition that is felsic to intermediate. The main finding of this study is that crustal structure is similar across all terrains, which span more than 4.0 Ga of earth history. There is no discernable difference in the crustal thicknesses and Poisson's ratios between the Archean and Proterozoic terrains, or between the Proterozoic terrains, unlike the variability in Precambrian crustal structure found in many other continents. In the second part of the thesis, a joint inversion of Rayleigh wave phase and group velocities and receiver functions was used to investigate the shear wave velocity structure of the crust and uppermost mantle beneath the Precambrian terrains of East Africa. In comparison with other areas of similar age in southern and western Africa where the same joint inversion method has been applied, I find that while there is little difference in the mean shear wave velocities for the entire crust across all of the Precambrian terrains, and also few differences in the thickness of the crust, there exists substantial variability in lower crustal structure. This variability is reflected primarily in the thickness of the lower crustal layers with shear wave velocities ≥ 4.0 km/s. This variability is found both within terrains of the same age (i

  4. Crustal structure of the Nordland region, northern Norway

    NASA Astrophysics Data System (ADS)

    Maystrenko, Yuriy P.; Olesen, Odleiv; Gernigon, Laurent; Gradmann, Sofie

    2016-04-01

    To understand the major structural features of the sedimentary cover and crystalline crust within the Nordland County area of Norway, a data-based 3D structural model has been constructed in the framework of the Neonor2 project, "Neotectonics in Nordland - implications for petroleum exploration". The 3D structural model covers the Lofoten Ridge, the Ribban and Vestfjorden basins and adjacent areas of the Norwegian mainland. The model also covers the northern part of the adjacent Vøring Basin. At the regional scale, the 3D model includes the rifted margin which is located at the transition from the exposed crystalline rocks of the Fennoscandian Shield in the east to the Cenozoic oceanic domain of the Norwegian-Greenland Sea in the west. During the construction of the 3D structural model, all recently published and/or released data have been compiled in order to set the initial model. This initial 3D model has been validated by a 3D density modelling in order to obtain a gravity-consistent 3D structural model of the entire study area. The 3D density modelling has been carried out by using the IGMAS plus software (the Interactive Gravity and Magnetic Application System). During the 3D density modelling, densities have been assigned as constant values for the crystalline rocks. In contrast, densities of sedimentary rocks have been set to be depth-dependent in order to reflect the compaction of sedimentary rocks with depth. According to the results of the 3D density modeling, the crystalline crust of the investigated region consists of several layers with different densities. The deepest crustal layer is the high-density lower crust which corresponds to the high-velocity lower crustal layer. The regional-scale gravity response associated with the positions of the Moho and lithosphere-asthenosphere boundary is one of the key factors for performing a proper 3D density model of the study area. At the regional scale, the Moho and lithosphere-asthenosphere boundary are

  5. 3-D crustal velocity model for Lithuania and its application to local event studies

    NASA Astrophysics Data System (ADS)

    Kozlovskaya, Elena; Budraitis, Mantas; Janutyte, Ilma; Motuza, Gediminas; Lazauskiene, Jurga; Passeq-Working Group

    2010-05-01

    PASSEQ 2006-2008 project (PASsive Seismic Experiment in TESZ) aimed at studying the lithosphere-asthenosphere system around the TransEuropean Suture Zone (TESZ)- the transition between old Proterozoic platform of north and east Europe and younger Phanerozoic platform in central and western Europe. The experiment was a seismic array research aiming to retrieve the structure of the crust and Earth's mantle down to the mantle transition zone, including mapping of upper mantle seismic velocity variations and discontinuities (Moho, lithosphere-asthenosphere boundary, mantle transition zone) using all available techniques. During the experiment 26 seismic stations (including four broadband stations) were installed in Lithuania. One of the main targets of PASSEQ deployment in Lithuania was identification and characterization of the local seismic activity. The PASSEQ stations in Lithuania were in operation since June, 2006 till January, 2008. During this period a number of local seismic events was recorded and preliminary event location was made using the LocSat algorithm and 1-D velocity model. This standard procedure is not enough precise for Lithuania, however, because the thickness of the crust varies significantly in the region (from 45 to 55 km). In order to improve event location, we separated the events into several groups and located each group separately using a VELEST algorithms and own 1-D velocity model for each group. We also compiled a 3-D seismic velocity of the crust down to a depth of 60 km. The model, consisting of four major layers (sediments, upper crust, middle crust, lower crust and uppermost mantle) was interpolated from 2-D velocity models along previous wide-angle reflection and refraction profiles into a regular grid. The quality of the approximation was analysed using comparison of travel times of P-waves recorded along previous controlled source profiles and synthetic travel times calculated using the 3-D velocity model. The model was converted

  6. Crustal structure of northeastern California

    NASA Astrophysics Data System (ADS)

    Zucca, John J.; Fuis, Gary S.; Milkereit, Bernd; Mooney, Walter D.; Catchings, Rufus D.

    1986-06-01

    velocity structure in between, underlying the Cascade Range. This model was converted to a density model, and observed Bouguer gravity data were matched. A general decrease in Bouguer gravity values eastward may be explained by a general decrease in the density of crustal layers and does not require a change in crustal thickness. Beneath the 4.5-km-thick surficial layer, the velocity model for the Modoc Plateau is similar to that determined by other researchers for a refraction line in the Sierra Nevada. It is unlike velocity models for rift areas, to which the Modoc Plateau has been likened by some authors. We theorize that beneath its surficial volcanic and sedimentary rocks, the Modoc Plateau is underlain by a basement of granitic and metamorphic rocks that are the roots of ancient magmatic arc(s). The fine layering in the Klamath model is consistent with the imbricate structure of the Klamath Mountains. Independent modeling of aeromagnetic data indicates that the base of the Trinity ultramafic sheet corresponds to a velocity step from 6.5 to 6.7 km/s at 7-km depth in our model. The 6.7 km/s layer beneath the Trinity ultramafic sheet apparently corresponds to rocks of the central metamorphic belt, mostly amphibole schists, which crop out west of the Trinity ultramafic sheet. Deeper velocity layers can likewise be correlated to terranes that crop out farther west. In our geologic cross section of northeastern California, derived from our velocity-density model for the east-west line, the Klamath Mountains are underlain by folded and thrust-faulted slices of oceanic crust. The Modoc Plateau and westernmost Basin and Range province are underlain by a section of volcanic and sedimentary rocks overlying granitic and metamorphic rocks, all tilted westward between an inferred fault under Medicine Lake volcano and the Surprise Valley fault. In the Cascade Range, geologic units appear to be discontinuous, and structures include horsts, grabens, and a 10-km step downward to the

  7. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

    The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.

  8. 3-D crust and mantle structure in southern Ontario, Canada via receiver function imaging

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Frederiksen, A. W.

    2013-11-01

    A teleseismic data set from the POLARIS project is used to obtain 3-D images of southern Ontario using two imaging techniques: scattering tomography and common-conversion-point stacking. The resulting images reveal a layered crust, the layering being interrupted by discontinuities associated with major crustal-scale faulting. Breaks in crustal continuity and Moho deflections associated with the Ottawa-Bonnechère Graben indicate that the graben is associated with faulting on a whole crust scale. We also detect similar discontinuities across the Mississauga Domain, supporting the previous interpretation that the domain is bounded by crustal-scale faults. We locate discontinuous sub-lithospheric negative-polarity arrivals which indicate complex three-dimensional structures within the lithosphere and may be associated with subduction remnants or a mid-lithosphere discontinuity.

  9. 3D numerical modeling of subduction dynamics: plate stagnation and segmentation, and crustal advection in the mantle transition zone

    NASA Astrophysics Data System (ADS)

    Yoshida, M.; Tajima, F.

    2012-04-01

    Water content in the mantle transition zone (MTZ) has been broadly debated in the Earth science community as a key issue for plate dynamics [e.g., Bercovici and Karato, 2003]. In this study, a systematic series of three-dimensional (3D) numerical simulation are performed in an attempt to verify two hypotheses for plate subduction with effects of deep water transport: (1) the small-scale behavior of subducted oceanic plate in the MTZ; and (2) the role of subducted crust in the MTZ. These hypotheses are postulated based on the seismic observations characterized by large-scale flattened high velocity anomalies (i.e., stagnant slabs) in the MTZ and discontinuity depth variations. The proposed model states that under wet conditions the subducted plate main body of peridotite (olivine rich) is abutted by subducted crustal materials (majorite rich) at the base of the MTZ. The computational domain of mantle convection is confined to 3D regional spherical-shell geometry with a thickness of 1000 km and a lateral extent of 10° × 30° in the latitudinal and longitudinal directions. A semi-dynamic model of subduction zone [Morishige et al., 2010] is applied to let the highly viscous, cold oceanic plate subduct. Weak (low-viscosity) fault zones (WFZs), which presumably correspond to the fault boundaries of large subduction earthquakes, are imposed on the top part of subducting plates. The phase transitions of olivine to wadsleyite and ringwoodite to perovskite+magnesiowüstite with Clapeyron slopes under both "dry" and "wet" conditions are considered based on recent high pressure experiments [e.g., Ohtani and Litasov, 2006]. Another recent experiment provides new evidence for lower-viscosity (weaker strength) of garnet-rich zones than the olivine dominant mantle under wet conditions [Katayama and Karato, 2008]. According to this, the effect of viscosity reduction of oceanic crust is considered under wet condition in the MTZ. Results show that there is a substantial difference

  10. 3D visualization of middle ear structures

    NASA Astrophysics Data System (ADS)

    Vogel, Uwe; Schmitt, Thomas

    1998-06-01

    The achievement of volume geometry data from middle ear structures and surrounding components performs a necessary supposition for the finite element simulation of the vibrational and transfer characteristics of the ossicular chain. So far those models base on generalized figures and size data from anatomy textbooks or particular manual and one- or two-dimensional distance measurements of single ossicles, mostly obtained by light microscopy, respectively. Therefore the goal of this study is to create a procedure for complete three-dimensional imaging of real middle ear structures (tympanic membrane, ossicles, ligaments) in vitro or even in vivo. The main problems are their microscopic size with relevant structures from 10 micrometer to 5 mm, representing various tissue properties (bone, soft tissue). Additionally, these structures are surrounded by the temporal bone, the most solid bone of the human body. Generally there exist several established diagnostic tools for medical imaging that could be used for geometry data acquisition, e.g., X-ray computed tomography and magnetic resonance imaging. Basically they image different tissue parameters, either bony structures (ossicles), or soft tissue (tympanic membrane, ligaments). But considering this application those standard techniques allow low spatial resolution only, usually in the 0.5 - 1mm range, at least in one spatial direction. Thus particular structures of the middle ear region could even be missed completely because of their spatial location. In vitro there is a way out by collecting three complete data sets, each distinguished by 90 degree rotation of a cube-shaped temporal bone specimen. That allows high-resolution imaging in three orthogonal planes, which essentially supports the three-dimensional interpolation of the unknown elements, starting from the regularly set elements of the cubic grid with an edge extension given by the original two-dimensional matrix. A different approach represents the

  11. Acetylcholinesterase: From 3D Structure to Function

    PubMed Central

    Dvir, Hay; Silman, Israel; Harel, Michal; Rosenberry, Terrone L.; Sussman, Joel L.

    2010-01-01

    By rapid hydrolysis of the neurotransmitter, acetylcholine, acetylcholinesterase terminates neurotransmission at cholinergic synapses. Acetylcholinesterase is a very fast enzyme, functioning at a rate approaching that of a diffusion-controlled reaction. The powerful toxicity of organophosphate poisons is attributed primarily to their potent inhibition of acetylcholinesterase. Acetylcholinesterase inhibitors are utilized in the treatment of various neurological disorders, and are the principal drugs approved thus far by the FDA for management of Alzheimer’s disease. Many organophosphates and carbamates serve as potent insecticides, by selectively inhibiting insect acetylcholinesterase. The determination of the crystal structure of Torpedo californica acetylcholinesterase permitted visualization, for the first time, at atomic resolution, of a binding pocket for acetylcholine. It also allowed identification of the active site of acetylcholinesterase, which, unexpectedly, is located at the bottom of a deep gorge lined largely by aromatic residues. The crystal structure of recombinant human acetylcholinesterase in its apo-state is similar in its overall features to that of the Torpedo enzyme; however, the unique crystal packing reveals a novel peptide sequence which blocks access to the active-site gorge. PMID:20138030

  12. Comparison of publically available Moho depth and crustal thickness grids with newly derived grids by 3D gravity inversion for the High Arctic region.

    NASA Astrophysics Data System (ADS)

    Lebedeva-Ivanova, Nina; Gaina, Carmen; Minakov, Alexander; Kashubin, Sergey

    2016-04-01

    deep Arctic Ocean: results of a 3D gravity modeling Russian Geology and Geophysics 54, 247-262. Jakobsson M, Mayer L, Coakley B, Dowdeswell JA, Forbes S, Fridman B, Hodnesdal H, Noormets R, Pedersen R, Rebesco M, Schenke HW, Zarayskaya Y, Accettella D, Armstrong A, Anderson RM, Bienhoff P, Camerlenghi A, Church I, Edwards M, Gardner JV, Hall JK, Hell B, Hestvik O, Krist-offersen Y, Marcussen C, Mohammad R, Mosher D, Nghiem SV, Pedrosa MT, Travaglini PG, Weatherall P (2012). The international bathymetric chart of the Arctic Ocean (IBCAO) version 3.0. Geophys Res Lett 39, L12609. Laske, G., Masters., G., Ma, Z. and Pasyanos, M. (2013). Update on CRUST1.0 - A 1-degree Global Model of Earth's Crust, Geophys. Res. Abstracts, 15, Abstract EGU2013-2658, 2013. Minakov A, Faleide JI, Glebovsky VY, Mjelde R (2012) Structure and evolution of the northern Barents-Kara Sea continental margin from integrated analysis of potential fields, bathymetry and sparse seismic data. Geophys J Int 188, 79-102. Petrov O., Smelror M., Shokalsky S., Morozov A., Kashubin S., Grikurov G., Sobolev N., Petrov E., (2013). A new international tectonic map of the Arctic (TeMAr) at 1:5 M scale and geodynamic evolution in the Arctic region. EGU2013-13481. Reguzzoni, M., & Sampietro, D. (2014). GEMMA: An Earth crustal model based on GOCE satellite data. International Journal of Applied Earth Observation and Geoinformation Spasojevic S. & Gurnis M., (2012). Sea level and vertical motion of continents from dynamic earth models since the late Cretaceous. American Association of Petroleum Geologists Bulletin, 96, pp. 2037-2064.

  13. Comparison of protein structures using 3D profile alignment.

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

    A novel method for protein structure comparison using 3D profile alignment is presented. The 3D profile is a position-dependent scoring matrix derived from three-dimensional structures and is basically used to estimate sequence-structure compatibility for prediction of protein structure. Our idea is to compare two 3D profiles using a dynamic programming algorithm to obtain optimal alignment and a similarity score between them. When the 3D profile of hemoglobin was compared with each of the profiles in the library, which contained 325 profiles of representative structures, all the profiles of other globins were detected with relatively high scores, and proteins in the same structural class followed the globins. Exhaustive comparison of 3D profiles in the library was also performed to depict protein relatedness in the structure space. Using multidimensional scaling, a planar projection of points in the protein structure space revealed an overall grouping in terms of structural classes, i.e., all-alpha, all-beta, alpha/beta, and alpha+beta. These results differ in implication from those obtained by the conventional structure-structure comparison method. Differences are discussed with respect to the structural divergence of proteins in the course of molecular evolution. PMID:9071025

  14. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

    Wang, Zhangang; Qu, Honggang; Wu, Zixing; Yang, Hongjun; Du, Qunle

    2016-05-01

    The development and widespread application of geological modeling methods has increased demands for the integration and sharing services of three dimensional (3D) geological data. However, theoretical research in the field of geological information sciences is limited despite the widespread use of Geographic Information Systems (GIS) in geology. In particular, fundamental research on the formal representations and standardized spatial descriptions of 3D structural models is required. This is necessary for accurate understanding and further applications of geological data in 3D space. In this paper, we propose a formal representation method for 3D structural models using the theory of point set topology, which produces a mathematical definition for the major types of geological objects. The spatial relationships between geologic boundaries, structures, and units are explained in detail using the 9-intersection model. Reasonable conditions for describing the topological space of 3D structural models are also provided. The results from this study can be used as potential support for the standardized representation and spatial quality evaluation of 3D structural models, as well as for specific needs related to model-based management, query, and analysis.

  15. Lateral Crustal Velocity Variations across the Andean Foreland in San Juan, Argentina from the JHD Analysis and 3D P and S Velocity inversion

    NASA Astrophysics Data System (ADS)

    Asmerom, B. B.; Chiu, J.; Pujol, J.; Smalley, R.

    2010-12-01

    Lateral crustal velocity variations across the Andean Foreland in San Juan Argentina are explored by joint hypocentral determination (JHD) analysis and 3D velocity inversion. JHD results show consistent positive station corrections beneath Precordillera and negative station corrections beneath Pie de Palo, corresponding to regions of low and high velocity, respectively. These observations are supported by the results from the 3D velocity inversion. A 20% increase in velocity is observed from the Precordilleras in the west to Pie de Palo in the east. The tomography result also reveals a narrow east dipping and NNE trending high velocity anomalous zone bisecting the southern half of Pie de Palo. This anomalous zone was previously identified by a magnetic study and was interpreted to represent the structure corresponding to the Grenvillian Precordillera-Pie de Palo tectonic boundary zone. Finally, P and S station corrections are calculated from the synthetic travel time obtained by using the resultant 3D P- and S- wave velocity model. The observed pattern and magnitude of the P- and S-wave station corrections are recovered successfully from the synthetic calculation, indicating that the resultant 3D velocity model is close to the real earth structure in the Andean Foreland region. Relocation of all intermediate events from the flat subducting slab using this newly acquired 3D velocity model shows a significant change in the slab geometry. The relocated hypocenter distribution is more clustered than previous studies obtained using a 1D model. The slab is simply flat and it resumes a normal subduction angle towards the east of the study area.

  16. 3D crustal seismic velocity model for the Gulf of Cadiz and adjacent areas (SW Iberia margin) based on seismic reflection and refraction profiles

    NASA Astrophysics Data System (ADS)

    Lozano, Lucía; Cantavella, Juan Vicente; Barco, Jaime; Carranza, Marta; Burforn, Elisa

    2016-04-01

    The Atlantic margin of the SW Iberian Peninsula and northern Morocco has been subject of study during the last 30 years. Many seismic reflection and refraction profiles have been carried out offshore, providing detailed information about the crustal structure of the main seafloor tectonic domains in the region, from the South Portuguese Zone and the Gulf of Cadiz to the Abyssal Plains and the Josephine Seamount. The interest to obtain a detailed and realistic velocity model for this area, integrating the available data from these studies, is clear, mainly to improve real-time earthquake hypocentral location and for tsunami and earthquake early warning. Since currently real-time seismic location tools allow the implementation of 3D velocity models, we aim to generate a full 3D crustal model. For this purpose we have reviewed more than 50 profiles obtained in different seismic surveys, from 1980 to 2008. Data from the most relevant and reliable 2D seismic velocity published profiles were retrieved. We first generated a Moho depth map of the studied area (latitude 32°N - 41°N and longitude 15°W - 5°W) by extracting Moho depths along each digitized profile with a 10 km spacing, and then interpolating this dataset using ordinary kriging method and generating the contour isodepth map. Then, a 3D crustal velocity model has been obtained. Selected vertical sections at different distances along each profile were considered to retrieve P-wave velocity values at each interface in order to reproduce the geometry and the velocity gradient within each layer. A double linear interpolation, both in distance and depth, with sampling rates of 10 km and 1 km respectively, was carried out to generate a (latitude, longitude, depth, velocity) matrix. This database of all the profiles was interpolated to obtain the P-wave velocity distribution map every kilometer of depth. The new 3D velocity model has been integrated in NonLinLoc location program to relocate several representative

  17. Capacitance extraction from complex 3D interconnect structures

    SciTech Connect

    Cartwright, D.; Csanak, G.; George, D.; Walker, R.; Kuprat, A.; Dengi, A.; Grobman, W.

    1999-06-01

    A new tool has been developed for calculating the capacitance matrix for complex 3D interconnect structures involving multiple layers of irregularly shaped interconnect, imbedded in different dielectric materials. This method utilizes a new 3D adaptive unstructured grid capability, and a linear finite element algorithm. The capacitance is determined from the minimum in the total system energy as the nodes are varied to minimize the error in the electric field in the dielectric(s).

  18. Crustal structure of northern California

    NASA Astrophysics Data System (ADS)

    Godfrey, Nicola Jane

    This thesis presents work from two regions in northern California, using seismic data collected during the Mendocino Triple Junction Experiment (1993 and 1994), and USGS data collected in 1977. Much of California geology records subduction processes active during much of the Mesozoic. About 29 Ma ago, the East Pacific Rise began interacting with the California subduction margin, and two triple junctions formed. One moved north and one moved south, with the San Andreas transform system between them. The northern triple junction, the Mendocino triple junction, is currently situated close to Cape Mendocino, northern California. Northern California geology now has the added complication of processes associated with the northward moving triple junction and lengthening San Andreas fault system. Chapters 1 and 2 focus on the Great Valley, a forearc basin associated with Mesozoic subduction. The three major parts of the subduction system are the magmatic arc (Sierra Nevada batholith), forearc basin (Great Valley basin) and accretionary prism (Franciscan complex). Chapter 1 presents evidence from seismic data, for a complete ophiolitic sequence, including an unserpentinized mantle section (velocities of 8.1 km.ssp{-1} at 5-18 km depth) beneath the northernmost Great Valley. A combination velocity/density model shows the ophiolite is underlain by low-density material associated with the Sierra Nevada. Chapter 2 presents geophysical models, (seismic reflection, refraction, gravity and magnetic models) published by different authors over the last 14 years from the entire Great Valley, to explore the nature of the Great Valley ophiolite along the length of the forearc basin. Chapter 3 focuses offshore, west of the San Andreas fault, on an anomalous piece of crust, the Vizcaino block, situated immediately southwest of the Mendocino triple junction. This chapter discusses the crustal thickness of the Vizcaino block, the nature of its accretionary prism basement, and deformation

  19. The Deep Structure of the South Atlantic Kwanza Basin - Insights from 3D Structural and Gravimetric modelling

    NASA Astrophysics Data System (ADS)

    Nicolai, Christina V.; Scheck-Wenderoth, Magdalena; Warsitzka, Michael

    2010-05-01

    Three dimensional geological models constrained by potential field data have proven to be powerful tools for the investigation of areas where conventional seismic surveying fails to deliver satisfactory results. Especially in basins containing thick sedimentary and/or evaporite layers, the detection of crustal structures such as synrift halfgrabens or basement highs is considerably enhanced by potential field data. Knowledge on the distribution and configuration of crustal structures is inalienable for the reconstruction of the tectonic history of a continental margin. In this study, we present results from 3D gravimetric modelling of the Kwanza Basin offshore Angola accomplished to investigate the formation of the basin in response to the opening of the South Atlantic. Although the post-rift evolution of the Kwanza Basin is well studied, little is known about the basins early history. This is mainly due to the missing knowledge of its crustal structure owing to the masking effect of an up to 3 km thick salt layer, which seismically obscures the underlying basement. To get an insight into the deeper structure of the Angolan margin we combined 3D structural, isostatic and gravimetric modelling. 2D seismic reflection data was used to determine the structural setting and the configuration of the stratigraphic units in the sedimentary part of the basin, whereas its crustal structure was constrained by isostatic and gravity modelling. The resulting geological model confirms and extends previous observations, and adds new details to the hitherto dim picture of the Kwanza Basins crustal architecture. In addition, it raises new questions on the volcanic or non-volcanic origin of the margin, and the potential of transfer faults to dissect the latter into independently evolving tectonic segments.

  20. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

    Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

    2009-02-01

    Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

  1. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

    Campbell, Leckey Cara A/; Miler, Corey A.; Hinders, Mark K.

    2011-01-01

    Structural health monitoring (SHM) for the detection of damage in aerospace materials is an important area of research at NASA. Ultrasonic guided Lamb waves are a promising SHM damage detection technique since the waves can propagate long distances. For complicated flaw geometries experimental signals can be difficult to interpret. High performance computing can now handle full 3-dimensional (3D) simulations of elastic wave propagation in materials. We have developed and implemented parallel 3D elastodynamic finite integration technique (3D EFIT) code to investigate ultrasound scattering from flaws in materials. EFIT results have been compared to experimental data and the simulations provide unique insight into details of the wave behavior. This type of insight is useful for developing optimized experimental SHM techniques. 3D EFIT can also be expanded to model wave propagation and scattering in anisotropic composite materials.

  2. Regional crustal structures of Pacific Northwest

    SciTech Connect

    Connard, G.; Couch, R.; Farooqui, S.; Pitts, G.S.; O'Malley, R.

    1986-04-01

    Long-wavelength gravity anomalies combined with regional seismic refraction data, obtained during the last two decades, allow a regional mapping of crustal thickness variations in the Pacific Northwest and the adjacent continental margin. When the effects of these variations in crustal thickness are removed from the gravity data, the residual gravity anomalies outline major upper crustal structures in the Pacific Northwest. Residual gravity anomalies show that the Cascade Range in Oregon fills a major north-south-trending graben. The graben is approximately 60 km wide and 160 km long, and is oriented approximately N10/sup 0/E. Its well-developed western wall exhibits a throw of 2-3 km. The Cascade Range and its associated graben overlie a prominent northeast-southwest structural trend that demarks a Mesozoic orocline. The oroclinal structure extends from the continental margin northwest of the Klamath Mountains in southwestern Oregon through the Blue Mountains in northeastern Oregon, and separates the late Mesozoic to early Tertiary basins of central Oregon and central Washington. A large regional gravity high observed over the Columbia basin in central Washington is attributed to both the thick surface layer of flood basalts and an anomalous lower crust. Gravity data integrated with seismic refraction and geologic data yield a computed model of the crustal structure of the Columbia Plateau. Removing the basalt layer of the model reveals a rift topography or complex graben structure that connects with or adjoins the Cascade graben on the southwest side of the basin and the Chiwaukun, Methow, and Republic grabens on the north side of the basin. These structures in the Pacific Northwest reflect generally east-west extension and wrench tectonics.

  3. Crustal high-velocity anomaly at the East European Craton margin in SE Poland (TESZ) modelled by 3-D seismic tomography of refracted and reflected arrivals

    NASA Astrophysics Data System (ADS)

    Środa, Piotr; Dec, Monika

    2016-04-01

    The area of Trans-European Suture Zone in SE Poland represents a contact of major tectonic units of different consolidation age - from the Precambrian East European Craton, through Palaeozoic West European Platform to Cenozoic Carpathian orogen. The region was built by several phases of crustal accretion, which resulted in a complex collage of tectonic blocks. In 2000, this region was studied by several seismic wide-angle profiles of CELEBRATION 2000 experiment, providing a dense coverage of seismic data in SE Poland and allowing for detailed investigations of the crustal structure and properties in this area. Beneath the marginal part of the EEC, the 2-D modelling of in-line data form several CELEBRATION profiles revealed a prominent high P-wave velocity anomaly in the upper crust, with Vp of 6.7-7.1 km/s, starting at 10-16 km depth (e.g., Środa et al., 2006). Anomalously high velocities are observed in the area located approximately beneath Lublin trough, to the NE of Teisseyre-Tornquist Zone. Based on 3-D tomography of first arrivals of in- and off-line CELEBRATION 2000 recordings (Malinowski et al., 2008), elevated velocities are also reported in the same area and seem to continue to the SW, off the craton margin. Gravimetric modelling also revealed anomalously high density in the same region at similar depths. High seismic velocities and densities are interpreted as indicative for a pronounced mafic intrusion, possibly related to extensional processes at the EEC margin. Previous 3-D models of the high-velocity intrusion were based on first arrivals (crustal refractions) only. In this study, also off-line reflections (not modelled up to now) are used, in order to enlarge the data set and to better constrain the geometry and properties of the velocity anomaly. A code for 3-D joint tomographic inversion of refracted and reflected arrivals, with model parametrization allowing for velocity discontinuities was used (Rawlinson, 2007). With this approach, besides the

  4. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

    Gong, Xingting; Cho, Yigil; Castle, Toen; Sussman, Daniel; Kamien, Randall

    2015-03-01

    The purpose of this talk is to explore how one can create 3D structures from 2D materials through the art of kirigami. Kirigami expands upon origami by allowing not only folds, but also cuts, into materials. If we take an incompressible material such as paper and remove a hole from it, the paper will buckle into the third dimension once that hole is sealed in order to relieve strain. Thus, orienting cuts and folds in certain places throughout a sheet of paper can influence its ``pop-up,'' 3D structure. To narrow down the inverse design problem, we confined ourselves to making only one kind of cut (which we call the ``5-7 cut'') on a honeycomb grid, and we show how this single cut can give rise to arbitrarily complex three dimensional structures. A simple set of rules exists: (a) one 5-7 cut divides the material into 2 sections which can choose to pop-up or down independently of each other, (b) rows of uniform cuts must pop up or down in unison, giving (nearly) arbitrary 2D structure, and (c) the 5-7 cuts can be arranged in various ways to create 6 basic pop-up ``modes,'' which can then be arranged to give (nearly) arbitrary 3D structure. These simple rules allow a framework for designing targeted 3D structure from an initial 2D sheet of material. This work was supported by NSF EFRI-ODISSEI Grant EFRI 13-31583.

  5. Crustal Structure in Central-Eastern Greenland

    NASA Astrophysics Data System (ADS)

    Shulgin, A.; Thybo, H.

    2013-12-01

    We present the seismic structure in the interior of Greenland based on the first measurements by the seismic refraction/wide angle reflection method. Previous seismic surveys have only been carried out offshore and near the coast of Greenland, where the crustal structure is affected by oceanic break-up and may not be representative of the interior of the island. Acquisition of geophysical data onshore Greenland is logistically complicated by the presence of an up to 3.4 km thick ice sheet, permanently covering most of the land mass. The seismic data was acquired by a team of six people during a two-month long experiment in summer of 2011 on the ice cap in the interior of central-eastern Greenland. The EW-trending profile extends 310 km inland from the approximate edge of the stable ice cap near Scoresby Sund across the centre of the ice cap. The planned extension of the profile by use of OBSs and air gun shooting in Scoresbysund Fjord to the east coast of Greenland was unfortunately cancelled, because navigation was prevented by ice drift. 350 Reftek Texan receivers recorded high-quality seismic data from 8 equidistant shots along the profile. Explosive charge sizes were 1 ton at the ends and ca. 500 kg along the profile, loaded with about 100 kg at 35-85 m depth in individual boreholes. Two-dimensional velocity model based on forward ray tracing and tomography modelling shows a decrease of crustal thickness from 47 km below the centre of Greenland in the western part to 40 km in the eastern part of the profile. Earlier studies show that crustal thickness further decreases eastward to ca. 30 km below the fjord system, but details of the changes are unknown. Relatively high lower crustal velocities (Vp 6.8 - 7.3) in the western part of the TopoGreenland profile may indicate past collision tectonics or may be related or to the passage of the Iceland mantle plume. The origin of the pronounced circum-Atlantic mountain ranges in Norway and eastern Greenland, which have

  6. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    PubMed

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  7. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures

    PubMed Central

    Rahrig, Ryan R.; Petrov, Anton I.; Leontis, Neocles B.; Zirbel, Craig L.

    2013-01-01

    The R3D Align web server provides online access to ‘RNA 3D Align’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  8. RNAComposer and RNA 3D structure prediction for nanotechnology.

    PubMed

    Biesiada, Marcin; Pachulska-Wieczorek, Katarzyna; Adamiak, Ryszard W; Purzycka, Katarzyna J

    2016-07-01

    RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary structure is fundamental to understand RNA functions beginning with transcription and ending with turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy when experimental data are integrated into the prediction, tertiary structure prediction of large RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is rapidly developing and new computational methods based on different strategies are emerging. RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500 nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary structure specified by the user. Importantly, this method allows incorporation of distance restraints derived from the experimental data to strengthen the 3D predictions. The potential and limitations of RNAComposer are discussed and an application to RNA design for nanotechnology is presented. PMID:27016145

  9. Crustal structure beneath southern Norway imaged by magnetotellurics

    NASA Astrophysics Data System (ADS)

    Cherevatova, M.; Smirnov, M.; Korja, T.; Kaikkonen, P.; Pedersen, L. B.; Hübert, J.; Kamm, J.; Kalscheuer, T.

    2014-07-01

    We use data from two magnetotelluric profiles, ToSca10 and ToSca'09, over the Scandinavian Mountains to study the crustal structure in southern Norway. The profiles cross the major tectonic structures of the Caledonian orogen as well as the western margin of the Precambrian Baltica. Dimensionality and strike analyses indicate generally 3-D behavior of the data. However, the majority of the used data distinguishes a preferable strike direction, which is supported by the geology of the region. Hence, we employ 2-D inversion and choose to invert the determinant of the impedance tensor to mitigate 3-D effects in the data on our 2-D models. Magnetotelluric data from both profiles are inverted using a damped least squares solution based on a singular value decomposition. We improved the solution by defining the inverse model covariance matrix through gradient or Laplacian smoothing operators. The two-dimensional inversion models of the ToSca'09 and ToSca'10 field data from southern Norway derived from the damped least squares scheme with the Laplacian inverse model covariance matrix are presented. Resistive rocks, extending to the surface, image the autochthonous Southwest Scandinavian Domain and the allochthonous Western Gneiss Region. Near-surface conductors, which are located between the resistive Caledonian nappes and Precambrian basement, delineate highly conductive shallow-sea sediments, so called alum shales. They exhibit a decollement along which the Caledonian nappes were overthrust. A deeper, upper to mid-crustal conducting layer in the Southwest Scandinavian Domain may depict the remnants of closed ocean basins formed during the accretions and collisions of various Sveconorwegian terranes. In ToSca'10, the Caledonian nappes, the conducting alum shales and the deeper conductor are terminated in the west by the Faltungsgraben shear complex which represents a crustal scale boundary between the Western Gneiss Region in the west and the Southwest Scandinavian

  10. Late Cretaceous Localized Crustal Thickening as a Primary Control on the 3-D Architecture and Exhumation Histories of Cordilleran Metamorphic Core Complexes

    NASA Astrophysics Data System (ADS)

    Gans, P. B.; Wong, M.

    2014-12-01

    The juxtaposition of mylonitic mid-crustal rocks and faulted supracrustal rocks in metamorphic core complexes (MMCs) is usually portrayed in 2 dimensions and attributed to a single event of large-scale slip ± isostatic doming along a low-angle "detachment fault"/ shear zone. This paradigm does not explain dramatic along strike (3-D) variations in slip magnitude, footwall architecture, and burial / exhumation histories of most MMCs. A fundamental question posed by MMCs is how did their earlier thickening and exhumation histories influence the geometric evolution and 3-D slip distribution on the subsequent detachment faults? New geologic mapping and 40Ar/39Ar thermochronology from the Snake Range-Kern Mts-Deep Creek Mts (SKDC) complex in eastern Nevada offer important insights into this question. Crustal shortening and thickening by large-scale non-cylindrical recumbent folds and associated thrust faults during the late Cretaceous (90-80 Ma) resulted in deep burial (650°C, 20-25 km) of the central part of the footwall, but metamorphic grade decreases dramatically to the N and S in concert with decreasing amplitude on the shortening structures. Subsequent Paleogene extensional exhumation by normal faulting and ESE-directed mylonitic shearing is greatest in areas of maximum earlier thickening and brought highest grade rocks back to depths of~10-12 km. After ≥15 Ma of quiescence, rapid E-directed slip initiated along the brittle Miocene Snake Range detachment at 20 Ma and reactivated the Eocene shear zone. The ≥200°C gradient across the footwall at this time implies that the Miocene slip surface originated as a moderately E-dipping normal fault. This Miocene slip surface can be tracked for more than 100 km along strike, but the greatest amount of Miocene slip also coincides with parts of the footwall that were most deeply buried in the Cretaceous. These relations indicate that not only is the SKDC MMC a composite feature, but that the crustal welt created by

  11. Oceanic crustal structure from seismic measurements

    NASA Astrophysics Data System (ADS)

    Grevemeyer, Ingo

    2014-05-01

    The primary source of our knowledge of the structure of oceanic crust is the interpretation of seismic refraction experiments. The first classic compilation of seismic data of Raitt (in The Sea, 1963) subdivided the crust into three distinct layers, which have formed the reference basis for seismic profiles for the last decades. Today we know that the upper igneous crust (layer 2) is a region of strong velocity gradients, while the lower crust (layer 3) is relatively homogeneous, although it does show an increase in velocity with depth. Further, the upper crust has been sub-divided the in Layer 2A, composed of extruded basalts, and Layer 2B, formed by basaltic sheeted dikes. The lower crust, or Layer 3, often called the "oceanic layer", is inferred to be composed of gabbros. As crust ages, sediments accumulate on the igneous basement, creating layer 1. The velocity structure of the oceanic crust formed by seafloor spreading is inherently related to the process of mantle melting. The amount of melt produced by adiabatic decompression of the mantle and the composition of the resultant igneous crust depend on the temperature, composition, and water content of the mantle source. Normal oceanic crust with a thickness of 6-7 km and Mid-Ocean Ridge Basalt (MORB) like composition is the result of decompressional melting of a mantle source composed of dry pyrolite with a mantle temperature of ~1300°C. Thus, crustal formation occurs as passive response to seafloor spreading (i.e., passive upwelling). Higher mantle temperatures or compositional anomalies may cause buoyant upwelling of the mantle (i.e. active upwelling). The combination of active upwelling and higher mantle temperatures, or the presence of a more fertile mantle source, will produce larger amounts of melting and, likely, a thicker crust. Steady state mantle melting models can be used to investigate the relationship between mantle temperature, upwelling, and mantle composition on one hand and lower crustal

  12. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

    Kaynia, Narges; Fang, Nicholas X.; Boyce, Mary C.

    2014-03-01

    Many structured composites found in nature possess undulating and wrinkled interfacial layers that regulate mechanical, chemical, acoustic, adhesive, thermal, electrical and optical functions of the material. This research focused on the complex instability and wrinkling pattern arising in 3D structured composites and the effect of the buckling pattern on the overall structural response. The 3D structured composites consisted of stiffer plates supported by soft matrix on both sides. Compression beyond the critical strain led to complex buckling patterns in the initially straight plates. The motivation of our work is to elaborate the formation of a system of prescribed periodic scatterers (metamaterials) due to buckling, and their effect to interfere wave propagation through the metamaterial structures. Such metamaterials made from elastomers enable large reversible deformation and, as a result, significant changes of the wave propagation properties. We developed analytical and finite element models to capture various aspects of the instability mechanism. Mechanical experiments were designed to further explore the modeling results. The ability to actively alter the 3D composite structure can enable on-demand tunability of many different functions, such as active control of wave propagation to create band-gaps and waveguides.

  13. Structured Light-Based 3D Reconstruction System for Plants

    PubMed Central

    Nguyen, Thuy Tuong; Slaughter, David C.; Max, Nelson; Maloof, Julin N.; Sinha, Neelima

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants.This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701

  14. Structured Light-Based 3D Reconstruction System for Plants.

    PubMed

    Nguyen, Thuy Tuong; Slaughter, David C; Max, Nelson; Maloof, Julin N; Sinha, Neelima

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701

  15. Constructing 3D isotropic and azimuthally anisotropic crustal models across USArray using Rayleigh wave phase velocity and ellipticity: inferring continental stress field

    NASA Astrophysics Data System (ADS)

    Lin, F. C.; Schmandt, B.; Tsai, V. C.

    2014-12-01

    The EarthScope USArray Transportable Array (TA) has provided a great opportunity for imaging the detailed lithospheric structure beneath the continental US. In this presentation, we will report our recent progress on constructing detailed 3D isotropic and anisotropic crustal models of the contiguous US using Rayleigh wave phase velocity and ellipticity measurements across TA. In particular, we will discuss our recent methodology development of extracting short period Rayleigh wave ellipticity, or Rayleigh-wave H/V (horizontal to vertical) amplitude ratios, using multicomponent noise cross-correlations. To retain the amplitude ratio information between vertical and horizontal components, for each station, we perform daily noise pre-processing (temporal normalization and spectrum whitening) simultaneously for all three components. For each station pair, amplitude measurements between cross-correlations of different components (radial-radial, radial-vertical, vertical-radial and vertical-vertical) are then used to determine the Rayleigh-wave H/V ratios at the two station locations. Measurements from all available station pairs are used to determine isotropic and directionally dependent Rayleigh-wave H/V ratios at each location between 8- and 24-second period. The isotropic H/V ratio maps, combined with previous longer period Rayleigh-wave H/V ratio maps from earthquakes and Rayleigh-wave phase velocity maps from both ambient noise and earthquakes, are used to invert for a new 3-D isotropic crustal and upper-mantle model in the western United States. The new model has an outstanding vertical resolution in the upper crust and tradeoffs between different parameters are mitigated. A clear 180-degree periodicity is observed in the directionally dependent H/V ratio measurements for many locations where upper crustal anisotropy is likely strong. Across the US, good correlation is observed between the inferred fast directions in the upper crust and documented maximum

  16. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

    Llewellyn-Jones, Thomas M.; Drinkwater, Bruce W.; Trask, Richard S.

    2016-02-01

    This paper shows the first application of in situ manipulation of discontinuous fibrous structure mid-print, within a 3D printed polymeric composite architecture. Currently, rapid prototyping methods (fused filament fabrication, stereolithography) are gaining increasing popularity within the engineering commnity to build structural components. Unfortunately, the full potential of these components is limited by the mechanical properties of the materials used. The aim of this study is to create and demonstrate a novel method to instantaneously orient micro-scale glass fibres within a selectively cured photocurable resin system, using ultrasonic forces to align the fibres in the desired 3D architecture. To achieve this we have mounted a switchable, focused laser module on the carriage of a three-axis 3D printing stage, above an in-house ultrasonic alignment rig containing a mixture of photocurable resin and discontinuous 14 μm diameter glass fibre reinforcement(50 μm length). In our study, a suitable print speed of 20 mm s-1 was used, which is comparable to conventional additive layer techniques. We show the ability to construct in-plane orthogonally aligned sections printed side by side, where the precise orientation of the configurations is controlled by switching the ultrasonic standing wave profile mid-print. This approach permits the realisation of complex fibrous architectures within a 3D printed landscape. The versatile nature of the ultrasonic manipulation technique also permits a wide range of particle types (diameters, aspect ratios and functions) and architectures (in-plane, and out-plane) to be patterned, leading to the creation of a new generation of fibrous reinforced composites for 3D printing.

  17. All dispenser printed flexible 3D structured thermoelectric generators

    NASA Astrophysics Data System (ADS)

    Cao, Z.; Shi, J. J.; Torah, R. N.; Tudor, M. J.; Beeby, S. P.

    2015-12-01

    This work presents a vertically fabricated 3D thermoelectric generator (TEG) by dispenser printing on flexible polyimide substrate. This direct-write technology only involves printing of electrodes, thermoelectric active materials and structure material, which needs no masks to transfer the patterns onto the substrate. The dimension for single thermoelectric element is 2 mm × 2 mm × 0.5 mm while the distance between adjacent cubes is 1.2 mm. The polymer structure layer was used to support the electrodes which are printed to connect the top ends of the thermoelectric material and ensure the flexibility as well. The advantages and the limitations of the dispenser printed 3D TEGs will also be evaluated in this paper. The proposed method is potential to be a low-cost and scalable fabrication solution for TEGs.

  18. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

    Siler, Drew L; Faulds, James E; Mayhew, Brett; McNamara, David

    2013-06-23

    Robust geothermal activity in the Great Basin, USA is a product of both anomalously high regional heat flow and active fault-controlled extension. Elevated permeability associated with some fault systems provides pathways for circulation of geothermal fluids. Constraining the local-scale 3D geometry of these structures and their roles as fluid flow conduits is crucial in order to mitigate both the costs and risks of geothermal exploration and to identify blind (no surface expression) geothermal resources. Ongoing studies have indicated that much of the robust geothermal activity in the Great Basin is associated with high density faulting at structurally complex fault intersection/interaction areas, such as accommodation/transfer zones between discrete fault systems, step-overs or relay ramps in fault systems, intersection zones between faults with different strikes or different senses of slip, and horse-tailing fault terminations. These conceptualized models are crucial for locating and characterizing geothermal systems in a regional context. At the local scale, however, pinpointing drilling targets and characterizing resource potential within known or probable geothermal areas requires precise 3D characterization of the system. Employing a variety of surface and subsurface data sets, we have conducted detailed 3D geologic analyses of two Great Basin geothermal systems. Using EarthVision (Dynamic Graphics Inc., Alameda, CA) we constructed 3D geologic models of both the actively producing Brady’s geothermal system and a ‘greenfield’ geothermal prospect at Astor Pass, NV. These 3D models allow spatial comparison of disparate data sets in 3D and are the basis for quantitative structural analyses that can aid geothermal resource assessment and be used to pinpoint discrete drilling targets. The relatively abundant data set at Brady’s, ~80 km NE of Reno, NV, includes 24 wells with lithologies interpreted from careful analysis of cuttings and core, a 1

  19. The 3-D inelastic analyses for computational structural mechanics

    NASA Technical Reports Server (NTRS)

    Hopkins, D. A.; Chamis, C. C.

    1989-01-01

    The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.

  20. 3D reconstruction methods of coronal structures by radio observations

    NASA Astrophysics Data System (ADS)

    Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.

    1992-11-01

    The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.

  1. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

    Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.

    1992-01-01

    The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.

  2. Detailed Northern Anatolian Fault Zone crustal structure from receiver functions

    NASA Astrophysics Data System (ADS)

    Cornwell, D. G.; Kahraman, M.; Thompson, D. A.; Houseman, G. A.; Rost, S.; Turkelli, N.; Teoman, U.; Altuncu Poyraz, S.; Gülen, L.; Utkucu, M.

    2013-12-01

    We present high resolution images derived from receiver functions of the continental crust in Northern Turkey that is dissected by two fault strands of the Northern Anatolian Fault Zone (NAFZ). The NAFZ is a major continental strike-slip fault system that is comparable in length and slip rate to the San Andreas Fault Zone. Recent large earthquakes occurred towards the western end of the NAFZ in 1999 at Izmit (M7.5) and Düzce (M7.2). As part of the multi-disciplinary Faultlab project, we aim to develop a model of NAFZ crustal structure and locate deformation by constraining variations in seismic properties and anisotropy in the upper and lower crust. The crustal model will be an input to test deformation scenarios in order to match geodetic observations from different phases of the earthquake loading cycle. We calculated receiver functions from teleseismic earthquakes recorded by a rectangular seismometer array spanning the NAFZ with 66 stations at a nominal inter-station spacing of 7 km and 7 additional stations further afield. This Dense Array for North Anatolia (DANA) was deployed from May 2012 until September 2013 and we selected large events (Mw>5.5) from the high quality seismological dataset to analyze further. Receiver functions were calculated for different frequency bands then collected into regional stacks before being inverted for crustal S-wave velocity structure beneath the entire DANA array footprint. In addition, we applied common conversion point (CCP) migration using a regional velocity model to construct a migrated 3D volume of P-to-S converted and multiple energy in order to identify the major crustal features and layer boundaries. We also performed the CCP migration with transverse receiver functions in order to identify regions of anisotropy within the crustal layers. Our preliminary results show a heterogeneous crust above a flat Moho that is typically at a depth of 33 km. We do not observe a prominent step in the Moho beneath the surface

  3. Dynactin 3D structure: implications for assembly and dynein binding.

    PubMed

    Imai, Hiroshi; Narita, Akihiro; Maéda, Yuichiro; Schroer, Trina A

    2014-09-23

    The multisubunit protein complex, dynactin, is an essential component of the cytoplasmic dynein motor. High-resolution structural work on dynactin and the dynein/dynactin supercomplex has been limited to small subunits and recombinant fragments that do not report fully on either ≈1MDa assembly. In the present study, we used negative-stain electron microscopy and image analysis based on random conical tilt reconstruction to obtain a three-dimensional (3D) structure of native vertebrate dynactin. The 35-nm-long dynactin molecule has a V-shaped shoulder at one end and a flattened tip at the other end, both offset relative to the long axis of the actin-related protein (Arp) backbone. The shoulder projects dramatically away from the Arp filament core in a way that cannot be appreciated in two-dimensional images, which has implications for the mechanism of dynein binding. The 3D structure allows the helical parameters of the entire Arp filament core, which includes the actin capping protein, CP, to be determined for the first time. This structure exhibits near identity to F-actin and can be well fitted into the dynactin envelope. Molecular fitting of modeled CP-Arp polymers into the envelope shows that the filament contains between 7 and 9 Arp protomers and is capped at both ends. In the 7 Arp model, which agrees best with measured Arp stoichiometry and other structural information, actin capping protein (CP) is not present at the distal tip of the structure, unlike what is seen in the other models. The 3D structure suggests a mechanism for dynactin assembly and length specification. PMID:25046383

  4. 3-D Structure of the Slave and Rae Cratons Provides Clues to Their Construction

    NASA Astrophysics Data System (ADS)

    Snyder, D. B.

    2013-12-01

    Deep geologic structures within cratons that make up continental cores were long neglected. Recently acquired geophysical data from large observational arrays and geochemical data resulting from exploration for diamond has now made possible co-registration of large-scale (400-km depth), truly 3-dimensional data sets. P-waves, surface waves and magnetotelluric observations provide 3-D wavespeed and conductivity models. Multi-azimuthal receiver functions map seismic discontinuity surfaces in 3-D. Xenolith suites erupted in kimberlites provide rock samples at key lithospheric depths, albeit at sparsely distributed locations. These multi-disciplinary models are becoming available for several key cratons worldwide; here the deep structure of the Slave and Rae cratons of the Canadian Shield is described. Lithospheric layers with tapered, wedge-shaped margins are common. Slave craton layers are sub-horizontal and indicate construction of the craton core at 2.7 Ga by underthrusting and flat stacking of lithosphere. The central Rae craton has predominantly dipping discontinuities that indicate construction at 1.9 Ga by thrusting similar to that observed in crustal ';thick-skinned' fold-and-thrust belts. 3-D mapping of conductivity and metasomatism, the latter via mineral recrystallization and resetting of isotopic ages, overprints primary structures in both cratons. Distribution of more conductivitve mantle suggests that assumed causative pervasive metasomatism occurs at 100-200 km depths with ';chimneys' reaching to shallower depths, typically in locations where kimberlites or mineralization has occurred.

  5. 3D precision surface measurement by dynamic structured light

    NASA Astrophysics Data System (ADS)

    Franke, Ernest A.; Magee, Michael J.; Mitchell, Joseph N.; Rigney, Michael P.

    2004-02-01

    This paper describes a 3-D imaging technique developed as an internal research project at Southwest Research Institute. The technique is based on an extension of structured light methods in which a projected pattern of parallel lines is rotated over the surface to be measured. A sequence of images is captured and the surface elevation at any location can then be determined from measurements of the temporal pattern, at any point, without considering any other points on the surface. The paper describes techniques for system calibration and surface measurement based on the method of projected quadric shells. Algorithms were developed for image and signal analysis and computer programs were written to calibrate the system and to calculate 3-D coordinates of points on a measured surface. A prototype of the Dynamic Structured Light (DSL) 3-D imaging system was assembled and typical parts were measured. The design procedure was verified and used to implement several different configurations with different measurement volumes and measurement accuracy. A small-parts measurement accuracy of 32 micrometers (.0012") RMS was verified by measuring the surface of a precision-machined plane. Large aircraft control surfaces were measured with a prototype setup that provided .02" depth resolution over a 4" by 8" field of view. Measurement times are typically less than three minutes for 300,000 points. A patent application has been filed.

  6. Myosin filament 3D structure in mammalian cardiac muscle☆

    PubMed Central

    AL-Khayat, Hind A.; Morris, Edward P.; Kensler, Robert W.; Squire, John M.

    2008-01-01

    A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac). PMID:18472277

  7. Deep structure of the Argentine margin inferred from 3D gravity and temperature modelling, Colorado Basin

    NASA Astrophysics Data System (ADS)

    Autin, J.; Scheck-Wenderoth, M.; Götze, H.-J.; Reichert, C.; Marchal, D.

    2016-04-01

    Following previous work on the Colorado Basin using a 3D crustal structural model, we now investigate the presence of lower crustal bodies at the base of the crust using 3D lithospheric gravity modelling and calculations of the conductive thermal field. Our first study highlighted two fault directions and depocentres associated with thinned crust (NW-SE in the West and NE-SW at the distal margin). Fault relative chronology argues for two periods of extension: (1) NW-SE faulting and thinning in the western Colorado Basin and (2) NE-SW faulting and thinning related to the continental breakup and formation of the NE-SW-striking volcanic margins of the Atlantic Ocean. In this study, the geometry of modelled high-density Lower Crustal Bodies (LCBs) enables the reproduction of the gravimetric field as well as of the temperature measured in wells down to 4500 m. The modelled LCBs correlate with geological observations: (1) NW-SE LCBs below the deepest depocentres in the West, (2) NE-SW LCBs below the distal margin faults and the seaward dipping reflectors. Thus the proposed poly-phased evolution of the margin could as well correspond to two emplacement phases of the LCBs. The calculated conductive thermal field fits the measured temperatures best if the thermal properties (thermal conductivity and radiogenic heat production) assigned to the LCBs correspond to either high-grade metamorphic rocks or to mafic magmatic intrusions. To explain the possible lithology of the LCBs, we propose that the two successive phases of extension are accompanied by magma supply, emplaced (1) in the thinnest crust below the older NW-SE depocentres, then (2) along the NE-SW continentward boundary of the distal margin and below the volcanic seaward dipping reflectors. The South African conjugate margin records only the second NE-SW event and we discuss hypotheses which could explain these differences between the conjugate margins.

  8. 3-D simulation of nanopore structure for DNA sequencing.

    PubMed

    Park, Jun-Mo; Pak, Y Eugene; Chun, Honggu; Lee, Jong-Ho

    2012-07-01

    In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures. PMID:22966538

  9. 3-D lookup: Fast protein structure database searches

    SciTech Connect

    Holm. L.; Sander, C.

    1995-12-31

    There are far fewer classes of three-dimensional protein folds than sequence families but the problem of detecting three-dimensional similarities is NP-complete. We present a novel heuristic for identifying 3-D similarities between a query structure and the database of known protein structures. Many methods for structure alignment use a bottom-up approach, identifying first local matches and then solving a combinatorial problem in building up larger clusters of matching substructures. Here the top-down approach is to start with the global comparison and select a rough superimposition using a fast 3-D lookup of secondary structure motifs. The superimposition is then extended to an alignment of C{sup {alpha}} atoms by an iterative dynamic programming step. An all-against-all comparison of 385-representative proteins (150,000 pair comparisons) took 1 day of computer time on a single R8000 processor. In other words, one query structure is scanned against the database in a matter of minutes. The method is rated at 90% reliability at capturing statistically significant similarities. It is useful as a rapid preprocessor to a comprehensive protein structure database search system.

  10. Structure and magnetic exchange in heterometallic 3d-3d transition metal triethanolamine clusters.

    PubMed

    Langley, Stuart K; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S

    2012-01-21

    Synthetic methods are described that have resulted in the formation of seven heterometallic complexes, all of which contain partially deprotonated forms of the ligand triethanolamine (teaH(3)). These compounds are [Mn(III)(4)Co(III)(2)Co(II)(2)O(2)(teaH(2))(2)(teaH)(0.82)(dea)(3.18)(O(2)CMe)(2)(OMe)(2)](BF(4))(2)(O(2)CMe)(2)·3.18MeOH·H(2)O (1), [Mn(II)(2)Mn(III)(2)Co(III)(2)(teaH)(4)(OMe)(2)(acac)(4)](NO(3))(2)·2MeOH (2), [Mn(III)(2)Ni(II)(4)(teaH)(4)(O(2)CMe)(6)]·2MeCN (3), [Mn(III)(2)Co(II)(2)(teaH)(2)(sal)(2)(acac)(2)(MeOH)(2)]·2MeOH (4), [Mn(II)(2)Fe(III)(2)(teaH)(2)(paa)(4)](NO(3))(2)·2MeOH·CH(2)Cl(2) (5), [Mn(II)Mn(III)(2)Co(III)(2)O(teaH)(2)(dea)(Iso)(OMe)(F)(2)(Phen)(2)](BF(4))(NO(3))·3MeOH (6) and [Mn(II)(2)Mn(III)Co(III)(2)(OH)(teaH)(3)(teaH(2))(acac)(3)](NO(3))(2)·3CH(2)Cl(2) (7). All of the compounds contain manganese, combined with 3d transition metal ions such as Fe, Co and Ni. The crystal structures are described and examples of 'rods', tetranuclear 'butterfly' and 'triangular' Mn(3) cluster motifs, flanked in some cases by diamagnetic cobalt(III) centres, are presented. Detailed DC and AC magnetic susceptibility and magnetization studies, combined with spin Hamiltonian analysis, have yielded J values and identified the spin ground states. In most cases, the energies of the low-lying excited states have also been obtained. The features of note include the 'inverse butterfly' spin arrangement in 2, 4 and 5. A S = 5/2 ground state occurs, for the first time, in the Mn(III)(2)Mn(II) triangular moiety within 6, the many other reported [Mn(3)O](6+) examples having S = ½ or 3/2 ground states. Compound 7 provides the first example of a Mn(II)(2)Mn(III) triangle, here within a pentanuclear Mn(3)Co(2) cluster. PMID:22113523

  11. Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions

    PubMed Central

    Jun, Sangmi; Zhao, Gongpu; Ning, Jiying; Gibson, Gregory A.; Watkins, Simon C.; Zhang, Peijun

    2013-01-01

    Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-physiological state1. However, direct visualization of individual viral complexes in their host cellular environment with cryoET is challenging2, due to the infrequent and dynamic nature of viral entry, particularly in the case of HIV-1. While time-lapse live-cell imaging has yielded a great deal of information about many aspects of the life cycle of HIV-13-7, the resolution afforded by live-cell microscopy is limited (~ 200 nm). Our work was aimed at developing a correlation method that permits direct visualization of early events of HIV-1 infection by combining live-cell fluorescent light microscopy, cryo-fluorescent microscopy, and cryoET. In this manner, live-cell and cryo-fluorescent signals can be used to accurately guide the sampling in cryoET. Furthermore, structural information obtained from cryoET can be complemented with the dynamic functional data gained through live-cell imaging of fluorescent labeled target. In this video article, we provide detailed methods and protocols for structural investigation of HIV-1 and host-cell interactions using 3D correlative high-speed live-cell imaging and high-resolution cryoET structural analysis. HeLa cells infected with HIV-1 particles were characterized first by confocal live-cell microscopy, and the region containing the same viral particle was then analyzed by cryo-electron tomography for 3D structural details. The correlation between two sets of imaging data, optical imaging and electron imaging, was achieved using a home-built cryo-fluorescence light microscopy stage. The approach detailed here will be valuable, not only for study of virus-host cell interactions, but also for broader applications in cell biology, such as cell signaling, membrane receptor trafficking, and many other dynamic cellular processes. PMID:23852318

  12. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

    A new image matching technique is described. It is implemented as an object-independent hierarchical structural juxtaposition algorithm based on an alphabet of simple object-independent contour structural elements. The structural matching applied implements an optimized method of walking through a truncated tree of all possible juxtapositions of two sets of structural elements. The algorithm was initially developed for dealing with 2D images such as the aerospace photographs, and it turned out to be sufficiently robust and reliable for matching successfully the pictures of natural landscapes taken in differing seasons from differing aspect angles by differing sensors (the visible optical, IR, and SAR pictures, as well as the depth maps and geographical vector-type maps). At present (in the reported version), the algorithm is enhanced based on additional use of information on third spatial coordinates of observed points of object surfaces. Thus, it is now capable of matching the images of 3D scenes in the tasks of automatic navigation of extremely low flying unmanned vehicles or autonomous terrestrial robots. The basic principles of 3D structural description and matching of images are described, and the examples of image matching are presented.

  13. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  14. Receiver function analysis of crustal structure beneath northeast Tibet

    NASA Astrophysics Data System (ADS)

    Li, X.; Shen, Y.; Li, H.; Shi, D.; Sandvol, E. A.; Li, A.

    2013-12-01

    The Tibetan Plateau has been the prime site to understand the processes of continental collision, mountain building, and the interaction between tectonics. More detailed studies of crustal structure in northeast Tibet can be of great benefit to the understanding of crustal deformation and plateau growth mechanisms. We investigat crustal structure beneath 64 seismic stations in the northeast Tibet using the receiver function method to estimate the crustal thickness by analyzing the collected three-component teleseismic data recorded by 29 stations between June, 2008 and July, 2010 deployed by China University of Geosciences and 35 Ascent stations deployed between May, 2007 and August, 2008. The distributions of the crustal thickness have a good correlation with the known geological tectonic features. The images of Moho depth suggests the lateral variations of the crustal thickness decreasing from the northeastern margin of the Tibet (~70 km) to the Ordos Block (~40 km). The observations disagree with the crustal composition beneath the northeastern margin of the Tibetan plateau. Our results of crustal structure in this study area not only reveal the lateral inhomogeneity of the crustal structure but also provide some constraints on understanding the mechanism of uplift and crustal thickening of the Tibet and insights into the geodynamic process between the Tibet and its adjacent blocks.

  15. Engineering extracellular matrix structure in 3D multiphase tissues

    PubMed Central

    Gillette, Brian M.; Rossen, Ninna S.; Das, Nikkan; Leong, Debra; Wang, Meixin; Dugar, Arushi; Sia, Samuel K.

    2011-01-01

    In native tissues, microscale variations in the extracellular matrix (ECM) structure can drive different cellular behaviors. Although control over ECM structure could prove useful in tissue engineering and in studies of cellular behavior, isotropic 3D matrices poorly replicate variations in local microenvironments. In this paper, we demonstrate a method to engineer local variations in the density and size of collagen fibers throughout 3D tissues. The results showed that, in engineered multiphase tissues, the structures of collagen fibers in both the bulk ECM phases (as measured by mesh size and width of fibers) as well as at tissue interfaces (as measured by density of fibers and thickness of tissue interfaces) could be modulated by varying the collagen concentrations and gelling temperatures. As the method makes use of a previously published technique for tissue bonding, we also confirmed that significant adhesion strength at tissue interfaces was achieved under all conditions tested. Hence, this study demonstrates how collagen fiber structures can be engineered within all regions of a tightly integrated multiphase tissue scaffold by exploiting knowledge of collagen assembly. PMID:21840047

  16. Complete Tem-Tomography: 3D Structure of Gems Cluster

    NASA Technical Reports Server (NTRS)

    Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

    2015-01-01

    GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

  17. Direct ambient noise tomography for 3-D near surface shear velocity structure: methodology and applications

    NASA Astrophysics Data System (ADS)

    Yao, H.; Fang, H.; Li, C.; Liu, Y.; Zhang, H.; van der Hilst, R. D.; Huang, Y. C.

    2014-12-01

    Ambient noise tomography has provided essential constraints on crustal and uppermost mantle shear velocity structure in global seismology. Recent studies demonstrate that high frequency (e.g., ~ 1 Hz) surface waves between receivers at short distances can be successfully retrieved from ambient noise cross-correlation and then be used for imaging near surface or shallow crustal shear velocity structures. This approach provides important information for strong ground motion prediction in seismically active area and overburden structure characterization in oil and gas fields. Here we propose a new tomographic method to invert all surface wave dispersion data for 3-D variations of shear wavespeed without the intermediate step of phase or group velocity maps.The method uses frequency-dependent propagation paths and a wavelet-based sparsity-constrained tomographic inversion. A fast marching method is used to compute, at each period, surface wave traveltimes and ray paths between sources and receivers. This avoids the assumption of great-circle propagation that is used in most surface wave tomographic studies, but which is not appropriate in complex media. The wavelet coefficients of the velocity model are estimated with an iteratively reweighted least squares (IRLS) algorithm, and upon iterations the surface wave ray paths and the data sensitivity matrix are updated from the newly obtained velocity model. We apply this new method to determine the 3-D near surface wavespeed variations in the Taipei basin of Taiwan, Hefei urban area and a shale and gas production field in China using the high-frequency interstation Rayleigh wave dispersion data extracted from ambient noisecross-correlation. The results reveal strong effects of off-great-circle propagation of high-frequency surface waves in these regions with above 30% shear wavespeed variations. The proposed approach is more efficient and robust than the traditional two-step surface wave tomography for imaging complex

  18. Characterizing 3D Vegetation Structure from Space: Mission Requirements

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G.; Bergen, Kathleen; Blair, James B.; Dubayah, Ralph; Houghton, Richard; Hurtt, George; Kellndorfer, Josef; Lefsky, Michael; Ranson, Jon; Saatchi, Sasan; Shugart, H. H.; Wickland, Diane

    2012-01-01

    Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral

  19. 3D Seismic Reflection Imaging of Crustal Formation Processes on the East Pacific Rise, 9°57-42'N

    NASA Astrophysics Data System (ADS)

    Purdy, G. M.; Mutter, J. C.; Carbotte, S. M.; Canales, J. P.; Nedimovic, M. R.; Carton, H.; Newman, K. R.; Marjanovic, M.; Xu, M.; Aghaei, O.; Stowe, L. C.

    2008-12-01

    Between June 29th and August 19th 2008 the research vessel Marcus G Langseth carried out its first multi- streamer 3D seismic reflection imaging cruise, MGL08-12, by conducting a program research on the East Pacific Rise centered around 9°50'N. The primary goals were to create an accurate 3D seismic reflection image of the magmatic-hydrothermal system at this Integrated Study Site of the Ridge2000 program by imaging the structure of the axial magma chamber (AMC) lid and oceanic crust at a resolution, accuracy, and scale comparable to seafloor observations. The vessel acquired data with four, 6-kilometer solid streamers each comprising 468 active channels deployed with a total separation of 450 meters. Four gun strings with total volume of 3300 cubic inches in two groups fired alternately provide the source for a shot spacing of 37.5 meters. This configuration yields eight CMP lines for each of the sail lines that were spaced 300 m apart, and a static bin size of 6.25 m × 37.5 m in the along-track and across-track directions, respectively, providing a nominal fold of 40. The cruise accomplished the acquisition of ~3,782 km of sail line data. There are 111 across axis lines that required 10 repeated lines and 14 infills. Average feathering during the cruise was 0° ± 5° (one standard deviation), with maximum values of up to 11°. This means that 18% of the total cross axis acquisition was needed for reshoots and infilling. A 25% multiplier on planned lines for a 3D grid is probably a useful figure to use in cruise planning and is fairly standard in the seismic industry. Data quality meets or exceeds industry standards. 3D coverage was achieved in two areas. The larger comprises a set of 93 equally spaced lines forming the 3D grid between 9°57'N and 9°42'N. This grid is made up of lines from all of racetracks #1 and #2 and the northern lines of racetrack#3 and covers two principal hydrothermal vent areas in a continuous fashion. The second 3D area is comprised

  20. Structural analysis of tropical cyclone using INSAT-3D observations

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

    The continuous observations from visible and thermal infrared (TIR) channels of geostationary satellites are highly useful for obtaining the features associated with the shape and dynamics of cloud structures within the tropical cyclones (TCs). As TC develops from an unstructured cloud cluster and intensifies, the cloud structures become more axisymmetric around the centre of the TC. To better understand the structure of TC during different stages of its evolution i.e. from its cyclogenesis to maturity and dissipation, the continuous satellite observations plays a key role. The high spatial and temporal resolution observations from geostationary satellites are very useful in order to analyze the cloud organization during the cyclogenesis. The gradient of the brightness temperatures measures the level of symmetry of each structure, which characterizes the degree of cloud organization of the TC. In the present work, the structural analysis of TC during its life period using the observations from Indian geostationary satellite INSAT-3D has been discussed. The visible and TIR observations from INSAT-3D satellite were used to fix the center position of the cyclone which is an input for the cyclone track and intensity prediction models. This data is also used to estimate the intensity of cyclone in the advanced Dvorak technique (ADT), and in the estimation of radius of maximum winds (Rmax) of TC which is an essential input parameter for the prediction of storm surge associated to the cyclones. The different patterns of cloud structure during the intensification stage, eye-wall formation and dissipation have been discussed. The early identification of these features helps in predicting the rapid intensification of TC which in turn improves the intensity predictions.

  1. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

    Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein

  2. 3D structure and conductive thermal field of the Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Bär, Kristian; Stiller, Manfred; Fritsche, Johann-Gerhard; Kracht, Matthias

    2016-04-01

    The Upper Rhine Graben (URG) was formed as part of the European Cenozoic Rift System in a complex extensional setting. At present-day, it has a large socioeconomic relevance as it provides a great potential for geothermal energy production in Germany and France. For the utilisation of this energy resource it is crucial to understand the structure and the observed temperature anomalies in the rift basin. In the framework of the EU-funded "IMAGE" project (Integrated Methods for Advanced Geothermal Exploration), we apply a data-driven numerical modelling approach to quantify the processes and properties controlling the spatial distribution of subsurface temperatures. Typically, reservoir-scale numerical models are developed for predictions on the subsurface hydrothermal conditions and for reducing the risk of drilling non-productive geothermal wells. One major problem related to such models is setting appropriate boundary conditions that define, for instance, how much heat enters the reservoir from greater depths. Therefore, we first build a regional lithospheric-scale 3D structural model, which covers not only the entire URG but also adjacent geological features like the Black Forest and the Vosges Mountains. In particular, we use a multidisciplinary dataset (e.g. well data, seismic reflection data, existing structural models, gravity) to construct the geometries of the sediments, the crust and the lithospheric mantle that control the spatial distribution of thermal conductivity and radiogenic heat production and hence temperatures. By applying a data-based and lithology-dependent parameterisation of this lithospheric-scale 3D structural model and a 3D finite element method, we calculate the steady-state conductive thermal field for the entire region. Available measured temperatures (down to depths of up to 5 km) are considered to validate the 3D thermal model. We present major characteristics of the lithospheric-scale 3D structural model and results of the 3D

  3. An Elastic/Viscoelastic Finite Element Analysis Method for Crustal Deformation using a 3D Island-scale High-fidelity Model

    NASA Astrophysics Data System (ADS)

    Ichimura, Tsuyoshi; Agata, Ryoichiro; Hori, Takane; Hirahara, Kazuro; Hashimoto, Chihiro; Hori, Muneo; Fukahata, Yukitoshi

    2016-04-01

    As a result of the accumulation of high-resolution observation data, three-dimensional high-fidelity crustal structure data for large domains are becoming available. However, it has been difficult to use such data to perform elastic/viscoelastic crustal deformation analyses in large domains with quality assurance of the numerical simulation that guarantees convergence of the numerical solution with respect to the discretisation size, because the costs of analysis are significantly high. This paper proposes a method of constructing a high-fidelity crustal structure finite element (FE) model using high-fidelity crustal structure data and fast FE analysis to reduce the costs of analysis (based on automatic FE model generation for parallel computation, OpenMP/MPI hybrid parallel computation on distributed memory computers, a geometric multigrid, variable preconditioning, and multiple precision arithmetic). Using the proposed methods, we construct 10 billion degree-of-freedom high-fidelity crustal structure FE models for the entire Japan, and conduct elastic/viscoelastic crustal deformation analysis using this model with enough high accuracy of the numerical simulation.

  4. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

    Clancy, Neil T.; Lin, Jianyu; Arya, Shobhit; Hanna, George B.; Elson, Daniel S.

    2015-03-01

    Intraoperative feedback on tissue function, such as blood volume and oxygenation would be useful to the surgeon in cases where current clinical practice relies on subjective measures, such as identification of ischaemic bowel or tissue viability during anastomosis formation. Also, tissue surface profiling may be used to detect and identify certain pathologies, as well as diagnosing aspects of tissue health such as gut motility. In this paper a dual modality laparoscopic system is presented that combines multispectral reflectance and 3D surface imaging. White light illumination from a xenon source is detected by a laparoscope-mounted fast filter wheel camera to assemble a multispectral image (MSI) cube. Surface shape is then calculated using a spectrally-encoded structured light (SL) pattern detected by the same camera and triangulated using an active stereo technique. Images of porcine small bowel were acquired during open surgery. Tissue reflectance spectra were acquired and blood volume was calculated at each spatial pixel across the bowel wall and mesentery. SL features were segmented and identified using a `normalised cut' algoritm and the colour vector of each spot. Using the 3D geometry defined by the camera coordinate system the multispectral data could be overlaid onto the surface mesh. Dual MSI and SL imaging has the potential to provide augmented views to the surgeon supplying diagnostic information related to blood supply health and organ function. Future work on this system will include filter optimisation to reduce noise in tissue optical property measurement, and minimise spot identification errors in the SL pattern.

  5. 3D crustal architecture of the Alps-Apennines join — a new view on seismic data

    NASA Astrophysics Data System (ADS)

    Schumacher, M. E.; Laubscher, H. P.

    1996-08-01

    Seismic data from the Alps-Apennines join have usually been interpreted in the form of 2D cross-sections, passing either through the Western Alps or the Ligurian Alps-Monferrato Apennines. However, the oblique SE-NW convergence of Adria and Europa and superimposed rotations imply a distinct 3D kinematic development around the Adriatic Indenter (AI), the westernmost spur of Adria. In order to develop kinematic models, data on motion at the different margins of AI must be coordinated. Along the northern margin, the dextrally transpressive Insubric line (IL) was active between 25 and 16 Ma (Insubric-Helvetic phase of Alpine orogeny). Contemporaneously, along the southern margin (Paleo-Apenninic phase), a complementary sinistral motion took place along the Villalvernia-Varzi line (VVL). It emplaced the Monferrato Apennines westward to the north of the Ligurian Alps by carrying them westward on top of AI. Between 14 and 6 Ma (Jura-Lombardic phase of Alpine orogeny) the Lombardic thrust belt developed on the northern margin of AI, now largely hidden under the Po plain. Its continuation to the southwest is impeded by older thrust masses along the Western Alps that consist largely of basement, their sediments having been eroded, as noted on the deep reflection line CROP ALPI-1 by earlier investigators. This line, moreover, contains a deep reflection band originating in the autochthonous Mesozoic of the Apenninic foredeep. In order to better visualize this origin and the relation of further elements identified on reflection lines around the northwestern end of the Monferrato Apennines, a 3D fence diagram was constructed. It helps in establishing a 3D structural-kinematic model of the Alps-Apennines join based on the kinematics of AI. This model features an underthrust of AI under the western Alps in the Paleo-Apenninic phase. In the course of this underthrust, the Paleo-Apenninic elements of the Monferrato moved under the marginal thrusts of the western Alps. Subsequent Neo

  6. 3D modelling of non-linear visco-elasto-plastic crustal and lithospheric processes using LaMEM

    NASA Astrophysics Data System (ADS)

    Popov, Anton; Kaus, Boris

    2016-04-01

    LaMEM (Lithosphere and Mantle Evolution Model) is a three-dimensional thermo-mechanical numerical code to simulate crustal and lithospheric deformation. The code is based on a staggered finite difference (FDSTAG) discretization in space, which is a stable and very efficient technique to solve the (nearly) incompressible Stokes equations that does not suffer from spurious pressure modes or artificial compressibility (a typical feature of low-order finite element techniques). Higher order finite element methods are more accurate than FDSTAG methods under idealized test cases where the jump in viscosity is exactly aligned with the boundaries of the elements. Yet, geodynamically more realistic cases involve evolving subduction zones, nonlinear rheologies or localized plastic shear bands. In these cases, the viscosity pattern evolves spontaneously during a simulation or even during nonlinear iterations, and the advantages of higher order methods disappear and they all converge with approximately first order accuracy, similar to that of FDSTAG [1]. Yet, since FDSTAG methods have considerably less degrees of freedom than quadratic finite element methods, they require about an order of magnitude less memory for the same number of nodes in 3D which also implies that every matrix-vector multiplication is significantly faster. LaMEM is build on top of the PETSc library and uses the particle-in-cell technique to track material properties, history variables which makes it straightforward to incorporate effects like phase changes or chemistry. An internal free surface is present, together with (simple) erosion and sedimentation processes, and a number of methods are available to import complex geometries into the code (e.g, http://geomio.bitbucket.org). Customized Galerkin coupled geometric multigrid preconditioners are implemented which resulted in a good parallel scalability of the code (we have tested LaMEM on 458'752 cores [2]). Yet, the drawback of using FDSTAG

  7. The deep geothermal potential of Berlin (Germany) - Predictions from 3D structural and thermal modelling

    NASA Astrophysics Data System (ADS)

    Sippel, Judith; Fuchs, Sven; Cacace, Mauro; Kastner, Oliver; Huenges, Ernst; Scheck-Wenderoth, Magdalena

    2013-04-01

    In the light of an aspired reduction of CO2 emissions for Germany's capital Berlin, one possible alternative for meeting the city's growing energy demands lies in deep geothermal energy. To minimise exploration risks, a profound knowledge about the subsurface temperature distribution is indispensable. We present a 3D structural model that is used for thermal modelling and thus correlates calculated subsurface temperatures with geothermally relevant structures in the deep subsurface of Berlin - an ideal base for improving the probability of finding adequate geothermal reservoirs. Berlin is located in the eastern part of the North German Basin which is filled with several thousand metres of Permian to Cenozoic sediments containing hot and water bearing aquifers to potentially be used as hydrothermal reservoirs. To characterise the geological underground, the 3D structural model integrates stratigraphical, petrophysical and well-log based information from local boreholes as well as stratigraphic trends from (seismic data based) regional 3D models. The model differentiates 21 geological units: 17 Permian-Cenozoic sedimentary layers, pre-Permian sediments, upper crust, lower crust and the lithospheric mantle. Based on this 3D geological model complemented by databased lithology-dependent thermal properties, two groups of numerical thermal simulations have been carried out: calculations of the steady-state conductive thermal field and simulations of coupled fluid and heat transport. The 3D thermal models predict large lateral variations in temperatures that are validated by high-precession temperature logs. These variations are mostly caused by three specific geological layers and their physical properties: the Permian Zechstein salt with its markedly high thermal conductivity and strong thickness variation (171-3442 m); the crystalline upper crustal layer with its high radiogenic heat production and decreasing thickness from east to west; and the Tertiary Rupelian

  8. 3D Shape and Indirect Appearance by Structured Light Transport.

    PubMed

    OToole, Matthew; Mather, John; Kutulakos, Kiriakos N

    2016-07-01

    We consider the problem of deliberately manipulating the direct and indirect light flowing through a time-varying, general scene in order to simplify its visual analysis. Our approach rests on a crucial link between stereo geometry and light transport: while direct light always obeys the epipolar geometry of a projector-camera pair, indirect light overwhelmingly does not. We show that it is possible to turn this observation into an imaging method that analyzes light transport in real time in the optical domain, prior to acquisition. This yields three key abilities that we demonstrate in an experimental camera prototype: (1) producing a live indirect-only video stream for any scene, regardless of geometric or photometric complexity; (2) capturing images that make existing structured-light shape recovery algorithms robust to indirect transport; and (3) turning them into one-shot methods for dynamic 3D shape capture. PMID:27295455

  9. Crustal structure of east central Oregon: Relation between Newberry Volcano and regional crustal structure

    NASA Astrophysics Data System (ADS)

    Catchings, R. D.; Mooney, W. D.

    1988-09-01

    A 180-km-long seismic refraction transect from the eastern High Cascades, across Newberry Volcano, to the eastern High Lava Plains is used to investigate the subvolcanic crustal and upper mantle velocity structure there. Near-surface volcanic flows and sedimentary debris (1.6-4.7 km/s), ranging from 3 to 5 km in thickness, overlie subvolcanic Basin and Range structures. East and west of Newberry Volcano, the subvolcanic basement (5.6 km/s) has been downwarped, producing 5-km-deep basins. The midcrust (8- to 28-km depth) is characterized by velocities ranging from 6.1 to 6.5 km/s and varies laterally in thicknesses. The lower crust is characterized by art unusually high velocity (about 7.4 km/s), and its geometry mirrors the subvolcanic basement geometry. The Moho is located at a depth of 37 km and represents a transition to an upper mantle velocity of 8.1 km/s. The shallow subsurface (1.2 km) beneath Newberry Volcano is characterized by high-velocity (5.6 km/s, versus 4.1 km/s for the surrounding area) intrusions and appears to be located on a basement high. Beneath the seismic refraction array at Newberry Volcano, an absence of low-velocity anomalies suggests that large silicic magma chambers do not exist in the upper crust, but apparent high attenuation of the seismic wave field may be consistent with either partial melts in small volumes, elevated crustal temperatures, and/or poor geophonerecording site coupling. The east central Oregon velocity structure is nearly identical to that of the northwestern Nevada Basin and Range and the Modoc Plateau of northeastern California, and variations in the deep crustal structure about Newberry Volcano are consistent with tectonism involving crustal underplating, melting, and extension. If paleomagnetic estimates of extension in the east central Oregon area are correct, the North American continent experienced significant growth through extension, underplating, and volcanism in east central Oregon. Comparison of east

  10. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

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

  11. Crustal structure of Mars from gravity and topography

    NASA Technical Reports Server (NTRS)

    Neumann, G. A.; Zuber, M. T.; Wieczorek, M. A.; McGovern, P. J.; Lemoine, F. G.; Smith, D. E.

    2004-01-01

    Mars Orbiter Laser Altimeter (MOLA) topography and gravity models from 5 years of Mars Global Surveyor (MGS) spacecraft tracking provide a window into the structure of the Martian crust and upper mantle. We apply a finite-amplitude terrain correction assuming uniform crustal density and additional corrections for the anomalous densities of the polar caps, the major volcanos, and the hydrostatic flattening of the core. A nonlinear inversion for Moho relief yields a crustal thickness model that obeys a plausible power law and resolves features as small as 300 km wavelength. On the basis of petrological and geophysical constraints, we invoke a mantle density contrast of 600 kg m-3; with this assumption, the Isidis and Hellas gravity anomalies constrain the global mean crustal thickness to be >45 km. The crust is characterized by a degree 1 structure that is several times larger than any higher degree harmonic component, representing the geophysical manifestation of the planet's hemispheric dichotomy. It corresponds to a distinction between modal crustal thicknesses of 32 km and 58 km in the northern and southern hemispheres, respectively. The Tharsis rise and Hellas annulus represent the strongest components in the degree 2 crustal thickness structure. A uniform highland crustal thickness suggests a single mechanism for its formation, with subsequent modification by the Hellas impact, erosion, and the volcanic construction of Tharsis. The largest surviving lowland impact, Utopia, post-dated formation of the crustal dichotomy. Its crustal structure is preserved, making it unlikely that the northern crust was subsequently thinned by internal processes.

  12. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

    Birch, Gabriel Carisle; Dagel, Amber Lynn; Kast, Brian A.; Smith, Collin S.

    2015-09-01

    Three-dimensional (3D) information in a physical security system is a highly useful dis- criminator. The two-dimensional data from an imaging systems fails to provide target dis- tance and three-dimensional motion vector, which can be used to reduce nuisance alarm rates and increase system effectiveness. However, 3D imaging devices designed primarily for use in physical security systems are uncommon. This report discusses an architecture favorable to physical security systems; an inexpensive snapshot 3D imaging system utilizing a simple illumination system. The method of acquiring 3D data, tests to understand illumination de- sign, and software modifications possible to maximize information gathering capability are discussed.

  13. An Efficient 3D Imaging using Structured Light Systems

    NASA Astrophysics Data System (ADS)

    Lee, Deokwoo

    Structured light 3D surface imaging has been crucial in the fields of image processing and computer vision, particularly in reconstruction, recognition and others. In this dissertation, we propose the approaches to development of an efficient 3D surface imaging system using structured light patterns including reconstruction, recognition and sampling criterion. To achieve an efficient reconstruction system, we address the problem in its many dimensions. In the first, we extract geometric 3D coordinates of an object which is illuminated by a set of concentric circular patterns and reflected to a 2D image plane. The relationship between the original and the deformed shape of the light patterns due to a surface shape provides sufficient 3D coordinates information. In the second, we consider system efficiency. The efficiency, which can be quantified by the size of data, is improved by reducing the number of circular patterns to be projected onto an object of interest. Akin to the Shannon-Nyquist Sampling Theorem, we derive the minimum number of circular patterns which sufficiently represents the target object with no considerable information loss. Specific geometric information (e.g. the highest curvature) of an object is key to deriving the minimum sampling density. In the third, the object, represented using the minimum number of patterns, has incomplete color information (i.e. color information is given a priori along with the curves). An interpolation is carried out to complete the photometric reconstruction. The results can be approximately reconstructed because the minimum number of the patterns may not exactly reconstruct the original object. But the result does not show considerable information loss, and the performance of an approximate reconstruction is evaluated by performing recognition or classification. In an object recognition, we use facial curves which are deformed circular curves (patterns) on a target object. We simply carry out comparison between the

  14. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

    Gritto, Roland; O'Connell, Daniel; Elobaid Elnaiem, Ali; Mohamed, Fathelrahman; Sadooni, Fadhil

    2016-04-01

    The Middle-East has seen a recent boom in construction including the planning and development of complete new sub-sections of metropolitan areas. Before planning and construction can commence, however, the development areas need to be investigated to determine their suitability for the planned project. Subsurface parameters such as the type of material (soil/rock), thickness of top soil or rock layers, depth and elastic parameters of basement, for example, comprise important information needed before a decision concerning the suitability of the site for construction can be made. A similar problem arises in environmental impact studies, when subsurface parameters are needed to assess the geological heterogeneity of the subsurface. Environmental impact studies are typically required for each construction project, particularly for the scale of the aforementioned building boom in the Middle East. The current study was conducted in Qatar at the location of a future highway interchange to evaluate a suite of 3D seismic techniques in their effectiveness to interrogate the subsurface for the presence of karst-like collapse structures. The survey comprised an area of approximately 10,000 m2 and consisted of 550 source- and 192 receiver locations. The seismic source was an accelerated weight drop while the geophones consisted of 3-component 10 Hz velocity sensors. At present, we analyzed over 100,000 P-wave phase arrivals and performed high-resolution 3-D tomographic imaging of the shallow subsurface. Furthermore, dispersion analysis of recorded surface waves will be performed to obtain S-wave velocity profiles of the subsurface. Both results, in conjunction with density estimates, will be utilized to determine the elastic moduli of the subsurface rock layers.

  15. Improved hybrid optimization algorithm for 3D protein structure prediction.

    PubMed

    Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins. PMID:25069136

  16. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

    Coronal Mass Ejections (CMEs) represent one of the most powerful energy release phenomena in the entire solar system and are a major driver of space weather. Prior to 2006, our observational access to CMEs was limited to single viewpoint remote sensing observations in the inner/outer corona, and in-situ observations further away, e.g. at 1 AU. Taking all these factors together, turned out to be a major obstacle in our understanding and characterizing of the 3D structure and evolution of CMEs. The situation improved dramatically with the availability of multi-viewpoint imaging observations of CMEs, all way through from the Sun to 1 AU, from the STEREO mission since 2006, combined with observations from other missions (SOHO, Hinode, SDO, IRIS). With this talk we will discuss several key recent results in CME science resulting from the analysis of multi-viewpoint observations. This includes: (1) shape and structure; (2) kinematics and energetics; (3) trajectories, deflections and rotations; (4) arrival times and velocities at 1 AU; (5) magnetic field structure; (6) relationships with coronal and interplanetary shocks and solar energetic particles. The implications of these results in terms of CME theories and models will be also addressed. We will conclude with a discussion of important open issues in our understanding of CMEs and how these could be addressed with upcoming (Solar Orbiter, Solar Probe Plus) and under-study missions (e.g., L5).

  17. The lithospheric-scale 3D structural configuration of the North Alpine Foreland Basin constrained by gravity modelling and the calculation of the 3D load distribution

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2014-05-01

    The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International

  18. 3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site

    NASA Astrophysics Data System (ADS)

    Schneeberger, Raphael; Kober, Florian; Berger, Alfons; Spillmann, Thomas; Herwegh, Marco

    2015-04-01

    each other, water flow is high. Our 3D structural model allows the recognition of such intersections in 3D space and the prediction of their spatial extent. The structural model developed with the introduction of the locally known hydraulic permeabilities and in combination with the results of on-going hydrochemical investigations will allow to estimate the location of the recently active water pathways. References Wehrens, P., Baumberger, R., Berger, A., & Herwegh, M. (in prep.). How is strain localized in a mid-crustal basement section? Spatial distribution of deformation in the Aar massif (Switzerland).

  19. Crustal Structure beneath Mexico from Receiver Functions

    NASA Astrophysics Data System (ADS)

    Espindola, V.; Quintanar, L.; Espindola, J.

    2011-12-01

    The Servicio Sismológico Nacional (SSN) is Mexico's official organism in charge of the observation of seismicity in the country. Operated by the Universidad Nacional Autonoma de Mexico, it counts with 32 broadband stations deployed throughout the country. The coverage includes most of the geologic provinces of the territory, which vary widely in their geologic characteristics. The availability of records from teleseisms at those stations makes feasible to obtain sound and homogeneous estimates of the structure of the crust in the Mexican territory through the analysis of receiver functions (RF). In this work we present the results of the analysis of RF obtained from events registered from 1998 to 2009 in the 32 stations of the SSN. The RF technique, which uses converted phases at major velocity discontinuities, is a well established technique to infer the velocity contrasts and thickness of the underlying crust. Using this method we were able to infer the depth of the Moho, a major intracrustal discontinuity and in some cases the depth to the base of the subducting plate. We present maps of crustal thickness in Mexico, which varies between about 29 km in the Yucatan peninsula to more than 40 km in central Mexico. Poisson's coefficient varies between 0.19 and 0.30. The position of the descending slab shows a large variation in the subduction angle (from about 6° in the SE margin of the Pacific coast to about 60° in the NW ) as has been found from other techniques.

  20. CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins

    PubMed Central

    Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function. PMID:24748753

  1. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

    Hopf, Thomas A.; Colwell, Lucy J.; Sheridan, Robert; Rost, Burkhard; Sander, Chris; Marks, Debora S.

    2012-01-01

    Summary We show that amino acid co-variation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this technique to predict previously unknown, 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. The prediction method (EVfold_membrane), applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. We benchmark the approach with blinded, de novo computation of known transmembrane protein structures from 23 families, demonstrating unprecedented accuracy of the method for large transmembrane proteins. We show how the method can predict oligomerization, functional sites, and conformational changes in transmembrane proteins. With the rapid rise in large-scale sequencing, more accurate and more comprehensive information on evolutionary constraints can be decoded from genetic variation, greatly expanding the repertoire of transmembrane proteins amenable to modelling by this method. PMID:22579045

  2. Simulating Seismic Wave Propagation in 3-D Structure: A Case Study For Istanbul City

    NASA Astrophysics Data System (ADS)

    Yelkenci, Seda; Aktar, Mustafa

    2013-04-01

    Investigation of the wave propagation around the Marmara Sea, in particular for the city of Istanbul is critical because this target area is identified as one of the megacities with the highest seismic risk in the world. This study makes an attempt for creating an integrated 3D seismic/geologic model and precise understanding of 3-D wave propagation in the city of Istanbul. The approach is based on generating synthetic seismograms using realistic velocity structures as well as accurate location, focal mechanism and source parameters of reference earthquakes. The modarate size reference earthquakes occured in the Marmara Sea and were recorded by the National Seismic Network of Turkey as well as the network of Istanbul Early Warning and Rapid Response System. The seismograms are simulated by means of a 3-D finite difference method operated on parallel processing environment. In the content of creating a robust velocity model; 1D velocity models which are derived fom previous crustal studies of Marmara region such as refraction seismic and receiver functions have been conducted firstly for depths greater than 1km. Velocity structure in shallower part of the study region is then derived from recent geophysical and geotechnical surveys. To construct 3-D model from the obtained 1-D model data, a variety of interpolation methods are considered. According to the observations on amplitude and arrival time based on comparison of simulated seismograms, the considered velocity model is refined the way that S delay times are compensated. Another important task of this work is an application of the finite difference method to estimate three-dimensional seismic responses for a specified basin structure including soft sediments with low shear velocities in respect of the surrounded area in the Asian part of Istanbul. The analysis performed both in the time and frequency domain, helps in understanding of the comprehensive wave propagation characteristics and the distribution of

  3. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

    Tarquis, A. M.; Gonzalez-Nieto, P. L.; Bird, N. R. A.

    2012-04-01

    Soil voids manifest the cumulative effect of local pedogenic processes and ultimately influence soil behavior - especially as it pertains to aeration and hydrophysical properties. Because of the relatively weak attenuation of X-rays by air, compared with liquids or solids, non-disruptive CT scanning has become a very attractive tool for generating three-dimensional imagery of soil voids. One of the main steps involved in this analysis is the thresholding required to transform the original (greyscale) images into the type of binary representation (e.g., pores in white, solids in black) needed for fractal analysis or simulation with Lattice-Boltzmann models (Baveye et al., 2010). The objective of the current work is to apply an innovative approach to quantifying soil voids and pore networks in original X-ray CT imagery using Relative Entropy (Bird et al., 2006; Tarquis et al., 2008). These will be illustrated using typical imagery representing contrasting soil structures. Particular attention will be given to the need to consider the full 3D context of the CT imagery, as well as scaling issues, in the application and interpretation of this index.

  4. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

    Previous studies have indicated that 2D, time accurate computations based on a pseudo-laminar zonal model of the slat cove region (within the framework of the Reynolds-Averaged Navier-Stokes equations) are inadequate for predicting the full unsteady dynamics of the slat cove flow field. Even though such computations could capture the large-scale, unsteady vorticity structures in the slat cove region without requiring any external forcing, the simulated vortices were excessively strong and the recirculation zone was unduly energetic in comparison with the PIV measurements for a generic high-lift configuration. To resolve this discrepancy and to help enable physics based predictions of slat aeroacoustics, the present paper is focused on 3D simulations of the slat cove flow over a computational domain of limited spanwise extent. Maintaining the pseudo-laminar approach, current results indicate that accounting for the three-dimensionality of flow fluctuations leads to considerable improvement in the accuracy of the unsteady, nearfield solution. Analysis of simulation data points to the likely significance of turbulent fluctuations near the reattachment region toward the generation of broadband slat noise. The computed acoustic characteristics (in terms of the frequency spectrum and spatial distribution) within short distances from the slat resemble the previously reported, subscale measurements of slat noise.

  5. Applications of detailed 3D P-wave velocity crustal model in Poland for local, regional and global seismic tomography

    NASA Astrophysics Data System (ADS)

    Polkowski, Marcin; Grad, Marek

    2015-04-01

    The 3D P-wave seismic velocity model was obtained by combining data from multiple studies during past 50 years. Data sources included refraction seismology, reflection seismology, geological boreholes, vertical seismic profiling, magnetotellurics and gravimetry. Use of many data sources allowed creation of detailed 3D P-wave velocity model that reaches to depth of 60 km and includes 6-layers of sediments and 3-layers of the crust. Purpose of this study is to analyze how 3D model influences local (accuracy of location and source time estimation for local events), regional (identification of wide-angle seismic phases) and global (teleseismic tomography) seismic travel times. Additionally we compare results of forward seismic wave propagation with signals observed on short period and broadband stations. National Science Centre Poland provided financial support for this work by NCN grant DEC-2011/02/A/ST10/00284.

  6. 3D structural model of the North Alpine Foreland Basin, Bavarian Part

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2013-04-01

    The continental collision of Europe and Africa leads to the rise of the European Alps, which gave way to the formation of the North Alpine Foreland Basin, also referred to as the Molasse Basin, since the Tertiary. This typically wedge formed "foredeep" basin is filled with predominantly clastic sediments originating from erosional processes of the Alps which overly a southward dipping Mesozoic and Paleozoic succession. With our project we want to contribute to the understanding of the structure and subsequently of the thermal configuration of the Molasse Basin and its underlying deposits on a basin wide scale. We constructed a 3D structural model of the basin down to the crust-mantle-boundary, beginning with the Bavarian part. Therefore we used an approach of already existing local to midscale 2D and 3D structural models (e.g. Lüschen et al. 2006) as well as surface maps, seismic, well and gravity data. This 3D structural model resolves 5 sedimentary layers of the Mesozoic, including the geothermally utilized carbonate Malm aquifer (e.g. Birner et al. 2011), as well as the combined Paleozoic basement. Assuming isostatic equilibrium of the system a lithosphere-asthenosphere-boundary (LAB) has been calculated and compared to other published LABs of the region. Subsequently the model has been further constrained by 3D gravity modeling. The outcomes show that Cretaceous sediments are restricted to a small region in the central to eastern model area and are mostly overlain by the Tertiary Molasse sediments. The Triassic sediments occur in the northern and western part of the model area and do not continue far under the Molasse basin proper, while the Jurassic can be tracked as far south as beneath the Alps. The evaluation of the gravity indicates that the crystalline crust consists of a lighter upper crust and a denser lower crust. Our final LAB is shallowest under the Triassic subbasin, descending below the Bohemian Massif and the Molasse Basin proper and rising again

  7. Crustal structure of China from deep seismic sounding profiles

    USGS Publications Warehouse

    Li, S.; Mooney, W.D.

    1998-01-01

    More than 36,000 km of Deep Seismic Sounding (DSS) profiles have been collected in China since 1958. However, the results of these profiles are not well known in the West due to the language barrier. In this paper, we summarize the crustal structure of China with a new contour map of crustal thickness, nine representative crustal columns, and maps showing profile locations, average crustal velocity, and Pn velocity. The most remarkable aspect of the crustal structure of China is the well known 70+ km thickness of the crust of the Tibetan Plateau. The thick (45-70 km) crust of western China is separated from the thinner (30-45 km) crust of eastern China by the north-south trending seismic belt (105??E). The average crustal velocity of China ranges from 6.15 to 6.45 km/s, indicating a felsic-to-intermediate bulk crustal composition. Upper mantle (Pn) velocities are 8.0 ?? 0.2 km/s, equal to the global continental average. We interpret these results in terms of the most recent thermo-tectonic events that have modified the crust. In much of eastern China, Cenoxoic crustal extension has produced a thin crust with a low average crustal velocity, similar to western Europe and the Basin and Range Province, western USA. In western China, Mesozoic and Cenoxoic arc-continent and continent-continent collisions have led to crustal growth and thickening. Inferences on the process of crustal thickening are provided by the deep crustal velocity structure as determined by DSS profiles and other seismological studies. A high velocity (7.0-7.4 km/s) lower-crustal layer has been reported in western China only beneath the southernmost Tibetan Plateau. We identity this high-velocity layer as the cold lower crust of the subducting Indian plate. As the Indian crust is injected northward into the Tibetan lower crust, it heats and assimilates by partial melting, a process that results in a reduction in the seismic velocity of the lower crust in the central and northern Tibetan Plateau

  8. SUBSIDENCE, CRUSTAL STRUCTURE, AND THERMAL EVOLUTION OF GEORGES BANK BASIN.

    USGS Publications Warehouse

    Swift, B. Ann; Sawyer, D.S.; Grow, J.A.; Klitgord, Kim D.

    1987-01-01

    A geographical study of Georges Bank basin defines a deep crustal structure that is interpreted in terms of the basin's tectonic and thermal history. Gravity models along three basin cross sections delineate two zones of crustal thinning at the basement hinge zone and oceanic crustal margins. These two zones bound rift-stage crust (about 25 km thick) which underlies the central portion of the basin. Subsidence analysis of the basin, using data from multichannel seismic reflection lines and two COST wells, suggests a rifting and (uniform) extensional origin. Two-dimensional finite difference modeling of the basin defines a crustal structure that concurs with the gravity and subsidence studies. The resulting isotherms show no major changes in the thermal structure since the Late Jurassic. In some areas of the basin, temperature sufficient for oil generation are determined from maturation studies of Jurassic sediments. Hydrocarbon generation is questionable, however, because of the probable lack of proper and sufficient kerogen in the Jurassic deposits.

  9. Imaging crustal structure variation across southeastern Australia

    NASA Astrophysics Data System (ADS)

    Fontaine, Fabrice R.; Tkalčić, Hrvoje; Kennett, Brian L. N.

    2013-01-01

    A broad-band seismic network of 28 three-component seismometers was deployed in southeastern Australia to examine variations in crustal thickness across the transition between Precambrian and Phanerozoic lithosphere. Receiver function observations and modelling of P-to-S conversions at the Mohorovičić discontinuity (Moho) have been employed to investigate: (i) the variations in the Moho depth across southeastern Australia, and (ii) the nature of the transition between crust and mantle. Data from temporary deployments were used together with data from the few permanent broad-band stations in the region. The extraction of P-receiver functions from high-quality seismic data recorded on these stations has enabled the determination of the crustal thickness across the region. The crustal thicknesses lie in the range 28-48 km. The Moho depth is generally well correlated with the Earth surface elevation in the southeastern Australia. The Moho estimates from receiver functions are in good agreement with results from reflection profiling. The average crustal thickness is found to be around 39 km beneath the Precambrian area in the west and even thicker beneath the Lachlan Orogen in the east (~ 43 km). The average crustal thickness in between, beneath the Murray Basin is thinner ~ 32 km. Interestingly, the crust in the Mount Gambier volcanic area is rather thick ~ 41 km, suggesting that the limit between the Delamerian and western Lachlan orogens is located east of Mount Gambier. Our results favour a position for the Tasman Line generally consistent with the interpretation by Direen and Crawford (2003) and thus to the east of the location favoured by many authors. The broader crust-mantle transition and thicker crust beneath the Lachlan Orogen suggest the presence of magmatic underplating at the base of the lower crust. The intermediate nature of the crust-mantle transition also suggests magmatic underplating beneath the Gawler Craton and the Curnamona Province.

  10. Impact of lithosphere rheology and pre-existing tectonic stress field on surface topography, crustal and mantle deformation during plume-lithosphere interactions in continents: insights from 3D numerical experiments

    NASA Astrophysics Data System (ADS)

    Koptev, Alexander; Burov, Evgueni; Gerya, Taras

    2014-05-01

    We implement high-resolution 3D thermo-mechanical numerical models to elucidate the impact of realistically implemented rheological structure of continental lithosphere and of far-field tectonic stress/strain field on the localization and style of deformation during the emplacement of a mantle plume at the bottom of continental lithosphere. Numerical models demonstrate strong dependence of crustal strain distributions and surface topography on the rheological composition of the lower crust and the initial thermal structure of the lithosphere. In contrast to the usual inferences from passive rifting models, distributed wide rifting takes place in case of cold (500° C at Moho depth) initial isotherm and mafic composition of the lower crust, whereas hotter geotherms and weaker (wet quartzite) lower crustal rheology lead to strong localization of rifting. Moreover, it appears that the prerequisite of strongly anisotropic strain localization (linear rift structures) refers to simultaneous presence of an active mantle plume and of some, even very weak, slow (< 3 mm/y) passive horizontal extension produced by far-field tectonic forces. Higher (than 1.5-3 mm/y) velocities of supplementary far-field extension expectedly lead to enlargement of the active fault zone for the same lapse of time. Yet, simultaneous rise of the lithospheric geotherm associated with active rifting has an opposite effect leading to the narrowing of the rift zone. Consequently, interplays between active and passive rifting result in highly varying rifts styles hence breaking common rift-style classifications. The importance of the rheological properties of the continental crust for deformation regime is demonstrated not only by considerable difference in surface morphology and crustal strain patterns between the models with different lower crustal rheology, but also by a noticeable distinction in deep distribution of the plume head material, with consequent effect for magmatic processes and mantle

  11. Deep Crustal Structure Northeastern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Christeson, Gail; Eddy, Drew; van Avendonk, Harm; Norton, Ian; Karner, Garry; Johnson, Chris; Kneller, Erik; Snedden, John

    2013-04-01

    The Gulf of Mexico is a small ocean basin between the US and Mexico that opened up soon after the breakup of Pangea. Although the area has been heavily surveyed with seismic reflection profiles, the deep structure of the region is poorly understood because of lack of penetration beneath the thick sediments and salt. We present the results of two wide-angle seismic refraction profiles in the northeastern Gulf of Mexico that constrain seismic velocities and thicknesses of the sediments and crust from the continental shelf to deep ocean basin. Profile GUMBO 3 extends 523 km from offshore Alabama south-southwest via the De Soto Canyon to the central Gulf of Mexico, while GUMBO 4 extends 507 km from the northwestern Florida peninsula across the Florida Escarpment to the central Gulf of Mexico. On both profiles, ocean bottom seismometers were positioned at 12-km spacing, and recorded air gun shots at offsets >100 km. We use a tomographic inversion of first-arrival and secondary travel time picks from these data to build a layered velocity model (water, sediments, crystalline crust, mantle) along each profile. On GUMBO 3 and GUMBO 4 the thickness of crystalline crust from the continental shelf to the deep basin decreases from ~25 km to ~7 km (GUMBO 4) or ~8 km (GUMBO 3) over a horizontal distance of ~150 km. Velocities of 7-7.5 km/s are observed at the base of the crust along most of GUMBO 3, while velocities of 6.5-7 km/s are observed at similar depths along GUMBO 4. We suggest that higher lower crustal velocities, and thicker oceanic crust, on GUMBO 3 compared to GUMBO 4 may be explained by elevated syn-rift mantle temperatures in the vicinity of the De Soto Canyon and South Georgia Rift during rifting and continental breakup. We have integrated seismic refraction, seismic reflection, and well data to interpret sequence stratigraphic units along GUMBO 3 and GUMBO 4. We have constructed a geologic history of the late-Jurassic/early-Cretaceous, beginning first with Louann

  12. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

    How graphics postprocessing techniques are currently used to examine the results of 3-D nonlinear analyses, some new techniques which take advantage of recent technology, and how these results relate to both the finite element model and its geometric parent are reviewed.

  13. Arbitrary and Parallel Nanofabrication of 3D Metal Structures with Polymer Brush Resists.

    PubMed

    Chen, Chaojian; Xie, Zhuang; Wei, Xiaoling; Zheng, Zijian

    2015-12-01

    3D polymer brushes are reported for the first time as ideal resists for the alignment-free nanofabrication of complex 3D metal structures with sub-100 nm lateral resolution and sub-10 nm vertical resolution. Since 3D polymer brushes can be serially fabricated in parallel, this method is effective to generate arbitrary 3D metal structures over a large area at a high throughput. PMID:26439441

  14. 3D velocity structure of upper crust beneath NW Bohemia/Vogtland

    NASA Astrophysics Data System (ADS)

    Javad Fallahi, Mohammad; Mousavi, Sima; Korn, Michael; Sens-Schönfelder, Christoph; Bauer, Klaus; Rößler, Dirk

    2013-04-01

    surrounding area. Surface wave tomography using ambient noise provides additional constraints on shear velocities. The detailed knowledge of the 3D structure is essential to select the optimal future borehole locations. we use the vertical and transverse component ambient noise data to estimate both Rayleigh and Love waves from ambient noise cross-correlation waveforms to investigate the crustal seismic structure of W-Bohemia/Vogtland. More than 2000 Rayleigh and Love group-velocity dispersion curves are obtained by time-frequency analysis of stacked ambient noise cross-correlation functions between station pairs. We used the data between 2002 and 2004 recorded at 43 seismic stations from BOHEMA experiment and between 2006 and 2008 recorded at 79 seismic stations from permanent station networks of Germany, Czech Academy of Sciences (WEBNET) and PASSEQ experiments. At each period between 1 and 10 s, group velocity maps are constructed, all corresponding to different sampling depths, and thus together giving an indication of the 3D shear wave velocity structure extending to a depth of about 15 km.

  15. The crustal structure of central East Greenland-II: From the Precambrian shield to the recent mid-oceanic ridges

    NASA Astrophysics Data System (ADS)

    Schmidt-Aursch, Mechita C.; Jokat, Wilfried

    2005-02-01

    We present a 3-D crustal model of the East Greenland Fjord Region between 69°N and 74°N. The model covers the Precambrian shield and the Caledonian orogenic belt, the adjoining Devonian and Mesozoic basins, the continent-ocean transition and the Cenozoic oceanic areas as far as the Kolbeinsey and the Mohns mid-oceanic ridges. Existing seismic models of the crustal structure are extrapolated into adjacent areas using 3-D gravity modelling. For this purpose, we compile a new regional-scale Bouguer anomaly map. The Precambrian shield, west of the Caledonian orogen (approximately west of 32°W), shows a mean thickness of 35 km with only small-scale undulations. This thickness is at the lower limit of the global range in shield thickness. The Caledonian orogen exhibits a pronounced mountain root with overall crustal thicknesses up to 51 km. Beside the Urals, the East Greenland Caledonides are one of the two Palaeozoic mountain belts where a crustal root has preserved to the present day. Continuation of the crustal model to the east, beyond the continent-ocean transition, yielded thicknesses of the crystalline oceanic crust from 9 km near the Kolbeinsey Ridge to 3 km west of the Mohns Ridge. Differences in the thermal structures of the old continental and the young oceanic lithosphere are responsible for the low-density mantle beneath the oceanic crust, which is also demonstrated by 3-D gravity modelling.

  16. Crustal structure of east central Oregon: relation between Newberry Volcano and regional crustal structure

    USGS Publications Warehouse

    Catchings, R.D.; Mooney, W.D.

    1988-01-01

    A 180-km-long seismic refraction transect from the eastern High Cascades, across Newberry Volcano, to the eastern High Lava Plains is used to investigate the subvolcanic crustal and upper mantle velocity structure there. Near-surface volcanic flows and sedimentary debris (1.6-4.7 km/s), ranging from 3 to 5 km in thickness, overlie subvolcanic Basin and Range structures. East and west of Newberry Volcano, the subvolcanic basement (5.6 km/s) has been downwarped, producing 5-km-deep basins. The midcrust (8- to 28-km depth) is characterized by velocities ranging from 6.1 to 6.5 km/s and varies laterally in thicknesses. The lower crust is characterized by an unusually high velocity (about 7.4 km/s), and its geometry mirrors the subvolcanic basement geometry. The Moho is located at a depth of 37 km and represents a transition to an upper mantle velocity of 8.1 km/s. The shallow subsurface (1.2 km) beneath Newberry Volcano is characterized by high-velocity 5.6 km/s, versus 4.1 km/s for the surrounding area) intrusions and appears to be located on a basement high. Beneath the seismic refraction array at Newberry Volcano, an absence of low-velocity anomalies suggests that large silicic magma chambers do not exist in the upper crust, but apparent high attenuation of the seismic wave field may be consistent with either partial melts in small volumes, elevated crustal temperatures, and/or poor geophone-recording site coupling. -Authors

  17. Real-time structured light intraoral 3D measurement pipeline

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

    Computer aided design and manufacturing (CAD/CAM) is increasingly becoming a standard feature and service provided to patients in dentist offices and denture manufacturing laboratories. Although the quality of the tools and data has slowly improved in the last years, due to various surface measurement challenges, practical, accurate, invivo, real-time 3D high quality data acquisition and processing still needs improving. Advances in GPU computational power have allowed for achieving near real-time 3D intraoral in-vivo scanning of patient's teeth. We explore in this paper, from a real-time perspective, a hardware-software-GPU solution that addresses all the requirements mentioned before. Moreover we exemplify and quantify the hard and soft deadlines required by such a system and illustrate how they are supported in our implementation.

  18. Imaging 3D anisotropic upper mantle shear velocity structure of Southeast Asia using seismic waveform inversion

    NASA Astrophysics Data System (ADS)

    Chong, J.; Yuan, H.; French, S. W.; Romanowicz, B. A.; Ni, S.

    2011-12-01

    Southeast Asia as a special region in the world which is seismically active and is surrounded by active tectonic belts, such as the Himalaya collision zone, western Pacific subduction zones and the Tianshan- Baikal tectonic belt. Seismic anisotropic tomography can shade light on the complex crust and upper mantle dynamics of this region, which is the subject of much debate. In this study, we applied full waveform time domain tomography to image 3D isotropic and anisotropic upper mantle shear velocity structure of Southeast Asia. Three component waveforms of teleseismic and far regional events (15 degree ≤ Δ≤ 165 degree) with magnitude ranges from Mw6.0 to Mw7.0 are collected from 91 permanent and 438 temporary broadband seismic stations in SE Asia. Wavepackets of both fundamental and overtone modes, filtered between 60 and 400 sec, are selected automatically according to the similarity between data and synthetic waveforms (Panning & Romanowicz, 2006). Wavepackets corresponding to event-station paths that sample the region considered are weighted according to path redundancy and signal to noise ratio. Higher modes and fundamental mode wavepackets are weighted separately in order to enhance the contribution of higher modes which are more sensitive to deeper structure compared to the fundamental mode. Synthetic waveforms and broadband sensitivity kernels are computed using normal mode asymptotic coupling theory (NACT, Li & Romanowicz, 1995). As a starting model, we consider a global anisotropic upper mantle shear velocity model based on waveform inversion using the Spectral Element Method (Lekic & Romanowicz, 2011), updated for more realistic crustal thickness (French et al., 2011) as our starting model, we correct waveforms for the effects of 3D structure outside of the region, and invert them for perturbations in the 3D structure of the target region only. We start with waveform inversion down to 60sec and after several iterations, we include shorter period

  19. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

    Laser scanning confocal microscopy was used to study the dynamics of 3D assemblies spontaneously formed in microtubule (MT) solutions. Microtubule solutions prepared by mixing and incubating tubulin in the presence of GTP and Oregon Green conjugated taxol in PM buffer were placed in long, sub-millimeter thin glass cells by the capillary action. Within 24 hours, starting with a uniform distribution, microtubules were found to be gradually separated into a few large ``buckled'' bundles along the long direction, and in the middle plane, of the sample cell. A well-defined wavelength of the buckling sinusoids was around 510 μm. The cross section of these round bundles was approximately 40 μm in diameter and the lengths were several centimeters. Detailed analysis of the 3-D image within the bundles revealed that each bundle seemed to consist of loosely packed MTs. It appeared that MTs were phase separated resulting from attractive interactions between charged MT fibers. The ``buckling'' behavior could be the result of geometrical constraints of the repulsive cell walls and the repulsive interaction between bundles. Detailed 3-D observations of the dynamic evolution of MT assembly could provide insight to the mechanisms of cellular MT organization and phase separation of charged colloidal rods.

  20. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  1. Crustal structure interpreted from magnetic anomalies

    NASA Technical Reports Server (NTRS)

    Phillips, Jeffrey D.; Reynolds, Richard L.; Frey, Herbert

    1991-01-01

    This review, discusses publications during the last quadrennium (1987-1990) that used aeromagnetic data, marine magnetic data, satellite magnetic data, and rock magnetic and petrologic data to provide information on the sources of magnetic anomalies. The publications reviewed reflect increased integration of rock magnetic property and petrologic studies with magnetic anomaly interpretation studies, particularly in deep crustal magnetization, exploration for hydrocarbons, and inversion of marine magnetic anomalies. Interpretations of aeromagnetic data featuring image display techniques and using the horizontal gradient method for locating magnetization boundaries became standard.

  2. Sedimentary and upper crustal structure of Australia from receiver functions

    USGS Publications Warehouse

    Clitheroe, G.; Gudmundsson, O.; Kennett, B.L.N.

    2000-01-01

    The initial coda of teleseismic P-waves contains considerable information about the crust and upper mantle structure directly beneath a receiver. When this information can be recovered for a dense network of seismographs much can be learned about the structure of the earth. Data from the high quality broadband seismic stations of the SKIPPY and KIMBA projects along with permanent stations are used to investigate the upper crustal structure of Australia. A dataset of 65 shear-velocity models derived from receiver functions has enabled the sedimentary and upper crustal structure of Australia to be summarised. Regions of thick soft sediment show good agreement with topographical lows. A simple relation between upper-crustal velocity and magnetisation, as has been suggested by other investigators, has not been observed, but this may be due to the magnetic signal being muted by overlying sediments. A prominent mid-crustal discontinuity is apparent in the Tasman and New England mega-elements. This may represent a mid-crustal decollement that had structural control during accretion.

  3. The SCEC 3D Community Fault Model (CFM-v5): An updated and expanded fault set of oblique crustal deformation and complex fault interaction for southern California

    NASA Astrophysics Data System (ADS)

    Nicholson, C.; Plesch, A.; Sorlien, C. C.; Shaw, J. H.; Hauksson, E.

    2014-12-01

    Southern California represents an ideal natural laboratory to investigate oblique deformation in 3D owing to its comprehensive datasets, complex tectonic history, evolving components of oblique slip, and continued crustal rotations about horizontal and vertical axes. As the SCEC Community Fault Model (CFM) aims to accurately reflect this 3D deformation, we present the results of an extensive update to the model by using primarily detailed fault trace, seismic reflection, relocated hypocenter and focal mechanism nodal plane data to generate improved, more realistic digital 3D fault surfaces. The results document a wide variety of oblique strain accommodation, including various aspects of strain partitioning and fault-related folding, sets of both high-angle and low-angle faults that mutually interact, significant non-planar, multi-stranded faults with variable dip along strike and with depth, and active mid-crustal detachments. In places, closely-spaced fault strands or fault systems can remain surprisingly subparallel to seismogenic depths, while in other areas, major strike-slip to oblique-slip faults can merge, such as the S-dipping Arroyo Parida-Mission Ridge and Santa Ynez faults with the N-dipping North Channel-Pitas Point-Red Mountain fault system, or diverge with depth. Examples of the latter include the steep-to-west-dipping Laguna Salada-Indiviso faults with the steep-to-east-dipping Sierra Cucapah faults, and the steep southern San Andreas fault with the adjacent NE-dipping Mecca Hills-Hidden Springs fault system. In addition, overprinting by steep predominantly strike-slip faulting can segment which parts of intersecting inherited low-angle faults are reactivated, or result in mutual cross-cutting relationships. The updated CFM 3D fault surfaces thus help characterize a more complex pattern of fault interactions at depth between various fault sets and linked fault systems, and a more complex fault geometry than typically inferred or expected from

  4. 3D Reconstruction of virtual colon structures from colonoscopy images.

    PubMed

    Hong, DongHo; Tavanapong, Wallapak; Wong, Johnny; Oh, JungHwan; de Groen, Piet C

    2014-01-01

    This paper presents the first fully automated reconstruction technique of 3D virtual colon segments from individual colonoscopy images. It is the basis of new software applications that may offer great benefits for improving quality of care for colonoscopy patients. For example, a 3D map of the areas inspected and uninspected during colonoscopy can be shown on request of the endoscopist during the procedure. The endoscopist may revisit the suggested uninspected areas to reduce the chance of missing polyps that reside in these areas. The percentage of the colon surface seen by the endoscopist can be used as a coarse objective indicator of the quality of the procedure. The derived virtual colon models can be stored for post-procedure training of new endoscopists to teach navigation techniques that result in a higher level of procedure quality. Our technique does not require a prior CT scan of the colon or any global positioning device. Our experiments on endoscopy images of an Olympus synthetic colon model reveal encouraging results with small average reconstruction errors (4.1 mm for the fold depths and 12.1 mm for the fold circumferences). PMID:24225230

  5. Crustal structure of Precambrian terranes in the southern African subcontinent with implications for secular variation in crustal genesis

    NASA Astrophysics Data System (ADS)

    Kachingwe, Marsella; Nyblade, Andrew; Julià, Jordi

    2015-07-01

    New estimates of crustal thickness, Poisson's ratio and crustal shear wave velocity have been obtained for 39 stations in Angola, Botswana, the Democratic Republic of Congo, Malawi, Mozambique, Namibia, Rwanda, Tanzania and Zambia by modelling P-wave receiver functions using the H-κ stacking method and jointly inverting the receiver functions with Rayleigh-wave phase and group velocities. These estimates, combined with similar results from previous studies, have been examined for secular trends in Precambrian crustal structure within the southern African subcontinent. In both Archean and Proterozoic terranes we find similar Moho depths [38-39 ± 3 km SD (standard deviation)], crustal Poisson's ratio (0.26 ± 0.01 SD), mean crustal shear wave velocity (3.7 ± 0.1 km s-1 SD), and amounts of heterogeneity in the thickness of the mafic lower crust, as defined by shear wave velocities ≥4.0 km s-1. In addition, the amount of variability in these crustal parameters is similar within each individual age grouping as between age groupings. Thus, the results provide little evidence for secular variation in Precambrian crustal structure, including between Meso- and Neoarchean crust. This finding suggests that (1) continental crustal has been generated by similar processes since the Mesoarchean or (2) plate tectonic processes have reworked and modified the crust through time, erasing variations in structure resulting from crustal genesis.

  6. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    On page 3712, E. Fantino, A. Chiappone, and co-workers fabricate conductive 3D hybrid structures by coupling the photo-reduction of metal precursors with 3D printing technology. The generated structures consist of metal nanoparticles embedded in a polymer matrix shaped into complex multilayered architectures. 3D conductive structures are fabricated with a digital light-processing printer incorporating silver salt into photocurable formulations. PMID:27167030

  7. Triangular framework mesh generation of 3D geological structure

    NASA Astrophysics Data System (ADS)

    Meng, Xianhai; Zhou, Kun; Li, Jigang; Yang, Qin

    2013-03-01

    The dynamic simulation of oil migration and accumulation is an important issue on the research of petroleum exploration, and it is a numerical simulation process with special requirement on the framework mesh of 3D geological models, which means that the mesh should have same geometry and topology relation near the intersected part of geological surfaces. In this paper, basing on the conforming Delaunay triangulation algorithm to construct mesh of individual geological stratum or fault, a novel link-Delaunay-triangulation method is presented to achieve the geometric and topological consistency in the intersected line between two surfaces, also with the analysis of termination of our algorithm. Finally, some examples of the geological framework mesh are provided and the experimental result proved that the algorithm's effectiveness in engineering practice.

  8. Image quality improvement for a 3D structure exhibiting multiple 2D patterns and its implementation.

    PubMed

    Hirayama, Ryuji; Nakayama, Hirotaka; Shiraki, Atsushi; Kakue, Takashi; Shimobaba, Tomoyoshi; Ito, Tomoyoshi

    2016-04-01

    A three-dimensional (3D) structure designed by our proposed algorithm can simultaneously exhibit multiple two-dimensional patterns. The 3D structure provides multiple patterns having directional characteristics by distributing the effects of the artefacts. In this study, we proposed an iterative algorithm to improve the image quality of the exhibited patterns and have verified the effectiveness of the proposed algorithm using numerical simulations. Moreover, we fabricated different 3D glass structures (an octagonal prism, a cube and a sphere) using the proposed algorithm. All 3D structures exhibit four patterns, and different patterns can be observed depending on the viewing direction. PMID:27137021

  9. Application of surface wave travel times and amplitude ratios interpreted through a 3D crustal model to locate and characterize regional seismic events in the US

    NASA Astrophysics Data System (ADS)

    Tian, Y.; Ritzwoller, M. H.; Shen, W.; Levshin, A. L.; Barmin, M. P.

    2014-12-01

    The error in the epicentral location of crustal earthquakes across the contiguous US is on the order of 10 km due to the inability of 1D seismic velocity models to capture regional body wave travel time variations. New high resolution 3D models of the crust and uppermost mantle have been constructed recently across the US by inverting surface wave dispersion from ambient noise and earthquakes, receiver functions, and Rayleigh wave H/V ratios using USArray data [e.g., Shen et al., 2013]. These are mostly S-wave models of the lithosphere, however, which are not optimal for predicting regional P-wave travel times. We explore the use of observations of surface waves to improve regional event characterization because the new 3D models are constructed explicitly to model their behavior. In particular, we use measurements of group and phase time delays and the amplitude ratio between different periods of surface waves to estimate the moment tensor, the epicentral location and the earthquake depth. Preliminary estimates of these variables are determined through a simulated annealing algorithm. Afterward, a Bayesian Monte Carlo method is applied to estimate the posterior distribution of all variables in order to assess uncertainties in source characteristics. The reliability and limitations of the location method are tested by systematic relocation of earthquakes across the contiguous US.

  10. Study on 3-D velocity structure of crust and upper mantle in Sichuan-yunnan region, China

    USGS Publications Warehouse

    Wang, C.; Mooney, W.D.; Wang, X.; Wu, J.; Lou, H.; Wang, F.

    2002-01-01

    Based on the first arrival P and S data of 4 625 regional earthquakes recorded at 174 stations dispersed in the Yunnan and Sichuan Provinces, the 3-D velocity structure of crust and upper mantle in the region is determined, incorporating with previous deep geophysical data. In the upper crust, a positive anomaly velocity zone exists in the Sichuan basin, whereas a negative anomaly velocity zone exists in the western Sichuan plateau. The boundary between the positive and negative anomaly zones is the Longmenshan fault zone. The images of lower crust and upper mantle in the Longmenshan fault, Xianshuihe fault, Honghe fault and others appear the characteristic of tectonic boundary, indicating that the faults litely penetrate the Moho discontinuity. The negative velocity anomalies at the depth of 50 km in the Tengchong volcanic area and the Panxi tectonic zone appear to be associated with the temperature and composition variations in the upper mantle. The overall features of the crustal and the upper mantle structures in the Sichuan-Yunnan region are the lower average velocity in both crust and uppermost mantle, the large crustal thickness variations, and the existence of high conductivity layer in the crust or/and upper mantle, and higher geothermal value. All these features are closely related to the collision between the Indian and the Asian plates. The crustal velocity in the Sichuan-Yunnan rhombic block generally shows normal.value or positive anomaly, while the negative anomaly exists in the area along the large strike-slip faults as the block boundary. It is conducive to the crustal block side-pressing out along the faults. In the major seismic zones, the seismicity is relative to the negative anomaly velocity. Most strong earthquakes occurred in the upper-mid crust with positive anomaly or normal velocity, where the negative anomaly zone generally exists below.

  11. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system. PMID:26992060

  12. 3D Modeling of Branching Structures for Anatomical Instruction

    PubMed Central

    Mattingly, William A.; Chariker, Julia H.; Paris, Richard; Chang, Dar-jen; Pani, John R.

    2015-01-01

    Branching tubular structures are prevalent in many different organic and synthetic settings. From trees and vegetation in nature, to vascular structures throughout human and animal biology, these structures are always candidates for new methods of graphical and visual expression. We present a modeling tool for the creation and interactive modification of these structures. Parameters such as thickness and position of branching structures can be modified, while geometric constraints ensure that the resulting mesh will have an accurate anatomical structure by not having inconsistent geometry. We apply this method to the creation of accurate representations of the different types of retinal cells in the human eye. This method allows a user to quickly produce anatomically accurate structures with low polygon counts that are suitable for rendering at interactive rates on commodity computers and mobile devices. PMID:27087764

  13. Deep structure beneath Lake Ontario: crustal-scale Greeneville subdivisions

    USGS Publications Warehouse

    Forsyth, D. A.; Zelt, Colin A.; White, D. J.; Easton, R. M.; Hutchinson, Deborah R.

    1994-01-01

    Lake Ontario marine seismic data reveal major Grenville crustal subdivisions beneath central and southern Lake Ontario separated by interpreted shear zones that extend to the lower crust. A shear zone bounded transition between the Elzevir and Frontenac terranes exposed north of Lake Ontario is linked to a seismically defined shear zone beneath central Lake Ontario by prominent aeromagnetic and gravity anomalies, easterly dipping wide-angle reflections, and fractures in Paleozoic strata. We suggest the central Lake Ontario zone represents crustal-scale deformation along an Elzevir–Frontenac boundary zone that extends from outcrop to the south shore of Lake Ontario.Seismic images from Lake Ontario and the exposed western Central Metasedimentary Belt are dominated by crustal-scale shear zones and reflection geometries featuring arcuate reflections truncated at their bases by apparent east-dipping linear reflections. The images show that zones analogous to the interpreted Grenville Front Tectonic Zone are also present within the Central Metasedimentary Belt and support models of northwest-directed crustal shortening for Grenvillian deep crustal deformation beneath most of southeastern Ontario.A Precambrian basement high, the Iroquoian high, is defined by a thinning of generally horizontal Paleozoic strata over a crestal area above the basement shear zone beneath central Lake Ontario. The Iroquoian high helps explain the peninsular extension into Lake Ontario forming Prince Edward County, the occurrence of Precambrian inlier outcrops in Prince Edward County, and Paleozoic fractures forming the Clarendon–Linden structure in New York.

  14. UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation

    PubMed Central

    Zhu, Jinhao; Wei, Bryan; Yuan, Yuan; Mi, Yongli

    2009-01-01

    A user-friendly software system, UNIQUIMER 3D, was developed to design DNA structures for nanotechnology applications. It consists of 3D visualization, internal energy minimization, sequence generation and construction of motif array simulations (2D tiles and 3D lattices) functionalities. The system can be used to check structural deformation and design errors under scaled-up conditions. UNIQUIMER 3D has been tested on the design of both existing motifs (holiday junction, 4 × 4 tile, double crossover, DNA tetrahedron, DNA cube, etc.) and nonexisting motifs (soccer ball). The results demonstrated UNIQUIMER 3D's capability in designing large complex structures. We also designed a de novo sequence generation algorithm. UNIQUIMER 3D was developed for the Windows environment and is provided free of charge to the nonprofit research institutions. PMID:19228709

  15. 3D Lithosphere density structure of southern Indian shield from joint inversion of gravity, geoid and topography data

    NASA Astrophysics Data System (ADS)

    Kumar, Niraj; Zeyen, Hermann; Singh, A. P.

    2014-08-01

    We present the 3D crustal and lithospheric structure and crustal average density distribution of southern Indian shield (south of 18°N), Sri Lanka and adjoining oceans. The model is based on the assumption of local isostatic equilibrium and is derived from joint inversion of free air gravity and geoid anomalies and topography data. The derived crustal thickness of 10-25 km in the oceanic region increases to 34-35 km along the coast. A crustal thickness of 34-38 km is obtained beneath the Eastern Dharwar Craton and 36-45 km beneath the Western Dharwar Craton and the Southern Granulite Terrain. Sri Lanka has a thinner crust of 30-35 km. The lithosphere-asthenosphere boundary is located at depths of 70-120 km under oceanic regions and ∼150-180 km below the Dharwar Craton and the Northern block of Southern Granulite Terrain. A notably thinned lithosphere of ∼130 km near Bangalore in the Eastern Dharwar Craton, ∼140 km beneath the Southern block of Southern Granulite Terrain and ∼130 km in Sri Lanka is observed. The thickness of the lithosphere (∼130 km) near Bangalore is inferred as the frozen in signature of a small fossil mantle plume and/or tectono-compositional effect of a rifted margin and a suture. Considerable stretching and/or convective removal of pristine lithosphere in the Southern block of Southern Granulite Terrain and adjoining Sri Lanka, before disappearing completely in the Archaean Northern block of Southern Granulite Terrain and Dharwar Craton, is suggested.

  16. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and 3-dimensional structural information

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

    SUMMARY Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of 3-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  17. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  18. GMOL: An Interactive Tool for 3D Genome Structure Visualization.

    PubMed

    Nowotny, Jackson; Wells, Avery; Oluwadare, Oluwatosin; Xu, Lingfei; Cao, Renzhi; Trieu, Tuan; He, Chenfeng; Cheng, Jianlin

    2016-01-01

    It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlighting structural relationships that may not be obvious when examining the sequence information alone. Here we present a desktop application, known as GMOL, designed to effectively visualize genome structures so that researchers may better analyze genomic data. GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences. Users can also interactively manipulate and measure the whole genome structure and extract static images and machine-readable data files in PDB format from the multi-scale structure. By using GMOL researchers will be able to better understand and analyze genome structure models and the impact their structural relations have on genome activity and DNA function. PMID:26868282

  19. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model. PMID:26853327

  20. Crustal structure and active tectonics in the Eastern Alps

    NASA Astrophysics Data System (ADS)

    Brückl, E.; Behm, M.; Decker, K.; Grad, M.; Guterch, A.; Keller, G. R.; Thybo, H.

    2010-04-01

    During the last decade, a series of controlled source seismic experiments brought new insight into the crustal and lithospheric structure of the Eastern Alps and their adjacent tectonic provinces. A fragmentation of the lithosphere into three blocks, Europe (EU), Adria (AD), and the new Pannonian fragment (PA), was interpreted and a triple junction was inferred. The goal of this study has been to relate these deep crustal structures to active tectonics. We used elastic plate modeling to reconsider the Moho fragmentation. We interpret subduction of EU below AD and PA from north to south and underthusting of AD mantle below PA from southwest to northeast. The Moho fragmentation correlates well with major upper crustal structures and is supported by gravity, seismic, and geodetic data. An analysis of crustal thickening suggests that active convergence is associated with continued thrusting and lateral extrusion in the central Eastern Alps and thickening of the Adriatic indenter under the Southern Alps. According to the velocity relations at the triple junction, PA moves relative to EU and AD along ENE and SE striking faults, mainly by strike slip. An eastward directed extensional component is compensated by the lateral extrusion of the central Eastern Alps. The Periadriatic (Insubric) line east of the triple junction and the mid-Hungarian fault zone have relatively recently lost their role as first-order active structures. We favor the idea that the Pannonian fragment and the TISZA block merged to a "soft" microplate surrounded by the Eastern and Southern Alpine, Carpathian, and Dinaric orogens.

  1. SAFAS: Unifying Form and Structure through Interactive 3D Simulation

    ERIC Educational Resources Information Center

    Polys, Nicholas F.; Bacim, Felipe; Setareh, Mehdi; Jones, Brett D.

    2015-01-01

    There has been a significant gap between the tools used for the design of a building's architectural form and those that evaluate the structural physics of that form. Seeking to bring the perspectives of visual design and structural engineering closer together, we developed and evaluated a design tool for students and practitioners to explore the…

  2. Determining 3-D motion and structure from image sequences

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

    A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.

  3. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

    We review the observational evidences concerning the three-dimensional structure of the Galactic bulge. Although the inner few kpc of our Galaxy are normally referred to as the bulge, all the observations demonstrate that this region is dominated by a bar, i.e., the bulge is a bar. The bar has a boxy/peanut (X-shaped) structure in its outer regions, while it seems to become less and less elongated in its innermost region. A thinner and longer structure departing from the main bar has also been found, although the observational evidences that support the scenario of two separate structures has been recently challenged. Metal-poor stars ([Fe/H] ≲ -0.5 dex) trace a different structure, and also have different kinematics.

  4. A new model of crustal structure of Siberia

    NASA Astrophysics Data System (ADS)

    Cherepanova, Y.; Artemieva, I. M.; Thybo, H.

    2010-12-01

    We report a new model of the structure of the crust in Siberia that encompasses two large tectonic regions, the Paleozoic West Siberian Basin and the Precambrian Siberian craton. The area of study covers a significant part of the north Eurasia and extends from the Ural mountains in the west to the Verkoyansk Ridge/Lena river in the east, and from the Arctic shelf in the north to the Tien Shan and Altay-Sayans mountains in the south. The new crustal model is based on our new ("from scratch") compilation of all available reliable seismic data and includes the results of seismic reflection, refraction and receiver functions studies, based on old and newly acquired seismic data (from the late 1960-ies until present). Seismic structure along seismic profiles is digitized with a 50 km lateral spacing which is comparable with the resolution of seismic models. Structural parameters based on gravity modeling, or tectonic similarities, or seismic data reported not along seismic reflection/refraction profiles but as interpolated contour maps are excluded from the new crustal database. Due to uneven quality of seismic data related both to data acquisition problems and interpretation limitations, a special attention is paid to the data quality problem, and quality parameters are incorporated into the new database of regional crustal structure. The present database comprises detailed and reliable information on the seismic structure of the crust for most of the tectonic structures of the region and provides valuable constraints for geophysical modeling of the mantle structure. We observe important spatial correlations between the crustal structure (thickness of the sediments, the basement, and different crustal layers, and average basement velocities) and tectonic and geological settings. Statistical analysis of age-dependence (we use tectono-thermal ages) of crustal parameters allows for distinguishing the effects of various tectonic processes on the crustal structure. The

  5. Accretion tectonics and crustal structure in Alaska

    USGS Publications Warehouse

    Coney, P.J.; Jones, D.L.

    1985-01-01

    The entire width of the North American Cordillera in Alaska is made up of "suspect terranes". Pre-Late Cretaceous paleogeography is poorly constrained and the ultimate origins of the many fragments which make up the state are unclear. The Prince William and Chugach terranes accreted since Late Cretaceous time and represent the collapse of much of the northeast Pacific Ocean swept into what today is southern Alaska. Greater Wrangellia, a composite terrane now dispersed into fragments scattered from Idaho to southern Alaska, apparently accreted into Alaska in Late Cretaceous time crushing an enormous deep-marine flysch basin on its inboard side. Most of interior eastern Alaska is the Yukon Tanana terrane, a very large entirely fault-bounded metamorphic-plutonic assemblage covering thousands of square kilometers in Canada as well as Alaska. The original stratigraphy and relationship to North America of the Yukon-Tanana terrane are both obscure. A collapsed Mesozoic flysch basin, similar to the one inboard of Wrangellia, lies along the northern margin. Much of Arctic Alaska was apparently a vast expanse of upper Paleozoic to Early Mesozoic deep marine sediments and mafic volcanic and plutonic rocks now scattered widely as large telescoped sheets and Klippen thrust over the Ruby geanticline and the Brooks Range, and probably underlying the Yukon-Koyukuk basin and the Yukon flats. The Brooks Range itself is a stack of north vergent nappes, the telescoping of which began in Early Cretaceous time. Despite compelling evidence for thousands of kilometers of relative displacement between the accreted terranes, and large amounts of telescoping, translation, and rotation since accretion, the resulting new continental crust added to North America in Alaska carries few obvious signatures that allow application of currently popular simple plate tectonic models. Intraplate telescoping and strike-slip translations, delamination at mid-crustal levels, and large-scale lithospheric

  6. An Improved Model of the Crustal Structure of Mars

    NASA Technical Reports Server (NTRS)

    Zuber, M. T.; Neumann, G. A.; McGovern, P. J.; Wieczorek, M. A.; Lemoine, F. G.; Smith, D. E.

    2004-01-01

    The first reliable model of the structure of the crust and upper mantle of Mars from remote observations was produced using data from the Mars Orbiter Laser Altimeter (MOLA) and the Radio Science investigation of Mars Global Surveyor (MGS). That model assumed a uniform crustal density and solved for the global variations in crustal thickness using a gravity field derived from preliminary MGS tracking. In that study, spherical harmonic potential coefficients were derived to degree and order 80, but crustal structure was interpreted cautiously to degree 60, or 360 km wavelength, owing to the presence of noise. Tracking normal equations have since been generated to degree 75, to degree 80 (supplemented by altimetric crossovers), and recently to degree 90, using new constants for the orientation of the spin pole and the rotation rate of Mars provided by the IAU2000 rotation model. Gravity models now incorporate tracking data coverage from the Primary and Extended MGS missions and the early phases of the Mars Odyssey mission. In the present study we exploit these advances in gravity modeling to present a refined crustal inversion, which we also interpret in the context of Mars' internal structure and thermal evolution.

  7. 3D Thermoelectric Structures Derived from a New Mixed Micromachining Process

    NASA Astrophysics Data System (ADS)

    Du, Chen-Hsun; Lee, Chengkuo

    2000-12-01

    This paper proposes an innovative 3D thermoelectric structure which significantly reduce the componet size without deterioration of sensor performance. Based on complementary metal-oxide-semiconductor (CMOS) transistor compatible process, this 3D thermoelectric structure is demonstrated and fabricated by combining front-side silicon anisotropic wet etching and aluminum sacrificial layer etching technique. The voltage responsivity of derived 3D thermoelectric structure with 180× 180 μm2 pixel size can be as high as 190 V/W in vacuum. This new thermoelectric structure shows its potential to be an excellent pixel structure of infrared sensor array for infrared recognition applications.

  8. Crustal and Lithospheric Structure at Isidis Planitia, Mars

    NASA Astrophysics Data System (ADS)

    Ritzer, J. A.; Hauck, S. A.

    2005-12-01

    Isidis Planitia is the site of a large free air gravity anomaly consistent with modification and sedimentary or magmatic filling of an impact basin. Mars Global Surveyor gravity and topography data of the Isidis basin on Mars are analyzed to elucidate the crustal and lithospheric structure near the dichotomy boundary in the Eastern hemisphere. Global gravity and topography datasets are inverted using an extension of Banerdt's [1986] model for deformation of a thin elastic shell and a nominal assumption that Isidis was isostatically compensated prior to modification by infilling. Using this model we attempt to constrain potential variations in (and trade-offs among) local crustal thickness, density and thickness of basin fill material, and lithospheric deformation. The permissible parameter space is limited by assuming that the local crustal thickness of the basin cannot be less than zero at the time of infilling. Our results suggest that the density of the fill inside Isidis must be more than 2500 kg/m3 and higher densities are probable. Recent work of Wieczorek and Zuber [2004] indicates that the most likely average crustal thickness of Mars is between 38 and 62 km. On the basis of this range of values for crustal thickness, we infer that the average density of the fill is more than 2900 kg/m3. A high fill density suggests that the material inside the basin is predominantly of igneous rather than sedimentary origin. Under the assumption of an average crustal density of 2900 kg/m3 the inferred thickness of the fill layer is at least 5 km, and could be significantly larger depending upon the degree of compensation of the basin before it was loaded by fill material. A comparison of the faulting observed at Nili Fossae to the predicted zone of extensional strain northwest of Isidis may further constrain the thickness of the elastic lithosphere beneath the basin at the time of loading.

  9. Crustal Viscosity Structure Estimated from Multi-Phase Mixing Theory

    NASA Astrophysics Data System (ADS)

    Shinevar, W. J.; Behn, M. D.; Hirth, G.

    2014-12-01

    Estimates of lower crustal viscosity are typically constrained by analyses of isostatic rebound, post seismic creep, and laboratory-derived flow laws for crustal rocks and minerals. Here we follow a new approach for calculating the viscosity structure of the lower continental crust. We use Perple_X to calculate mineral assemblages for different crustal compositions. Effective viscosity is then calculated using the rheologic mixing model of Huet et al. (2014) incorporating flow laws for each mineral phase. Calculations are performed along geotherms appropriate for the Basin and Range, Tibetan Plateau, Colorado Plateau, and the San Andreas Fault. To assess the role of crustal composition on viscosity, we examined two compositional gradients extending from an upper crust with ~67 wt% SiO2 to a lower crust that is either: (i) basaltic with ~53 wt% SiO2 (Rudnick and Gao, 2003), or (ii) andesitic with ~64% SiO2 (Hacker et al., 2011). In all cases, the middle continental crust has a viscosity that is 2-3 orders of magnitude greater than that inferred for wet quartz, a common proxy for mid-crustal viscosities. An andesitic lower crust results in viscosities of 1020-1021 Pa-s and 1021-1022 Pa-s for hotter and colder crustal geotherms, respectively. A mafic lower crust predicts viscosities that are an order of magnitude higher for the same geotherm. In all cases, the viscosity calculated from the mixing model decreases less with depth compared to single-phase estimates. Lastly, for anhydrous conditions in which alpha quartz is stable, we find that there is a strong correlation between Vp/Vs and bulk viscosity; in contrast, little to no correlation exists for hydrous conditions.

  10. LV motion tracking from 3D echocardiography using textural and structural information.

    PubMed

    Myronenko, Andriy; Song, Xubo; Sahn, David J

    2007-01-01

    Automated motion reconstruction of the left ventricle (LV) from 3D echocardiography provides insight into myocardium architecture and function. Low image quality and artifacts make 3D ultrasound image processing a challenging problem. We introduce a LV tracking method, which combines textural and structural information to overcome the image quality limitations. Our method automatically reconstructs the motion of the LV contour (endocardium and epicardium) from a sequence of 3D ultrasound images. PMID:18044597

  11. Crustal structure of southwestern Saudi Arabia

    USGS Publications Warehouse

    Gettings, M.E.; Blank, H.R.; Mooney, W.D.; Healy, J.H.

    1983-01-01

    The southwestern Arabian Shield is composed of uplifted Proterozoic metamorphic and plutonic rocks. The Shield is bordered on the southwest by Cenozoic sedimentary and igneous rocks of the Red Sea paar and on the east by the Arabian Platform, an area of basin sedimentation throughout Phanerozoic time. The Shield appears to have been formed by successive episodes of island arc volcanism and sea-floor spreading, followed by several cycles of compressive tectonism and metamorphism. An interpretation and synthesis of a deep-refraction seismic profile from the Riyadh area to the Farasan Islands, and regional gravity, aeromagnetic, heat flow, and surface geologic data have yielded a self-consistent regional-scale model of the crust and upper mantle for this area. The model consists of two 20 km-thick layers of crust with an average compressional wave velocity in the upper crust of about 6.3 km/s and an average velocity in the lower. crust of about 7.0 km/s. This crust thins abruptly to less than 20 km near the southwestern end of the profile where Precambrian outcrops abut the Cenozoic rocks and to 8 km beneath the Farasan Islands. The data over the coastal plain and Red Sea shelf areas are fit satisfactorily by an oceanic crustal model. A major lateral velocity inhomogeneity in the crust is inferred about 25 km northeast of Sabhah and is supported by surface geologic evidence. The major velocity discontinuities occur at about the same depth across the entire Shield and are interpreted to indicate horizontal metamorphic stratification of the Precambrian crust. Several lateral inhomogenities in both the upper and lower .crust of the . Shield are interpreted, to indicate bulk compositional variations. The subcrustal portion of the model is composed of a hot, low-density lithosphere beneath the Red Sea which is systematically cooler and denser to the northeast. This model provides a mechanism which explains the observed topographic uplift, regional gravity pattern, heat

  12. Delineation of nuclear structures in 3D multicellular systems

    2013-09-13

    A pipeline, implemented within the Insight Segmentation and Registration Toolkit (ITK) and The Visualization Toolkit (VTK) framework, to delineate each nucleus and to profile morphometric and colony organization. At an abstract level, our approach is an extension of a previously developed method for monolayer call structure models.

  13. TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants.

    PubMed

    Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

    2014-01-01

    The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure-activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein-ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. PMID:24930145

  14. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side.

  15. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  16. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors.

    PubMed

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III-V, and II-VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain-low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  17. Precision and Accuracy Parameters in Structured Light 3-D Scanning

    NASA Astrophysics Data System (ADS)

    Eiríksson, E. R.; Wilm, J.; Pedersen, D. B.; Aanæs, H.

    2016-04-01

    Structured light systems are popular in part because they can be constructed from off-the-shelf low cost components. In this paper we quantitatively show how common design parameters affect precision and accuracy in such systems, supplying a much needed guide for practitioners. Our quantitative measure is the established VDI/VDE 2634 (Part 2) guideline using precision made calibration artifacts. Experiments are performed on our own structured light setup, consisting of two cameras and a projector. We place our focus on the influence of calibration design parameters, the calibration procedure and encoding strategy and present our findings. Finally, we compare our setup to a state of the art metrology grade commercial scanner. Our results show that comparable, and in some cases better, results can be obtained using the parameter settings determined in this study.

  18. ProSAT+: visualizing sequence annotations on 3D structure.

    PubMed

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org. PMID:27284084

  19. 3D Anisotropic structure of the south-central Mongolia from Rayleigh and Love wave tomography

    NASA Astrophysics Data System (ADS)

    Yu, D.; Wu, Q.; Montagner, J. P.

    2014-12-01

    A better understanding of the geodynamics of the crust and mantle below Baikal-Mongolia is required to identify the role of mantle processes versus that of far-field tectonic effects from India-Asia collision. Anisotropy tomography can provide new perspective to the continental growth mechanism. In order to study the 3D anisotropic structure of the upper mantle in the south-central Mongolia, we collected the vertical and transverse components of seismograms recorded at 69 broadband seismic stations. We have measured inter-station phase velocities of 7181 Rayleigh waves and 901 Love waves using the frequency-time analysis of wavelet transformation method for the fundamental mode at period range 10~80s. The lateral phase velocity variations are computed by using a regionalization method. These phase velocities have been inverted to obtain the first anisotropic model including Sv velocities, azimuthal and radial anisotropy. The Middle Gobi is associated with low velocity. Based on the distribution of the Cenozoic basalts in the Middle Gobi, it refers that the low velocity anomaly is related to the Cenozoic volcanism. In the northern domain, near to Baikal zone, the azimuthal anisotropy is normal to the Baikal rift and consistent with the fast direction of previous SKS splitting measurements. In the South Gobi, north to Main Mongolian Lineament, the azimuthal anisotropy is NEE-SWW in the crust and NW-SE in the mantle. It indicates that the crust and mantle are decoupled. We propose that the crustal deformation is related to the far-field effects of India-Asia collision and that the mantle flow is correlated with the Baikal rift activity. Further study in process will provide more evidence and insight to better understand the geodynamics in this region.

  20. Code System for Analysis of 3-D Reinforced Concrete Structures.

    1999-11-22

    Version 00 NONSAP-C is a finite element program for determining the static and dynamic response of three-dimensional reinforced concrete structures. Long-term, or creep, behavior of concrete structures can also be analyzed. Nonlinear constitutive relations for concrete under short-term loads are incorporated in two time-independent models, a variable-modulus approach with orthotropic behavior induced in the concrete due to the development of different tangent moduli in different directions and an elastic-plastic model in which the concrete ismore » assumed to be a continuous, isotropic, and linearly elastic-plastic strain-hardening-fracture material. A viscoelastic constitutive model for long-term thermal creep of concrete is included. Three-dimensional finite elements available in NONSAP-C include a truss element, a multinode tendon element for prestressed and post tensioned concrete structures, an elastic-plastic membrane element to represent the behavior of cavity liners, and a general isoparametric element with a variable number of nodes for analysis of solids and thick shells.« less

  1. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

    Roddy, P. A.; Huang, C. Y.; Lyke, J.; Baur, J.; Durstock, M.; MacDonald, E.

    2013-12-01

    Three-dimensional printing, more formally Additive Manufacturing (AM), is being explored by groups worldwide for use in space missions, but we recognize the amazing potential of this emerging technology to produce space weather environmental sensors at costs commensurate with declining research budgets. We present here a plan to go substantially beyond the novelty stage of this technology by developing a foundation for using AM in high-assurance space system missions. Our two-pronged approach involves (1) a disciplined investigation of material properties and reliability (electrical, mechanical, radiation) of AM and (2) the extension of this knowledge to make complex structures that can exploit the advantages of AM. We address the design, manufacture, and optimization of multifunctional space structures using multi-physics design methods, integrated computational models, and AM. Integrated multifunctional structures have significant advantage in flexibility, size, weight, and power in comparison to formally attached elements, but their design and fabrication can be complex. The complexity and range in element shape, processing method, material properties and vehicle integration make this an ideal problem to advance the current state of the art methods for multiphysics mechanism design and strengthening AM processing science.

  2. Designing self-assembling 3D structures of microcapsules

    NASA Astrophysics Data System (ADS)

    Li, Like; Shum, Henry; Shklyaev, Oleg; Yashin, Victor; Balazs, Anna

    Self-assembly of complex, three-dimensional structures is commonly achieved by biological cells but difficult to realize in synthetic systems with micron-scale or larger components. Some previous modeling studies have considered only the planar self-assembly of microcapsules on a substrate. In this work, nanoparticles released from the capsules bind to the substrate and to the shells of nearby capsules. The non-uniform nanoparticle deposition on a capsule's surface leads to adhesion gradients, which drive the capsules to effectively ``climb'' on top of one another and self-organize in the vertical direction. We determine conditions that favor this structural organization. In particular, we study how the vertical structuring depends on the background fluid flow, the topography of the microcapsules and the underlying surface, the capsule-capsule interaction and that between the capsules and the substrate. The findings can provide design rules for the autonomous creation of novel nanocomposites, where the layers are formed from nanoparticle-containing and nanoparticle-decorated microcapsules.

  3. 3D P and S Wave Velocity Structure and Tremor Locations in the Parkfield Region

    NASA Astrophysics Data System (ADS)

    Zeng, X.; Thurber, C. H.; Shelly, D. R.; Bennington, N. L.; Cochran, E. S.; Harrington, R. M.

    2014-12-01

    We have assembled a new dataset to refine the 3D seismic velocity model in the Parkfield region. The S arrivals from 184 earthquakes recorded by the Parkfield Experiment to Record MIcroseismicity and Tremor array (PERMIT) during 2010-2011 were picked by a new S wave picker, which is based on machine learning. 74 blasts have been assigned to four quarries, whose locations were identified with Google Earth. About 1000 P and S wave arrivals from these blasts at permanent seismic network were also incorporated. Low frequency earthquakes (LFEs) occurring within non-volcanic tremor (NVT) are valuable for improving the precision of NVT location and the seismic velocity model at greater depths. Based on previous work (Shelley and Hardebeck, 2010), waveforms of hundreds of LFEs in same family were stacked to improve signal qualify. In a previous study (McClement et al., 2013), stacked traces of more than 30 LFE families at the Parkfileld Array Seismic Observatory (PASO) have been picked. We expanded our work to include LFEs recorded by the PERMIT array. The time-frequency Phase Weight Stacking (tf-PWS) method was introduced to improve the stack quality, as direct stacking does not produce clear S-wave arrivals on the PERMIT stations. This technique uses the coherence of the instantaneous phase among the stacked signals to enhance the signal-to-noise ratio (SNR) of the stack. We found that it is extremely effective for picking LFE arrivals (Thurber et al., 2014). More than 500 P and about 1000 S arrivals from 58 LFE families were picked at the PERMIT and PASO arrays. Since the depths of LFEs are much deeper than earthquakes, we are able to extend model resolution to lower crustal depths. Both P and S wave velocity structure have been obtained with the tomoDD method. The result suggests that there is a low velocity zone (LVZ) in the lower crust and the location of the LVZ is consistent with the high conductivity zone beneath the southern segment of the Rinconada fault that

  4. Structural 3d Monitoring Using a New Sinusoidal Fitting Adjustment

    NASA Astrophysics Data System (ADS)

    Detchev, I.; Habib, A.; Lichti, D.; El-Badry, M.

    2016-06-01

    Digital photogrammetric systems combined with image processing techniques have been used for structural monitoring purposes for more than a decade. For applications requiring sub-millimetre level precision, the use of off-the-shelf DSLR cameras is a suitable choice, especially when the low cost of the involved sensors is a priority. The disadvantage in the use of entry level DSLRs is that there is a trade-off between frame rate and burst rate - a high frame rate is either not available or it cannot be sustained long enough. This problem must be overcome when monitoring a structural element undergoing a dynamic test, where a range of loads are cycled through multiple times a second. In order to estimate deflections during such a scenario, this paper proposes a new least-squares adjustment for sinusoidal fitting. The new technique is capable of processing multiple back-to-back bursts of data within the same adjustment, which synthetically increases the de-facto temporal resolution of the system. The paper describes a beam deformation test done in a structures laboratory. The experimental results were assessed in terms of both their precision and accuracy. The new method increased the effective sampling frequency three-fold, which improved the standard deviations of the estimated parameters with up to two orders of magnitude. A residual RMSE as low as 30 μm was attained, and likewise the RMSE of the computed amplitudes between the photogrammetric system and the control laser transducers was as small as 34 μm.

  5. High Resolution 3-D Waveform Tomography of the Lithospheric Structure of the Hellenic Subduction Zone

    NASA Astrophysics Data System (ADS)

    Lamara, Samir; Friederich, Wolfgang; Schumacher, Florian; Meier, Thomas; Egelados Working Group

    2015-04-01

    in 67320 model parameters. Adding the smoothing and damping constraints we solved in total a system of 274780 equations for 67320 unknowns. The 3D tomographic model obtained from the full waveform inversion of the shear-wave velocity resolves in high details the crustal structure of the Hellenic subduction zone and images distinctly the eastern part of the volcanic arc where most of the actual volcanic activity is concentrated. Thinning of the crust in the Gulf of Corinth and many special features of the forearc such as low velocity anomalies throughout its upper 40 km depth are also well imaged. The crustal thickness in the southern Aegean shows strong variations in the whole region with a shallower Moho in the volcanic arc and the Cretan Sea (from 18 km to 25 km) and a thicker one beneath the entire forearc especially in its south-eastern part (from 45 to 50 km).

  6. TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants

    PubMed Central

    Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

    2014-01-01

    The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure–activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein–ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. PMID:24930145

  7. Formation of 3D structures in a volumetric photocurable material via a holographic method

    NASA Astrophysics Data System (ADS)

    Vorzobova, N. D.; Bulgakova, V. G.; Veselov, V. O.

    2015-12-01

    The principle of forming 3D polymer structures is considered, based on the display of the 3D intensity distribution of radiation formed by a hologram in the bulk of a photocurable material. The conditions are determined for limiting the cure depth and reproducing the projected wavefront configuration.

  8. Central Andean crustal structure from receiver function analysis

    NASA Astrophysics Data System (ADS)

    Ryan, Jamie; Beck, Susan; Zandt, George; Wagner, Lara; Minaya, Estela; Tavera, Hernado

    2016-07-01

    The Central Andean Plateau (15°-27°S) is a high plateau in excess of 3 km elevation, associated with thickened crust along the western edge of the South America plate, in the convergent margin between the subducting Nazca plate and the Brazilian craton. We have calculated receiver functions using seismic data from a recent portable deployment of broadband seismometers in the Bolivian orocline (12°-21°S) region and combined them with waveforms from 38 other stations in the region to investigate crustal thickness and crust and mantle structures. Results from the receiver functions provide a more detailed map of crustal thickness than previously existed, and highlight mid-crustal features that match well with prior studies. The active volcanic arc and Altiplano have thick crust with Moho depths increasing from the central Altiplano (65 km) to the northern Altiplano (75 km). The Eastern Cordillera shows large along strike variations in crustal thickness. Along a densely sampled SW-NE profile through the Bolivian orocline there is a small region of thin crust beneath the high peaks of the Cordillera Real where the average elevations are near 4 km, and the Moho depth varies from 55 to 60 km, implying the crust is undercompensated by ~ 5 km. In comparison, a broader region of high elevations in the Eastern Cordillera to the southeast near ~ 20°S has a deeper Moho at ~ 65-70 km and appears close to isostatic equilibrium at the Moho. Assuming the modern-day pattern of high precipitation on the flanks of the Andean plateau has existed since the late Miocene, we suggest that climate induced exhumation can explain some of the variations in present day crustal structure across the Bolivian orocline. We also suggest that south of the orocline at ~ 20°S, the thicker and isostatically compensated crust is due to the absence of erosional exhumation and the occurrence of lithospheric delamination.

  9. Stress Recovery and Error Estimation for 3-D Shell Structures

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

    The C1-continuous stress fields obtained from finite element analyses are in general lower- order accurate than are the corresponding displacement fields. Much effort has focussed on increasing their accuracy and/or their continuity, both for improved stress prediction and especially error estimation. A previous project developed a penalized, discrete least squares variational procedure that increases the accuracy and continuity of the stress field. The variational problem is solved by a post-processing, 'finite-element-type' analysis to recover a smooth, more accurate, C1-continuous stress field given the 'raw' finite element stresses. This analysis has been named the SEA/PDLS. The recovered stress field can be used in a posteriori error estimators, such as the Zienkiewicz-Zhu error estimator or equilibrium error estimators. The procedure was well-developed for the two-dimensional (plane) case involving low-order finite elements. It has been demonstrated that, if optimal finite element stresses are used for the post-processing, the recovered stress field is globally superconvergent. Extension of this work to three dimensional solids is straightforward. Attachment: Stress recovery and error estimation for shell structure (abstract only). A 4-node, shear-deformable flat shell element developed via explicit Kirchhoff constraints (abstract only). A novel four-node quadrilateral smoothing element for stress enhancement and error estimation (abstract only).

  10. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

  11. 3D structures of the crust and upper mantle in Atlas Mountains of Morocco from magnetotelluric data

    NASA Astrophysics Data System (ADS)

    Kiyan, D.; Jones, A.; Ledo, J.; Fullea, J.; Sinischalchi, A.; Romano, G.; Campanya, J.

    2012-04-01

    As a part of the PICASSO (Program to Investigate Convective Alboran Sea System Overturn) and concomitant TopoMed (Plate re-organization in the western Mediterranean: Lithospheric causes and topographic consequences - an ESF EUROCORES TOPO-EUROPE project) projects, a multi-institutional magnetotelluric (MT) experiment across the Atlas Mountains initiated in September 2009 and ended in February 2010. The overarching objective of the project is to provide new constrains on the lithospheric structure of the Atlas Mountains, and to aid in discriminating between competing models describing the tectonics of the region. The experiment comprised acquisition of broad-band (crustal probing) and long period (mantle probing) MT data along two profiles: a N-S oriented profile crossing the Middle Atlas through the Central High Atlas to the east (profile MEK) and a NE-SW oriented profile crossing the western High Atlas towards the Anti Atlas in the west (profile MAR). Our MT inversion results from the MEK profile (Ledo et al., 2011), assuming that the Earth can be validly represented by two-dimensional (2D) structures, reveal two major mid- to lower crustal scale conductive features. The first anomaly is stretching from the Middle Atlas southward towards the High Moulouya basin and the second one is located beneath the Anti Atlas. There is a gradual increase in mantle resistivity to the south which may indicate a thickening lithosphere beneath the Anti Atlas. To validate the 2D inversion results, the MT data on the same profile were inverted for 3D electrical resistivity structure using both WSINV3DMT (Siripunvaraporn et al., 2005a) and ModEM (Egbert et al., 2011). We ran inversions with the full impedance tensor and also with only the off-diagonal components. Following the paper of Patro and Egbert (2011), we are testing the effect of using different length scales in the along-strike and across strike directions. As expected, the 3D inversion results provide a better fit to the

  12. 3D Structured Grid Generation Codes for Turbomachinery

    NASA Technical Reports Server (NTRS)

    Loellbach, James; Tsung, Fu-Lin

    1999-01-01

    This report describes the research tasks during the past year. The research was mainly in the area of computational grid generation in support of CFD analyses of turbomachinery components. In addition to the grid generation work, a numerical simulation was obtained for the flow through a centrifugal gas compressor using an unstructured Navier-Stokes solver. Other tasks involved many different turbomachinery component analyses. These analyses were performed for NASA projects or for industrial applications. The work includes both centrifugal and axial machines, single and multiple blade rows, and steady and unsteady analyses. Over the past five years, a set of structured grid generation codes were developed that allow grids to be obtained fairly quickly for the large majority of configurations we encounter. These codes do not comprise a generalized grid generation package; they are noninteractive codes specifically designed for turbomachinery blade row geometries. But because of this limited scope, the codes are small, fast, and portable, and they can be run in the batch mode on small workstations. During the past year, these programs were used to generate computational grids were modified for a wide variety of configurations. In particular, the codes or wrote supplementary codes to improve our grid generation capabilities for multiple blade row configurations. This involves generating separate grids for each blade row, and then making them match and overlap by a few grid points at their common interface so that fluid properties are communicated across the interface. Unsteady rotor/stator analyses were performed for an axial turbine, a centrifugal compressor, and a centrifugal pump. Steady-state single-blade-row analyses were made for a study of blade sweep in transonic compressors. There was also cooperation on the application of an unstructured Navier-Stokes solver for turbomachinery flow simulations. In particular, the unstructured solver was used to analyze the

  13. A 3-D fluorescence imaging system incorporating structured illumination technology

    NASA Astrophysics Data System (ADS)

    Antos, L.; Emord, P.; Luquette, B.; McGee, B.; Nguyen, D.; Phipps, A.; Phillips, D.; Helguera, M.

    2010-02-01

    A currently available 2-D high-resolution, optical molecular imaging system was modified by the addition of a structured illumination source, OptigridTM, to investigate the feasibility of providing depth resolution along the optical axis. The modification involved the insertion of the OptigridTM and a lens in the path between the light source and the image plane, as well as control and signal processing software. Projection of the OptigridTM onto the imaging surface at an angle, was resolved applying the Scheimpflug principle. The illumination system implements modulation of the light source and provides a framework for capturing depth resolved mages. The system is capable of in-focus projection of the OptigridTM at different spatial frequencies, and supports the use of different lenses. A calibration process was developed for the system to achieve consistent phase shifts of the OptigridTM. Post-processing extracted depth information using depth modulation analysis using a phantom block with fluorescent sheets at different depths. An important aspect of this effort was that it was carried out by a multidisciplinary team of engineering and science students as part of a capstone senior design program. The disciplines represented are mechanical engineering, electrical engineering and imaging science. The project was sponsored by a financial grant from New York State with equipment support from two industrial concerns. The students were provided with a basic imaging concept and charged with developing, implementing, testing and validating a feasible proof-of-concept prototype system that was returned to the originator of the concept for further evaluation and characterization.

  14. The lithosphere-asthenosphere system beneath Ireland from integrated geophysical-petrological modeling II: 3D thermal and compositional structure

    NASA Astrophysics Data System (ADS)

    Fullea, J.; Muller, M. R.; Jones, A. G.; Afonso, J. C.

    2014-02-01

    The lithosphere-asthenosphere boundary (LAB) depth represents a fundamental parameter in any quantitative lithospheric model, controlling to a large extent the temperature distribution within the crust and the uppermost mantle. The tectonic history of Ireland includes early Paleozoic closure of the Iapetus Ocean across the Iapetus Suture Zone (ISZ), and in northeastern Ireland late Paleozoic to early Mesozoic crustal extension, during which thick Permo-Triassic sedimentary successions were deposited, followed by early Cenozoic extrusion of large scale flood basalts. Although the crustal structure in Ireland and neighboring offshore areas is fairly well constrained, with the notable exception of the crust beneath Northern Ireland, the Irish uppermost mantle remains to date relatively unknown. In particular, the nature and extent of a hypothetical interaction between a putative proto Icelandic mantle plume and the Irish and Scottish lithosphere during the Tertiary opening of the North Atlantic has long been discussed in the literature with diverging conclusions. In this work, the present-day thermal and compositional structure of the lithosphere in Ireland is modeled based on a geophysical-petrological approach (LitMod3D) that combines comprehensively a large variety of data (namely elevation, surface heat flow, potential fields, xenoliths and seismic tomography models), reducing the inherent uncertainties and trade-offs associated with classical modeling of those individual data sets. The preferred 3D lithospheric models show moderate lateral density variations in Ireland characterized by a slightly thickened lithosphere along the SW-NE trending ISZ, and a progressive lithospheric thinning from southern Ireland towards the north. The mantle composition in the southern half of Ireland (East Avalonia) is relatively and uniformly fertile (i.e., typical Phanerozoic mantle), whereas the lithospheric composition in the northern half of Ireland (Laurentia) seems to vary

  15. Crustal structure of the Levant Basin, eastern Mediterranean

    NASA Astrophysics Data System (ADS)

    Ben-Avraham, Zvi; Ginzburg, Avihu; Makris, Jannis; Eppelbaum, Lev

    2002-02-01

    A seismic refraction/wide-angle reflection experiment was undertaken in the Levant Basin, eastern Mediterranean. Two roughly east-west profiles extend from the continental shelf of Israel toward the Levant Basin. The northern profile crosses the Eratosthenes Seamount and the southern profile crosses several distinct magnetic anomalies. The marine operation used 16 ocean bottom seismometers deployed along the profiles with an air gun array and explosive charges as energy sources. The results of this study strongly suggest the existence of oceanic crust under portions of the Levant Basin and continental crust under the Eratosthenes Seamount. The seismic refraction data also indicate a large sedimentary sequence, 10-14 km thick, in the Levant Basin and below the Levant continental margin. Assuming the crust is of Cretaceous age, this gives a fairly high sedimentation rate. The sequence can be divided into several units. A prominent unit is the 4.2 km/s layer, which is probably composed of the Messinian evaporites. Overlying the evaporitic layer are layers composed of Plio-Pleistocene sediments, whose velocity is 2.0 km/s. The refraction profiles and gravity and magnetic models indicate that a transition from a two layer continental to a single-layer oceanic crust takes place along the Levant margin. The transition in the structure along the southern profile is located beyond the continental margin and it is quite gradual. The northern profile, north of the Carmel structure, presents a different structure. The continental crust is much thinner there and the transition in the crustal structure is more rapid. The crustal thinning begins under western Galilee and terminates at the continental slope. The results of the present study indicate that the Levant Basin is composed of distinct crustal units and that the Levant continental margin is divided into at least two provinces of different crustal structure.

  16. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

    Madura, T. I.; Clementel, N.; Gull, T. R.; Kruip, C. J. H.; Paardekooper, J.-P.

    2015-06-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (≳120 M⊙), highly eccentric (e ˜ 0.9) binary star system η Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF (Portable Document Format) journal publication and the benefits of using 3D visualization and 3D printing as tools to analyse data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of η Carinae's inner (r ˜ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown `finger-like' structures at orbital phases shortly after periastron (φ ˜ 1.045) that protrude radially outwards from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively cooled layer of dense post-shock primary-star wind and the fast (3000 km s-1), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  17. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    NASA Astrophysics Data System (ADS)

    Babu, Sabarish; Liao, Pao-Chuan; Shin, Min C.; Tsap, Leonid V.

    2006-12-01

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell, and its state. Analysis of chromosome structure is significant in the detection of diseases, identification of chromosomal abnormalities, study of DNA structural conformation, in-depth study of chromosomal surface morphology, observation of in vivo behavior of the chromosomes over time, and in monitoring environmental gene mutations. The methodology incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  18. Sensitivity of an MT Array to 3D Structure Outside the Array Footprint

    NASA Astrophysics Data System (ADS)

    Booker, J. R.; Mackie, R. L.; Burd, A. I.; Pomposiello, M. C.; Favetto, A. B.

    2015-12-01

    Standard data collection strategy in magnetotellurics (MT) is to deploy a profile or array of sites that spans the target of interest. There is no expectation that structure can be imaged outside the area covered by sites. We have inverted two MT arrays for 3D structure under Argentina. The two arrays do not overlap, but serendipitously the 3D model for the northern array overlaps the position of a prominent 3D deep conductive structure seen in the inversion of the southern array. To our surprise this deep southern feature is also imaged by the northern array even though it is well outside the footprint of the northern array. It therefore appears that typical intuition about one's ability to image structure outside the span of the sites is not always true. We present model studies to demonstrate why this is so and under what conditions one can expect a 3D array to be capable of imaging structure outside the array.

  19. Imaging Crustal Structure Beneath Southern Australia: SoC Preliminary Results

    NASA Astrophysics Data System (ADS)

    Fontaine, F. R.; Tkalcic, H.; Kennett, B.

    2008-12-01

    We deployed in Southern Australia a broad-band seismic network of 28 three-component seismometers between December 2005 and August 2008 for a nine months period at most site. This seismic experiment called SoC (Structure of Cratons) should provide 3-D images of the lithosphere and constraints on the variation in crustal and lithospheric thickness through exploitation of recordings of distant earthquakes in a corridor extending from the Curnamona craton to the east coast of Australia, crossing the transition from Precambrian to Phanerozoic belts. We also analyze data from permanent broad-band stations: one GEOSCOPE station and eight stations from Geoscience Australia network. SoC is designed to be complementary of previous broad-band deployments in the region (SKIPPY and TASMAL). Including data from previous experiments we estimate if the lithosphere thins gradually toward the east and we also look at potential underplating of materials at the base of the crust. We present preliminary results obtained with teleseismic P receiver functions. We compare results from receiver functions computed in the ZRT coordinate system and receiver functions obtained from a rotation into the ray coordinate system L, Q and T. Two different inversion techniques are used to determine the crust and upper mantle structure that can explain the observed receiver functions. The 1-D velocity structure will be used to invert for seismic moment tensor of regional earthquakes. The crustal Vp/Vs ratio and the crust thickness can be estimated from the analysis of the travel times of waves converted at the Moho and of crustal multiples converted phases. The comparison between Moho topography and crustal Vp/Vs ratio give us the possibility to discuss the nature of the basement of the lithosphere beneath Mount Gambier and the Murray Basin: whether it is oceanic or continental.

  20. Crustal and Lithospheric Structure across the Boundary of the East European Craton from Receiver Functions

    NASA Astrophysics Data System (ADS)

    Knapmeyer-Endrun, B.; Krueger, F.

    2014-12-01

    The Trans-European Suture Zone (TESZ), which extends from the North Sea to the Black Sea, marks a fundamental lithospheric boundary in Europe. It separates the East European Craton to the north-east, which has been stable for at least 1.45 Ga, from the younger lithosphere of Phanerozoic Europe to the south-west. In this study we use a large dataset of more than 40,000 teleseismic P- and S-receiver functions from almost 500 seismological stations to image crustal and lithospheric structure across central and eastern Europe between the Benelux and the Baltic countries. An important data source is the PASSEQ project, which deployed close to 200 temporary stations between Germany and Lithuania for two years with the aim to obtain detailed, 3D information on the upper mantle structure across the TESZ. Combining P and S observations, we find a stepwise transition in crustal thickness, spread over 200 km laterally, from on average of 30 km in Phanerozoic Europe to more than 45 km beneath the East European Craton. Individual Paleoproterozoic terranes in Lithuania can also be distinguished based on crustal thickness. Crustal layering is not resolved with the receiver functions, but a high Poisson's ratio of 0.27 is obtained for the craton, compared to 0.25 for Phanerozoic Europe, which is consistent with a thick mafic lower crust. Moho depth results show an excellent correlation with the interpretation of a seismic line in the area, lending confidence to the interpretation of deeper structures. The lithosphere-asthenosphere boundary (LAB), as mapped by S-receiver functions, is located at an average depth of 90 km beneath Phanerozoic Europe. Towards the east, the LAB is dipping to about 125 km depth beneath the Elbe Line. Below the craton, a mid-lithospheric discontinuity is found at about 80 km depth, whereas weak indications of the LAB are found at an average depth of 260 km.

  1. Crustal subsidence, seismicity, and structure near Medicine Lake Volcano, California

    USGS Publications Warehouse

    Dzurisin, D.; Donnelly-Nolan, J. M.; Evans, J.R.; Walter, S.R.

    1991-01-01

    The pattern of historical ground deformation, seismicity, and crustal structure near Medicine Lake volcano illustrates a close relation between magmatism and tectonism near the margin of the Cascade volcanic chain and the Basin and Range tectonic province. Subsidence occurs mainly by aseismic creep within 25km of the summit, where the crust has been heated and weakened by intrusions, and by normal faulting during episodic earthquake swarms in surrounding, cooler terrain. -from Authors

  2. mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome.

    PubMed

    Meyer, Michael J; Lapcevic, Ryan; Romero, Alfonso E; Yoon, Mark; Das, Jishnu; Beltrán, Juan Felipe; Mort, Matthew; Stenson, Peter D; Cooper, David N; Paccanaro, Alberto; Yu, Haiyuan

    2016-05-01

    A new algorithm and Web server, mutation3D (http://mutation3d.org), proposes driver genes in cancer by identifying clusters of amino acid substitutions within tertiary protein structures. We demonstrate the feasibility of using a 3D clustering approach to implicate proteins in cancer based on explorations of single proteins using the mutation3D Web interface. On a large scale, we show that clustering with mutation3D is able to separate functional from nonfunctional mutations by analyzing a combination of 8,869 known inherited disease mutations and 2,004 SNPs overlaid together upon the same sets of crystal structures and homology models. Further, we present a systematic analysis of whole-genome and whole-exome cancer datasets to demonstrate that mutation3D identifies many known cancer genes as well as previously underexplored target genes. The mutation3D Web interface allows users to analyze their own mutation data in a variety of popular formats and provides seamless access to explore mutation clusters derived from over 975,000 somatic mutations reported by 6,811 cancer sequencing studies. The mutation3D Web interface is freely available with all major browsers supported. PMID:26841357

  3. Laser direct writing 3D structures for microfluidic channels: flow meter and mixer

    NASA Astrophysics Data System (ADS)

    Lin, Chih-Lang; Liu, Yi-Jui; Lin, Zheng-Da; Wu, Bo-Long; Lee, Yi-Hsiung; Shin, Chow-Shing; Baldeck, Patrice L.

    2015-03-01

    The 3D laser direct-writing technology is aimed at the modeling of arbitrary three-dimensional (3D) complex microstructures by scanning a laser-focusing point along predetermined trajectories. Through the perspective technique, the details of designed 3D structures can be properly fabricated in a microchannel. This study introduces a direct reading flow meter and a 3D passive mixer fabricated by laser direct writing for microfluidic applications. The flow meter consists of two rod-shaped springs, a pillar, an anchor, and a wedge-shaped indicator, installed inside a microfluidic channel. The indicator is deflected by the flowing fluid while restrained by the spring to establish an equilibrium indication according to the flow rate. The measurement is readily carried out by optical microscopy observation. The 3D passive Archimedes-screw-shaped mixer is designed to disturb the laminar flow 3D direction for enhancing the mixing efficiency. The simulation results indicate that the screw provides 3D disturbance of streamlines in the microchannel. The mixing demonstration for fluids flowing in the micrchannel approximately agrees with the simulation result. Thanks to the advantage of the laser direct writing technology, this study performs the ingenious applications of 3D structures for microchannels.

  4. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

    Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

    2015-07-01

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

  5. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

    A 3D printer is used to prepare a variety of models representing potential energy as a function of two geometric coordinates. These models facilitate the teaching of structure-energy relationships in molecular conformations and in chemical reactions.

  6. Mare volcanism and lunar crustal structure

    NASA Technical Reports Server (NTRS)

    Solomon, S. C.

    1975-01-01

    It is pointed out that the concept of hydrostatic head, the height to which a fluid at a given pressure will rise in a gravitational field, can be usefully applied to magmatic liquids and to a number of problems in volcanology. For the moon, hydrostatic head arguments are an essential ingredient to explanations of mascons and of the scarcity of farside maria. In the reported investigation, simple hydrostatic concepts are extended to synthesize results from experimental petrology, lunar chronology, thermal history models, seismology, and gravity. Attention is given to a scenario for early lunar history, the density of lunar rocks and basaltic liquids, the thickness of the lunar crust, the source depth of mare basalt versus time, hydrostatic considerations with respect to the occurrence of high-titanium and low-titanium mare basalts, the structure of mascons, and the extension of the concepts of hydrostatics to the parent liquids of other basaltic rocks returned from the lunar surface.

  7. 3D P-wave velocity structure of the deep Galicia rifted margin: A first analysis of the Galicia 3D wide-angle seismic dataset

    NASA Astrophysics Data System (ADS)

    Bayrakci, Gaye; Minshull, Timothy A.; Davy, Richard G.; Karplus, Marianne S.; Kaeschen, Dirk; Papenberg, Cord; Krabbenhoeft, Anne; Sawyer, Dale; Reston, Timothy J.; Shillington, Donna J.; Ranero, César R.

    2014-05-01

    Galicia 3D, a reflection-refraction and long offset seismic experiment was carried out from May through September 2013, at the Galicia rifted margin (in the northeast Atlantic Ocean, west of Spain) as a collaboration between US, UK, German and Spanish groups. The 3D multichannel seismic acquisition conducted by R/V Marcus Langseth covered a 64 km by 20 km (1280 km2) zone where the main geological features are the Peridotite Ridge (PR), composed of serpentinized peridotite and thought be upper mantle exhumed to the seafloor during rifting, and the S reflector which has been interpreted to be a low angle detachment fault overlain by fault bounded, rotated, continental crustal blocks. In the 3D box, two airgun arrays of 3300 cu.in. were fired alternately (in flip-flop configuration) every 37.5 m. All shots are recorded by 44 short period four component ocean bottom seismometers (OBS) and 26 ocean bottom hydrophones (OBH) deployed and recovered by R/V Poseidon, as well as four 6 km hydrophone streamers with 12.5 m channel spacing towed by R/V Marcus Langseth. We present the preliminary results of the first arrival time tomography study which is carried out with a subset of the wide-angle dataset, in order to generate a 3D P-wave velocity volume for the entire depth sampled by the reflection data. After the relocation of OBSs and OBHs, an automatic first-arrival time picking approach is applied to a subset of the dataset, which comprises more than 5.5 million source-receiver pairs. Then, the first-arrival times are checked visually, in 3-dimensions. The a priori model used for the first-arrival time tomography is built up using information from previous seismic surveys carried out at the Galicia margin (e.g. ISE, 1997). The FAST algorithm of Zelt and Barton (1998) is used for the first-arrival time inversion. The 3D P-wave velocity volume can be used in interpreting the reflection dataset, as a starting point for migration, to quantify the thinning of the crustal layers

  8. Effect of 3d doping on the electronic structure of BaFe2As2.

    PubMed

    McLeod, J A; Buling, A; Green, R J; Boyko, T D; Skorikov, N A; Kurmaev, E Z; Neumann, M; Finkelstein, L D; Ni, N; Thaler, A; Bud'ko, S L; Canfield, P C; Moewes, A

    2012-05-30

    The electronic structure of BaFe(2)As(2) doped with Co, Ni and Cu has been studied by a variety of experimental and theoretical methods, but a clear picture of the dopant 3d states has not yet emerged. Herein we provide experimental evidence of the distribution of Co, Ni and Cu 3d states in the valence band. We conclude that the Co and Ni 3d states provide additional free carriers to the Fermi level, while the Cu 3d states are found at the bottom of the valence band in a localized 3d(10) shell. These findings help shed light on why superconductivity can occur in BaFe(2)As(2) doped with Co and Ni but not Cu. PMID:22534111

  9. Effect of 3d doping on the electronic structure of BaFe2As2

    SciTech Connect

    McLeod, John A.; Buling, A.; Green, R.J.; Boyko, T.D.; Skorikov, N.A.; Kurmaev, E.Z.; Neumann, M.; Finkelstein, L.D.; Ni, Ni; Thaler, Alexander; Budko, Serguei L.; Canfield, Paul; Moewes, A.

    2012-04-25

    The electronic structure of BaFe2As2 doped with Co, Ni and Cu has been studied by a variety of experimental and theoretical methods, but a clear picture of the dopant 3d states has not yet emerged. Herein we provide experimental evidence of the distribution of Co, Ni and Cu 3d states in the valence band. We conclude that the Co and Ni 3d states provide additional free carriers to the Fermi level, while the Cu 3d states are found at the bottom of the valence band in a localized 3d10 shell. These findings help shed light on why superconductivity can occur in BaFe2As2 doped with Co and Ni but not Cu.

  10. Crustal Thickness and Moho Character of the Fast-Spreading East Pacific Rise Between 9º37.5'N and 9º57'N From Poststack and Prestack Time Migrated 3D MCS data

    NASA Astrophysics Data System (ADS)

    Nedimovic, M. R.; Aghaei, O.; Carbotte, S. M.; Carton, H. D.; Canales, J. P.

    2014-12-01

    We measured crustal thickness and mapped Moho transition zone (MTZ) character over an 880 km2 section of the fast-spreading East Pacific Rise (EPR) using the first full 3D multichannel seismic (MCS) dataset collected across a mid-ocean ridge (MOR). The 9°42'-9°57'N area was initially investigated using 3D poststack time migration, which was followed by application of 3D prestack time migration (PSTM) to the whole dataset. This first attempt at applying 3D PSTM to MCS data from a MOR environment resulted in the most detailed reflection images of a spreading center to date. MTZ reflections are for the first time imaged below the ridge axis away from axial discontinuities indicating that Moho is formed at zero age at least at some sections of the MOR system. The average crustal thickness and crustal velocity derived from PSTM are 5920±320 m and 6320±290 m/s, respectively. The average crustal thickness varies little from Pacific to Cocos plate suggesting mostly uniform crustal production in the last ~180 Ka. However, the crust thins by ~400 m from south to north. The MTZ reflections were imaged within ~92% of the study area, with ~66% of the total characterized by impulsive reflections interpreted to originate from a thin MTZ and 26% characterized by diffusive reflections interpreted to originate from a thick MTZ. The MTZ is dominantly diffusive at the southern (9°37.5'-9°40'N) and northern (9°51'-9°57'N) ends of the study area, and it is impulsive in the central region (9°42'-9°51'N). No data were collected between 9°40'N and 9°42'N. More efficient mantle melt extraction is inferred within the central region with greater proportion of the lower crust accreted from the axial magma lens than within the northern and southern sections. This along-axis variation in the crustal accretion style may be caused by interaction between the melt sources for the ridge and the local seamounts, which are present within the northern and southern survey sections. Third

  11. Crustal structure of the Appalachian Highlands in Tennessee

    USGS Publications Warehouse

    Prodehl, C.; Schlittenhardt, J.; Stewart, S.W.

    1984-01-01

    Crustal structure of the southern Appalachians and adjacent Interior Low Plateaus in Tennessee is derived from seismic-refraction measurements observed by the U.S. Geological Survey in 1965 along reversed lines, normal (NW-SE) and parallel (NE-SW) to the structure of the Appalachian Highlands' major geologic divisions. Its easternmost part is located approximately 80 km southwest of the westernmost part of the COCORP seismic-reflection traverse within the Blue Ridge province. The velocity-depth models derived for both observational directions consist of three crustal layers with surprisingly high velocities, being about 6.1-6.2 km/s in the upper crust down to 7-10 km depth, 6.7-6.8 km/s for the middle crust between about 17 and 34 km and varying from 7.1 to 7.4 km/s for the lower crust at about 40-47 km depth. The boundaries between the three crustal layers as well as the crust-mantle boundary are transition zones of up to 11 km thickness. Similar to old orogens in other parts of the earth, the main result is a thick crust, at places in excess of 50 km, with high average velocity and a broad crust-mantle transition zone. ?? 1984.

  12. Crustal structure of the Eastern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Nwafor, Emeka

    The Gulf of Mexico initiated in the Late Triassic as South America and Africa separated from North America during the break up of Pangea. Previous studies indicate three models for the opening of the GOM. These include counter clockwise rotation of the Yucatan Block, rotation of the Yucatan Block about the same pole of rotation as those describing seafloor spreading in the central North Atlantic, and clockwise rotation of the Yucatan Block. There is much debate about the margin type and the crustal structure of the Eastern Gulf of Mexico (EGOM), especially below the depth of 6 km where crustal structure is poorly imaged on seismic reflection data. Two 2.5-D forward gravity and magnetic models across the margin are presented. These are constrained by basement picks from sparse seismic reflection and refraction data, spectral analysis of gravity data to determine the depth to source, magnetic susceptibility derived from results from other margins, the empirical relationship between P-wave velocity and density, and crustal scale isostatic modeling. The models, combined with a kinematic reconstruction of the GOM, show that: 1) it is a rifted margin; 2) the point where the Moho deepens downward from ˜17 km to ˜32 km is approximately 50 km outboard of the topographic shelf edge; 3) the carbonate bank retreated by several kilometers from its original termination due to the action of contourite currents; 4) extension and subsidence was accommodated with little shallow brittle faulting; 5) oceanic lithosphere is possibly outboard of the EGOM continental slope.

  13. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    SciTech Connect

    Babu, S; Liao, P; Shin, M C; Tsap, L V

    2004-04-28

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell and its state. Chromosome analysis is significant in the detection of deceases and in monitoring environmental gene mutations. The algorithm incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  14. New geophysical models of Palmer Deep crustal structure

    NASA Astrophysics Data System (ADS)

    Yakymchuk, M. A.; Levashov, S. P.; Korchagin, I. N.; Bachmutov, V. G.; Solovyov, V. D.

    2009-04-01

    The 2004 (9th) and 2006 (11th) Ukrainian Antarctic expeditions acquired new geoelectrical data (‘short-impulse electromagnetic field formation' - FSPEF, and ‘vertical electric-resonance sounding' - VERS) along profiles across Drake Passage and along Bransfield Strait, Antarctic Peninsula, with the aim of studying the crustal structure of these features down to depths of >30 km. The sounding on this depth in Antarctic region was the first experience of deep modification of the VERS method using. Modelling experience of deep crustal structure by geophysical data with VERS method shows that there is a possibility to investigate the fluid regime, tectonic disturbances and crush zones in basement and local places of submarine volcanic activity too. This technology also gives a possibility to efficiently divide the cross-section on separate stratigraphic subsections in the sounding site and to determine its depth with high accuracy (Levashov et al., 2003; Levashov et al., 2007). Geophysical surveys enabled to yield new data set with information about Drake Passage and Palmer Deep inner crustal structure on broad continental margin of Antarctic Peninsula. Palmer Deep is located on continental (Pacific) shelf of the Antarctic Peninsula near Anvers Island and consists of three deep basins with depths from 1200м to 1500м. These basins were part of glacial outlet during glaciation's period (Rebesco et al., 1998). Geoelectrical models of Palmer Deep crustal structure along three profiles were built on the sounding data in separate points of continental shelf. Heterogeneity of Palmer Deep earth's crust obtained from VERS data modelling testified to processes of tectonic transformations of internal shelf structures. Tectonic factor explains some conformities of the most recent glaciomarine sediments and glacial streams forming during recent shelf-wide glaciations. New information about sediment distribution and inner crustal structure has an important value for searching

  15. Deep Crustal Structure Northern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Christeson, G. L.; Van Avendonk, H. J.; Eddy, D. R.; Norton, I. O.; Karner, G. D.; Johnson, C. A.; Kneller, E. A.; Snedden, J.

    2013-12-01

    The Gulf of Mexico is a small ocean basin between the US and Mexico that opened up soon after the breakup of Pangea. Although the area has been heavily surveyed with seismic reflection profiles, the deep structure of the region is poorly understood because of lack of penetration beneath the thick sediments and salt. We present the results of the GUMBO (GUlf of Mexico Basin Opening) project that constrains seismic velocities and thicknesses of the sediments and crust from the continental shelf to deep ocean basin in the northern Gulf of Mexico. Data were acquired in 2010 along four profiles 300-500 km in length, using the industry vessel R/V Iron Cat and ocean bottom seismometers at 10-12 km spacing. Plate tectonic models for the Gulf of Mexico region have rifting initiating in the Late Triassic or Early Jurassic, with seafloor spreading beginning ~166-154 Ma in the western Gulf, propagating to the eastern Gulf, and ending ~154-135 Ma. Many models include transform motion along the Florida margin during initiation of continental rifting. We observe a strong change in rifting style from west to east across the ocean basin. Our western profile, offshore Texas, images highly heterogeneous crust with sediment velocities directly overlying Moho in some locations. These observations are consistent with either sedimentary basins within rifted continental crust or ultra-slow-spreading oceanic crust. The profile offshore Lousiana images thicker, faster, and more homogeneous crust. This could suggest an eastward increase in magmatic output during rifting. The eastern profiles offshore Alabama and Florida image the ocean-continent boundary and extensive regions of oceanic crust. The thickness of crystalline crust from the continental shelf to the deep basin decreases from ~25 km to 6-7 km over a horizontal distance of 150 km in the eastern Gulf of Mexico. The profile offshore Alabama, near a region where syn-rift volcanism has been interpreted on seismic reflection data, has

  16. Contribution of 3D inversion of Electrical Resistivity Tomography data applied to volcanic structures

    NASA Astrophysics Data System (ADS)

    Portal, Angélie; Fargier, Yannick; Lénat, Jean-François; Labazuy, Philippe

    2016-04-01

    The electrical resistivity tomography (ERT) method, initially developed for environmental and engineering exploration, is now commonly used for geological structures imaging. Such structures can present complex characteristics that conventional 2D inversion processes cannot perfectly integrate. Here we present a new 3D inversion algorithm named EResI, firstly developed for levee investigation, and presently applied to the study of a complex lava dome (the Puy de Dôme volcano, France). EResI algorithm is based on a conventional regularized Gauss-Newton inversion scheme and a 3D non-structured discretization of the model (double grid method based on tetrahedrons). This discretization allows to accurately model the topography of investigated structure (without a mesh deformation procedure) and also permits a precise location of the electrodes. Moreover, we demonstrate that a complete 3D unstructured discretization limits the number of inversion cells and is better adapted to the resolution capacity of tomography than a structured discretization. This study shows that a 3D inversion with a non-structured parametrization has some advantages compared to classical 2D inversions. The first advantage comes from the fact that a 2D inversion leads to artefacts due to 3D effects (3D topography, 3D internal resistivity). The second advantage comes from the fact that the capacity to experimentally align electrodes along an axis (for 2D surveys) depends on the constrains on the field (topography...). In this case, a 2D assumption induced by 2.5D inversion software prevents its capacity to model electrodes outside this axis leading to artefacts in the inversion result. The last limitation comes from the use of mesh deformation techniques used to accurately model the topography in 2D softwares. This technique used for structured discretization (Res2dinv) is prohibed for strong topography (>60 %) and leads to a small computational errors. A wide geophysical survey was carried out

  17. Imaging the Crustal and Subducted Slab Structure Beneath Puerto Rico Using Receiver Function Analysis

    NASA Astrophysics Data System (ADS)

    Vanacore, E. A.; Lopez, A. M.; Huerfano Moreno, V. A.

    2015-12-01

    The determination of earthquake locations are dependent on the velocity model selected. Consequently, the refinement and updating of the velocity models used at the local and regional network level is a critical component for network efficiency through location accuracy. With the expansion of broadband instruments within the Puerto Rico -Virgin Islands region, updating the velocity model is a current long term goal of the Puerto Rico Seismic Network (PRSN). As a first step to this long term goal, receiver functions of ~20 broadband stations with data between 2010 and 2015 were calculated using iterative time domain deconvolution. The receiver function analysis not only provides insight into the crustal velocity structure but also leads to a better understanding of the region's larger tectonic structure. Preliminary results of the receiver function analysis exhibit evidence of a "slab signal"; the receiver function backazimuth sweeps for some stations particularly on the northern side of the island contain a strong P to S conversion at approximately 7 seconds which likely corresponds to the top of the slab beneath Puerto Rico. This strong slab signal implies that simple 1-D analyses of the data (e.g. H-K stacking) may lead to misleading results. To further understand the crustal structure of PRVI, we employ a 3D common-conversion-point analysis. This analysis yields a Moho beneath the island between 32-42km and a possible southward dipping slab structure between 60-80km depth. Further analysis is needed to determine the 2D or 3D velocity structure of Puerto Rico and the surrounding environs such as waveform modeling. Given the current geometry of the available array, detailed imaging of the slab and mantle wedge beneath Puerto Rico is limited. PRSN is currently seeking to install denser temporary networks to improve local imaging that will help understand the nature of the crust, mantle wedge and slab structure beneath the island as well as the structure's influence

  18. Transfer printing of 3D hierarchical gold structures using a sequentially imprinted polymer stamp.

    PubMed

    Zhang, Fengxiang; Low, Hong Yee

    2008-10-15

    Complex three-dimensional (3D) hierarchical structures on polymeric materials are fabricated through a process referred to as sequential imprinting. In this work, the sequentially imprinted polystyrene film is used as a soft stamp to replicate hierarchical structures onto gold (Au) films, and the Au structures are then transferred to a substrate by transfer printing at an elevated temperature and pressure. Continuous and isolated 3D structures can be selectively fabricated with the assistance of thermo-mechanical deformation of the polymer stamp. Hierarchical Au structures are achieved without the need for a corresponding three-dimensionally patterned mold. PMID:21832645

  19. Self-Discovery of Structural Geology Concepts using Interactive 3D Visualization

    NASA Astrophysics Data System (ADS)

    Billen, M. I.; Saunders, J.

    2010-12-01

    Mastering structural geology concepts that depend on understanding three-dimensional (3D) geometries and imagining relationships among unseen subsurface structures are fundamental skills for geologists. Traditionally these skills are developed first, through use of 2D drawings of 3D structures that can be difficult to decipher or 3D physical block models that show only a limited set of relationships on the surfaces of the blocks, followed by application and testing of concepts in field settings. We hypothesize that this learning process can be improved by providing repeated opportunities to evaluate and explore synthetic 3D structures using interactive 3D visualization software. We present laboratory modules designed for undergraduate structural geology curriculum using a self-discovery approach to teach concepts such as: the Rule of V’s, structure separation versus fault slip, and the more general dependence of structural exposure on surface topography. The laboratory modules are structured to allow students to discover and articulate each concept from observations of synthetic data both on traditional maps and using the volume visualization software 3DVisualizer. Modules lead students through exploration of data (e.g., a dipping layered structure exposed in ridge-valley topography or obliquely offset across a fault) by allowing them to interactively view (rotate, pan, zoom) the exposure of structures on topographic surfaces and to toggle on/off the full 3D structure as a transparent colored volume. This tool allows student to easily visually understand the relationships between, for example a dipping structure and its exposure on valley walls, as well as how the structure extends beneath the surface. Using this method gives students more opportunities to build a mental library of previously-seen relationships from which to draw-on when applying concepts in the field setting. These laboratory modules, the data and software are freely available from KeckCAVES.

  20. Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

    3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

  1. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data

    PubMed Central

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUSstart) and after (3D-iCEUSend) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUSstart and 3D-iCEUSend data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  2. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data.

    PubMed

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUS s t a r t ) and after (3D-iCEUS e n d ) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUS s t a r t and 3D-iCEUS e n d data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  3. Metal nanoparticle direct inkjet printing for low-temperature 3D micro metal structure fabrication

    NASA Astrophysics Data System (ADS)

    Ko, Seung Hwan; Chung, Jaewon; Hotz, Nico; Nam, Koo Hyun; Grigoropoulos, Costas P.

    2010-12-01

    Inkjet printing of functional materials is a key technology toward ultra-low-cost, large-area electronics. We demonstrate low-temperature 3D micro metal structure fabrication by direct inkjet printing of metal nanoparticles (NPs) as a versatile, direct 3D metal structuring approach representing an alternative to conventional vacuum deposition and photolithographic methods. Metal NP ink was inkjet-printed to exploit the large melting temperature drop of the nanomaterial and the ease of the NP ink formulation. Parametric studies on the basic conditions for stable 3D inkjet printing of NP ink were carried out. Furthermore, diverse 3D metal microstructures, including micro metal pillar arrays, helices, zigzag and micro bridges were demonstrated and electrical characterization was performed. Since the process requires low temperature, it carries substantial potential for fabrication of electronics on a plastic substrate.

  4. Crustal thickness and Moho character of the fast-spreading East Pacific Rise from 9°42'N to 9°57'N from poststack-migrated 3-D MCS data

    NASA Astrophysics Data System (ADS)

    Aghaei, Omid; Nedimović, Mladen R.; Carton, Helene; Carbotte, Suzanne M.; Canales, J. Pablo; Mutter, John C.

    2014-03-01

    computed crustal thickness (5740 ± 270 m) and mapped Moho reflection character using 3-D seismic data covering 658 km2 of the fast-spreading East Pacific Rise (EPR) from 9°42'N to 9°57'N. Moho reflections are imaged within ˜87% of the study area. Average crustal thickness varies little between large sections of the study area suggesting regionally uniform crustal production in the last ˜180 Ka. However, individual crustal thickness measurements differ by as much as 1.75 km indicating that the mantle melt delivery has not been uniform. Third-order, but not fourth-order ridge discontinuities are associated with changes in the Moho reflection character and/or near-axis crustal thickness. This suggests that the third-order segmentation is governed by melt distribution processes within the uppermost mantle while the fourth-order ridge segmentation arises from midcrustal to upper-crustal processes. In this light, we assign fourth-order ridge discontinuity status to the debated ridge segment boundary at ˜9°45'N and third-order status at ˜9°51.5'N to the ridge segment boundary previously interpreted as a fourth-order discontinuity. Our seismic results also suggest that the mechanism of lower-crustal accretion varies along the investigated section of the EPR but that the volume of melt delivered to the crust is mostly uniform. More efficient mantle melt extraction is inferred within the southern half of our survey area with greater proportion of the lower crust accreted from the axial magma lens than that for the northern half. This south-to-north variation in the crustal accretion style may be caused by interaction between the melt sources for the ridge and the Lamont seamounts.

  5. Laser fabrication of 2D and 3D metal nanoparticle structures and arrays.

    PubMed

    Kuznetsov, A I; Kiyan, R; Chichkov, B N

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated. PMID:20941016

  6. Air-structured optical fibre drawn from a 3D-printed preform

    NASA Astrophysics Data System (ADS)

    Cook, Kevin; Leon-Saval, Sergio; Canning, John; Reid, Zane; Hossain, Md. Arafat; Peng, Gang-Ding

    2015-09-01

    We report the first optical fibre drawn from a 3D-printed preform. An air-structured polymer preform is printed using a modified butadiene plastic called Bendlay as opposed to the more-common Acrylonitrile Butadiene Styrene (ABS). The preform is subsequently drawn to fibre form at a relatively low temperature of 160 °C and maintains its air-structured cladding holes. Such ability to freely-design and 3D-print complex preform structures, such as photonic bandgap and photonic crystal structures, opens up an exciting new front in optical fibre fabrication.

  7. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

    PubMed Central

    Rodriguez-Palacios, Alex; Kodani, Tomohiro; Kaydo, Lindsey; Pietropaoli, Davide; Corridoni, Daniele; Howell, Scott; Katz, Jeffry; Xin, Wei; Pizarro, Theresa T.; Cominelli, Fabio

    2015-01-01

    Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes (‘cobblestones' versus ‘villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals ‘liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD. PMID:26154811

  8. A finite element analysis of a 3D auxetic textile structure for composite reinforcement

    NASA Astrophysics Data System (ADS)

    Ge, Zhaoyang; Hu, Hong; Liu, Yanping

    2013-08-01

    This paper reports the finite element analysis of an innovative 3D auxetic textile structure consisting of three yarn systems (weft, warp and stitch yarns). Different from conventional 3D textile structures, the proposed structure exhibits an auxetic behaviour under compression and can be used as a reinforcement to manufacture auxetic composites. The geometry of the structure is first described. Then a 3D finite element model is established using ANSYS software and validated by the experimental results. The deformation process of the structure at different compression strains is demonstrated, and the validated finite element model is finally used to simulate the auxetic behaviour of the structure with different structural parameters and yarn properties. The results show that the auxetic behaviour of the proposed structure increases with increasing compression strain, and all the structural parameters and yarn properties have significant effects on the auxetic behaviour of the structure. It is expected that the study could provide a better understanding of 3D auxetic textile structures and could promote their application in auxetic composites.

  9. Gene3D: structural assignments for the biologist and bioinformaticist alike

    PubMed Central

    Buchan, Daniel W. A.; Rison, Stuart C. G.; Bray, James E.; Lee, David; Pearl, Frances; Thornton, Janet M.; Orengo, Christine A.

    2003-01-01

    The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH. PMID:12520054

  10. Lithographically-generated 3D lamella layers and their structural color

    NASA Astrophysics Data System (ADS)

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-01

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ~ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  11. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography

    PubMed Central

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

  12. Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.

    PubMed

    Sillitoe, Ian; Lewis, Tony; Orengo, Christine

    2015-01-01

    The CATH database is a classification of protein structures found in the Protein Data Bank (PDB). Protein structures are chopped into individual units of structural domains, and these domains are grouped together into superfamilies if there is sufficient evidence that they have diverged from a common ancestor during the process of evolution. A sister resource, Gene3D, extends this information by scanning sequence profiles of these CATH domain superfamilies against many millions of known proteins to identify related sequences. Thus the combined CATH-Gene3D resource provides confident predictions of the likely structural fold, domain organisation, and evolutionary relatives of these proteins. In addition, this resource incorporates annotations from a large number of external databases such as known enzyme active sites, GO molecular functions, physical interactions, and mutations. This unit details how to access and understand the information contained within the CATH-Gene3D Web pages, the downloadable data files, and the remotely accessible Web services. PMID:26087950

  13. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

    Nugraha, Andri Dian; Syahputra, Ahmad; Fatkhan,; Sule, Rachmat

    2013-09-09

    We conducted delay time tomography to determine 3-D seismic velocity structures (Vp, Vs, and Vp/Vs ratio) using micro-seismic events in the geothermal field. The P-and S-wave arrival times of these micro-seismic events have been used as input for the tomographic inversion. Our preliminary seismic velocity results show that the subsurface condition of geothermal field can be fairly delineated the characteristic of reservoir. We then extended our understanding of the subsurface physical properties through determining of attenuation structures (Qp, Qs, and Qs/Qp ratio) using micro-seismic waveform. We combined seismic velocities and attenuation structures to get much better interpretation of the reservoir characteristic. Our preliminary attanuation structures results show reservoir characterization can be more clearly by using the 3-D attenuation model of Qp, Qs, and Qs/Qp ratio combined with 3-D seismic velocity model of Vp, Vs, and Vp/Vs ratio.

  14. Lithographically-generated 3D lamella layers and their structural color.

    PubMed

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-28

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ∼ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc. PMID:27087577

  15. Estimating the complexity of 3D structural models using machine learning methods

    NASA Astrophysics Data System (ADS)

    Mejía-Herrera, Pablo; Kakurina, Maria; Royer, Jean-Jacques

    2016-04-01

    Quantifying the complexity of 3D geological structural models can play a major role in natural resources exploration surveys, for predicting environmental hazards or for forecasting fossil resources. This paper proposes a structural complexity index which can be used to help in defining the degree of effort necessary to build a 3D model for a given degree of confidence, and also to identify locations where addition efforts are required to meet a given acceptable risk of uncertainty. In this work, it is considered that the structural complexity index can be estimated using machine learning methods on raw geo-data. More precisely, the metrics for measuring the complexity can be approximated as the difficulty degree associated to the prediction of the geological objects distribution calculated based on partial information on the actual structural distribution of materials. The proposed methodology is tested on a set of 3D synthetic structural models for which the degree of effort during their building is assessed using various parameters (such as number of faults, number of part in a surface object, number of borders, ...), the rank of geological elements contained in each model, and, finally, their level of deformation (folding and faulting). The results show how the estimated complexity in a 3D model can be approximated by the quantity of partial data necessaries to simulated at a given precision the actual 3D model without error using machine learning algorithms.

  16. Crustal shear wave velocity structure of the western United States inferred from ambient seismic noise and earthquake data

    NASA Astrophysics Data System (ADS)

    Moschetti, M. P.; Ritzwoller, M. H.; Lin, F.-C.; Yang, Y.

    2010-10-01

    Surface wave dispersion measurements from ambient seismic noise and array-based measurements from teleseismic earthquakes observed with the EarthScope/USArray Transportable Array (TA) are inverted using a Monte Carlo method for a 3-D VS model of the crust and uppermost mantle beneath the western United States. The combination of data from these methods produces exceptionally broadband dispersion information from 6 to 100 s period, which constrains shear wave velocity structures in the crust and uppermost mantle to a depth of more than 100 km. The high lateral resolution produced by the TA network and the broadbandedness of the dispersion information motivate the question of the appropriate parameterization for a 3-D model, particularly for the crustal part of the model. We show that a relatively simple model in which VS increases monotonically with depth in the crust can fit the data well across more than 90% of the study region, except in eight discrete areas where greater crustal complexity apparently exists. The regions of greater crustal complexity are the Olympic Peninsula, the MendocinoTriple Junction, the Yakima Fold Belt, the southern Cascadia back arc, the Great Central Valley of California, the Salton Trough, the Snake River Plain, and the Wasatch Mountains. We also show that a strong Rayleigh-Love discrepancy exists across much of the western United States, which can be resolved by introducing radial anisotropy in both the mantle and notably the crust. We focus our analysis on demonstrating the existence of crustal radial anisotropy and primarily discuss the crustal part of the isotropic model that results from the radially anisotropic model by Voigt averaging. Model uncertainties from the Monte Carlo inversion are used to identify robust isotropic features in the model. The uppermost mantle beneath the western United States is principally composed of four large-scale shear wave velocity features, but lower crustal velocity structure exhibits far greater

  17. System for conveyor belt part picking using structured light and 3D pose estimation

    NASA Astrophysics Data System (ADS)

    Thielemann, J.; Skotheim, Ø.; Nygaard, J. O.; Vollset, T.

    2009-01-01

    Automatic picking of parts is an important challenge to solve within factory automation, because it can remove tedious manual work and save labor costs. One such application involves parts that arrive with random position and orientation on a conveyor belt. The parts should be picked off the conveyor belt and placed systematically into bins. We describe a system that consists of a structured light instrument for capturing 3D data and robust methods for aligning an input 3D template with a 3D image of the scene. The method uses general and robust pre-processing steps based on geometric primitives that allow the well-known Iterative Closest Point algorithm to converge quickly and robustly to the correct solution. The method has been demonstrated for localization of car parts with random position and orientation. We believe that the method is applicable for a wide range of industrial automation problems where precise localization of 3D objects in a scene is needed.

  18. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

    3D printing is a form of additive manufacturing whereby the building up of layers of material creates objects. The selective laser sintering process (SLS) uses a laser beam to sinter powdered material to create objects. This paper builds upon previous research into 3D printed textile based material exploring the use of SLS using nylon powder to create flexible weft knitted structures. The results show the potential to print flexible textile based structures that exhibit the properties of traditional knitted textile structures along with the mechanical properties of the material used, whilst describing the challenges regarding fineness of printing resolution. The conclusion highlights the potential future development and application of such pieces.

  19. Effects of shallow density structure on the inversion for crustal shear wavespeeds in surface wave tomography

    NASA Astrophysics Data System (ADS)

    Xing, Guangchi; Niu, Fenglin; Chen, Min; Yang, Yingjie

    2016-03-01

    Surface wave tomography routinely uses empirically scaled density model in the inversion of dispersion curves for shear wavespeeds of the crust and uppermost mantle. An improperly selected empirical scaling relationship between density and shear wavespeedcan lead to unrealistic density models beneath certain tectonic formations such as sedimentary basins. Taking the Sichuan basin east to the Tibetan plateau as an example, we investigate the differences between density profiles calculated from four scaling methods and their effects on Rayleigh wave phase velocities. Analytical equations for 1-D layered models and adjoint tomography for 3-D models are used to examine the tradeoff between density and S-wave velocity structures at different depth ranges. We demonstrate that shallow density structure can significantly influence phase velocities at short periods, and thereby affect the shear wavespeed inversion from phase velocity data. In particular, a deviation of 25% in the initial density model can introduce an error up to 5% in the inverted shear velocity at middle and lower crustal depths. Therefore one must pay enough attention in choosing a proper velocity-density scaling relationship in constructing initial density model in Rayleigh wave inversion for crustal shear velocity structure.

  20. Acquisition of 3d Information for Vanished Structure by Using Only AN Ancient Picture

    NASA Astrophysics Data System (ADS)

    Kunii, Y.; Sakamoto, R.

    2016-06-01

    In order to acquire 3D information for reconstruction of vanished historical structure, grasp of 3D shape of such structure was attempted by using an ancient picture. Generally, 3D information of a structure is acquired by photogrammetric theory which requires two or more pictures. This paper clarifies that the geometrical information of the structure was obtained only from an ancient picture, and 3D information was acquired. This kind of method was applied for an ancient picture of the Old Imperial Theatre. The Old Imperial Theatre in the picture is constituted by two-point perspective. Therefore, estimated value of focal length of camera, length of camera to the Old Imperial Theatre and some parameters were calculated by estimation of field angle, using body height as an index of length and some geometrical information. Consequently, 3D coordinate of 120 measurement points on the surface of the Old Imperial Theatre were calculated respectively, and 3DCG modeling of the Old Imperial Theatre was realized.

  1. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation. PMID:26930179

  2. 3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures

    NASA Astrophysics Data System (ADS)

    Zawadzki, Robert J.; Fuller, Alfred R.; Zhao, Mingtao; Wiley, David F.; Choi, Stacey S.; Bower, Bradley A.; Hamann, Bernd; Izatt, Joseph A.; Werner, John S.

    2006-02-01

    The acquisition speed of current FD-OCT (Fourier Domain - Optical Coherence Tomography) instruments allows rapid screening of three-dimensional (3D) volumes of human retinas in clinical settings. To take advantage of this ability requires software used by physicians to be capable of displaying and accessing volumetric data as well as supporting post processing in order to access important quantitative information such as thickness maps and segmented volumes. We describe our clinical FD-OCT system used to acquire 3D data from the human retina over the macula and optic nerve head. B-scans are registered to remove motion artifacts and post-processed with customized 3D visualization and analysis software. Our analysis software includes standard 3D visualization techniques along with a machine learning support vector machine (SVM) algorithm that allows a user to semi-automatically segment different retinal structures and layers. Our program makes possible measurements of the retinal layer thickness as well as volumes of structures of interest, despite the presence of noise and structural deformations associated with retinal pathology. Our software has been tested successfully in clinical settings for its efficacy in assessing 3D retinal structures in healthy as well as diseased cases. Our tool facilitates diagnosis and treatment monitoring of retinal diseases.

  3. Reinterpretation of nappe structures in the Central Alps Evidence from 3D foliation field modelling

    NASA Astrophysics Data System (ADS)

    Maxelon, M.; Mancktelow, N. S.

    2003-04-01

    The Lepontine Alps represent the classic region for both, fold nappe development at mid-crustal levels and fold interference patterns from outcrop to regional scale. They have also been proposed as models for rapid burial and exhumation. However, before such models can be applied or critically assessed, the geometry of the units involved must be accurately known in three dimensions and this is a challenging task in this complex region. The three-dimensional geometry of the Lepontine nappes is not established unequivocally, as the integration and visualisation of structural data reflecting at least five different deformation phases has not yet been achieved satisfactorily. The present study focusses on a combination of new structural mapping in critical and/or contradictory areas, existing observations and their geostatistical assessment with modern computer-based tools (Editeur Géologique, Gocad) in order to develop a testable three-dimensional model of the geometry of the Lepontine Nappes in the Central Alps. Here we present a regional-scale three dimensional model of the southern central part of the Lepontine Region, bordered by the Swiss-Italian frontier in the east and Valle Leventina to the west and by Biasca and Locarno to the north and south. The model visualises a geostatistical calculation of the dominant foliation field in three dimensions, based on field measurements. The present day tectonostratigraphy and nappe geometry are mainly influenced by the three earliest recognisable Alpine deformation phases D_1 to D_3. D_1 structures are associated with first-time crustal nappe emplacement. Lithologies that are interpreted as nappe separators - mainly Mesozoic sediments such as "Bündnerschiefer" - have mostly been interleaved between the nappes during D_1, which entails strong isoclinal folding and pronounced boudinage of the infolded lithologies, with the development of a penetrative foliation S_1. S_1 and the infolded Mesozoic have been intensely

  4. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  5. Structural response to 3D simulated earthquake motions in San Bernardino Valley

    USGS Publications Warehouse

    Safak, E.; Frankel, A.

    1994-01-01

    Structural repsonse to one- and three-dimensional (3D) simulated motions in San Bernardino Valley from a hypothetical earthquake along the San Andreas fault with moment magnitude 6.5 and rupture length of 30km is investigated. The results show that the ground motions and the structural response vary dramatically with the type of simulation and the location. -from Authors

  6. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Fiedler, Susanne; Schmid, Volker J; Schermelleh, Lothar; Cremer, Thomas; Cremer, Marion

    2012-05-01

    Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization. PMID:22508100

  7. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

    Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

  8. Crustal structure beneath northeast India inferred from receiver function modeling

    NASA Astrophysics Data System (ADS)

    Borah, Kajaljyoti; Bora, Dipok K.; Goyal, Ayush; Kumar, Raju

    2016-09-01

    We estimated crustal shear velocity structure beneath ten broadband seismic stations of northeast India, by using H-Vp/Vs stacking method and a non-linear direct search approach, Neighbourhood Algorithm (NA) technique followed by joint inversion of Rayleigh wave group velocity and receiver function, calculated from teleseismic earthquakes data. Results show significant variations of thickness, shear velocities (Vs) and Vp/Vs ratio in the crust of the study region. The inverted shear wave velocity models show crustal thickness variations of 32-36 km in Shillong Plateau (North), 36-40 in Assam Valley and ∼44 km in Lesser Himalaya (South). Average Vp/Vs ratio in Shillong Plateau is less (1.73-1.77) compared to Assam Valley and Lesser Himalaya (∼1.80). Average crustal shear velocity beneath the study region varies from 3.4 to 3.5 km/s. Sediment structure beneath Shillong Plateau and Assam Valley shows 1-2 km thick sediment layer with low Vs (2.5-2.9 km/s) and high Vp/Vs ratio (1.8-2.1), while it is observed to be of greater thickness (4 km) with similar Vs and high Vp/Vs (∼2.5) in RUP (Lesser Himalaya). Both Shillong Plateau and Assam Valley show thick upper and middle crust (10-20 km), and thin (4-9 km) lower crust. Average Vp/Vs ratio in Assam Valley and Shillong Plateau suggest that the crust is felsic-to-intermediate and intermediate-to-mafic beneath Shillong Plateau and Assam Valley, respectively. Results show that lower crust rocks beneath the Shillong Plateau and Assam Valley lies between mafic granulite and mafic garnet granulite.

  9. A close-up on the southern Apennines crustal structure

    NASA Astrophysics Data System (ADS)

    Bianchi, Irene; Pio Lucente, Francesco; Chiarabba, Claudio; Piana Agostinetti, Nicola

    2015-04-01

    The southern Apennines of Italy undergoes intense tectonic activity and has been theater of large and destructive earthquakes. The region is characterized by deep structural complexities, which have been investigated in this study through the application and analysis of receiver function data. The structural complexities are reflected in the computed receiver functions, that in most cases lack of a clear P-direct phase on the radial component, hint of very low velocities in the first kilometers; the receiver functions also show strong amplitudes in the transverse component, hint of strong anisotropy. However the large data-set analyzed and the technique adopted for the analysis allowed us to reconstruct the crustal structures to some degree of detail. At shallow depth our analysis, accordingly with previous studies, reveals basin sequences and flysch units overriding limestone from former carbonate platform. In the middle crust, at about 20 km depth, an anisotropic layer has been detected, with anisotropy reaching up to 15%. We interpret this layer as the transition between the upper and the lower crust, and infer that its strong anisotropic signature is due to the texture acquired by the rocks behaving plastically under the rigid movements of upper crustal blocks during the Plio-Pleistocene collisional phase which lead to the growth of the Apennines.

  10. Imaging the Western Iberia Crustal Structure by Noise Analysis

    NASA Astrophysics Data System (ADS)

    Silveira, G. M.; Dias, N. A.; Custodio, S.; Kiselev, S.; Dündar, S.

    2014-12-01

    Portugal lies close to the Eurasian-African boundary, a region of tectonic regime transition from convergence in the Mediterranean to strike-slip in the Atlantic. Such broad convergence area, characterized by a slow rate of about 4.5-5.6 mm/yr, translates unto a scattered seismicity concentrated mainly in the offshore. Therefore, the irregular source-receiver geometry resulting from the inland seismic stations networks does not permit to derive high-resolution models of the Portuguese crustal structure using traditional passive seismology. Seismic interferometry/ambient noise surface-waves tomography allows imaging regions with a resolution that mainly depends on the seismic network coverage. Over the last decade, both Portuguese and Spanish permanent broadband (BB) seismic networks expanded significantly. This densification enabled to build a detailed image of the crustal structure of the Iberian Peninsula using ambient seismic noise. However, due to the existing network gaps towards west, the crustal image of Western Iberia is on the limit of resolution. The two years temporary deployment by the WILAS project contributed to fill those gaps and provide an excellent opportunity to study the Portuguese crustal structure. Dispersion measurements were computed for each pair of stations using empirical Green's functions generated by cross-correlating one-day-length seismic ambient-noise records. To improve the signal-to-noise ratio of the empirical Green functions computed from ambient noise records, we applied a phase cross-correlation method, followed by time-frequency domain phase weighted stack. Group-velocities were computed using the S-transform and we use the Fast Marching Surface Tomography algoritm to compute group velocity perturbation maps. Group velocities were then inverted as a function of depth to obtain S-wave velocity maps for diferent depths. The models will be compared with results from Ps receiver functions. The results obtained for the crust using

  11. Advanced methods for 3-D inelastic structural analysis for hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1989-01-01

    Three-dimensional Inelastic Analysis Methods are described. These methods were incorporated into a series of new computer codes embodying a progression of mathematical models (mechanics of materials, specialty finite element, boundary element) for streamlined analysis of hot engine structures such as: (1) combustor liners, (2) turbine blades, and (3) turbine vanes. These models address the effects of high temperatures and thermal/mechanical loadings on the local (stress/strain) and global (displacements, frequencies, amplitudes, buckling) structural behavior of the three respective components. The methods and the three computer codes, referred to as MOMM (Mechanics Of Materials Model), MHOST (MARC-Hot Section Technology), and BEST3D (Boundary Element Stress Technology), have been developed and are briefly described.

  12. The Crustal Structure of the Falkland Plateau from Wide-angle Seismic Data

    NASA Astrophysics Data System (ADS)

    Klemt, C. M.; Jokat, W.

    2015-12-01

    The Falkland Plateau is situated in the South Atlantic Ocean and stretches from the Falkland Islands more than 1500 km eastward to Georgia Basin. The Falkland Plateau Basin is located on the Falkland Plateau between the Falkland Islands in the west and a bathymetric high, the Maurice Ewing Bank, in the east. According to geodynamic models, the Falkland Plateau had a different shape during the Jurassic whereas the Falkland Islands were part of the supercontinent Gondwana. While the Falkland Islands and Maurice Ewing Bank are proved to be of continental composition, the nature and structure of the crust beneath the Falkland Plateau Basin in between is debatable. The first crustal model derived from sonobuoy data contradicts a recently published 3D-gravity model. To enhance the understanding of Gondwana break-up considering timing, geometry and amount of volcanism, further knowledge about the structure and thickness of the crust is inevitable. During the ANT-XXIX/5 Polarstern cruise, seismic refraction measurements were conducted using Ocean Bottom Seismometers (OBS) and REF TEK land stations onshore of East Falkland. The OBS were deployed at 78 locations along an approximately 1500 km east-west stretching profile. Based on this data, a P-wave velocity model was calculated using 2D-raytracing techniques. Beneath the Falkland Plateau Basin the crust exhibits a thickness ranging between 16 km and 22 km and a two-layered velocity structure. The velocity distribution is similar to average oceanic crust with a larger gradient in the upper part and a smaller gradient in the lower part. Lower crustal velocities are up to 7.6 km/s. For Maurice Ewing Bank a different velocity distribution can be observed. The crust is thicker (about 30 km) and velocities do not exceed 7.0 km/s. Considering crustal thickness and velocity distribution, we interpret the Falkland Plateau with the exception of Maurice Ewing Bank to consist of thickened oceanic crust.

  13. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  14. Deep-crustal magma reservoirs beneath the Nicaraguan volcanic arc, revealed by 2-D and semi 3-D inversion of magnetotelluric data

    NASA Astrophysics Data System (ADS)

    Brasse, Heinrich; Schäfer, Anja; Díaz, Daniel; Alvarado, Guillermo E.; Muñoz, Angélica; Mütschard, Lutz

    2015-11-01

    A long-period magnetotelluric (MT) experiment was conducted in early 2009 in western Nicaragua to study the electrical resistivity and thus fluid/melt distribution at the Central American continental margin where the Cocos plate subducts beneath the Caribbean plate. Strike analysis yields a preference direction perpendicular to the profile, with moderate deviation from two-dimensionality, however. Two-dimensional modeling maps the sediments of the Nicaraguan Depression and a high-conductivity zone in the mid-crust, slightly offset from the arc. Further conductors are modeled in the backarc. However, these features are probably artifacts when a 2-D program is applied to data which show moderate 3-D characteristics. 3-D inversion clarifies the situation, and the major remaining conductive structure is now quasi directly beneath the volcanic chain and interpreted as a deep-seated magma deposit. Conductivity in the backarc is also relatively high and may either be caused by still existing partial melts beneath the Paleocene to Miocene volcanic arcs or by related metallic deposits in the aureoles of hydrothermal alteration.

  15. Direct-growth carbon nanotubes on 3D structural microelectrodes for electrophysiological recording.

    PubMed

    Pan, Alice Ian; Lin, Min-Hsuan; Chung, Hui-Wen; Chen, Hsin; Yeh, Shih-Rung; Chuang, Yung-Jen; Chang, Yen-Chung; Yew, Tri-Rung

    2016-01-01

    A novel 3D carbon nanotube (CNT) microelectrode was developed through direct growth of CNTs on a gold pin-shaped 3D microelectrode at a low temperature (400 °C) for applications in neural and cardiac recording. With an electroplated Ni catalyst layer covering the entire surface of the pin-shaped structure, CNTs were synthesized on a 3D microelectrode by catalytic thermal chemical vapor deposition (CVD). According to the analyses by electrochemical impedance spectroscopy, the impedance of 3D microelectrodes after CNT growth and UV/O3 treatment decreased from 9.3 Ω mm(-2) to 1.2 Ω mm(-2) and the capacitance increased largely from 2.2 mF cm(-2) to 73.3 mF cm(-2). The existence of UVO3-treated CNT led to a large improvement of interfacial capacitance, contributing to the decrease of impedance. The electrophysiological detection capability of this 3D CNT microelectrode was demonstrated by the distinguished P waves, QRS complex and T waves in the electrocardiogram of the zebrafish heart and the action potential recorded from individual rat hippocampal neurons. The compatibility of integration with ICs, high resolution in space, electrophysiological signals, and non-invasive long-term recording suggest that the 3D CNT microelectrode exhibits promising potential for applications in electrophysiological research and clinical trials. PMID:26588673

  16. Modeling 3D soil and sediment distributions for assessing catchment structure and hydrological feedbacks

    NASA Astrophysics Data System (ADS)

    Maurer, Thomas; Brück, Yasemine; Hinz, Christoph; Gerke, Horst H.

    2015-04-01

    Structural heterogeneity, namely the spatial distribution of soils and sediments (represented by mineral particles), characterizes catchment hydrological behavior. In natural catchments, local geology and the specific geomorphic processes determine the characteristics and spatial distribution of structures. In constructed catchments, structural features are determined primarily by the construction processes and the geological origin of the parent material. Objectives are scenarios of 3D catchment structures in form of complete 3D description of soil hydraulic properties generated from the knowledge of the formation processes. The constructed hydrological catchment 'Hühnerwasser' (Lower Lusatia, Brandenburg, Germany) was used for the calibration and validation of model results due to its well-known conditions. For the modelling of structural features, a structure generator was used to model i) quasi-deterministic sediment distributions using input data from a geological model of the parent material excavation site; ii) sediment distributions that are conditioned to measurement data from soil sampling; and iii) stochastic component sediment distributions. All three approaches allow a randomization within definable limits. Furthermore, the spoil cone / spoil ridge orientation, internal layering, surface compaction and internal spoil cone compaction were modified. These generated structural models were incorporated in a gridded 3D volume model constructed with the GOCAD software. For selected scenarios, the impact of structure variation was assessed by hydrological modelling with HYDRUS 2D/3D software. For that purpose, 3D distributions of soil hydraulic properties were estimated based on generated sediment properties using adapted pedotransfer functions. Results from the hydrological model were compared them to measured discharges from the catchment. The impact of structural feature variation on flow behaviour was analysed by comparing different simulation scenarios

  17. Crustal Structure of Northeastern Sicily, South Italy, From Tomographic Inversion of Local Earthquake Arrival-times

    NASA Astrophysics Data System (ADS)

    Orecchio, B.; Aloisi, M.; Barberi, G.; Neri, G.

    After integrating the databases of the local and national seismic networks relative to lithospheric seismicity that occurred in and around Northeastern Sicily bet ween 1978 and 2001, we selected 932 events for 3D local tomography of P- and S-wave velocity. A dataset of 10241 P and 5597 S arrival times was inverted for Vp, Vs and hypocenter distributions using the SIMULPS12 algorithm. Analysis of the Derivative Weight Sum and Spread Function detected a rather good level of constraint of velocity at nodes of a grid with horizontal and vertical spacing of 10 and 6 km respectively, spanning the upper 30 Km beneath the area including Central and Northeastern Sicily, Southern Calabria and the Southeasternmost Tyrrhenian Sea. Standard deviation of arrival-time residuals after 3D inversion was about 20% lower than obtained by locating the same earthquakes using the minimum 1D model. Four main spatial domains can be distinguished in the obtained velocity structure: i) a high-velocity domain corresponding to Tyrrhenian structural units; ii) low-velocity domain corresponding to Sicilian units; iii) a domain corresponding to the Calabrian Arc characterized by positive velocity anomalies at shallow depth (nodes in the range 0-12 Km) and by negative velocity ones below (18-30 Km); iv) positive anomalies at deep nodes (18-30 Km) and negative anomalies above, in the area including the Etna volcano and the Ionian coast of Sicily near the volcanic edifice. Velocity distributions were analyzed jointly with the geophysical and geological information available in the literature in order to improve our knowledge of the crustal structure in the study area. Furthermore, comparisons were made with the most recent regional geodynamic models and led us to state that the crustal features evidenced in the present investigation match well with the model assuming gravity- induced southeastward roll-back of an Ionian lithospheric slab subducting beneath the Tyrrhenian sea.

  18. 2D and 3D X-Ray Structural Microscopy Using Submicron-Resolution Laue Microdiffraction

    SciTech Connect

    Budai, John D.; Yang, Wenge; Larson, Bennett C.; Tischler, Jonathan Z.; Liu, Wenjun; Ice, Gene E.

    2010-11-10

    We have developed a scanning, polychromatic x-ray microscopy technique with submicron spatial resolution at the Advanced Photon Source. In this technique, white undulator radiation is focused to submicron diameter using elliptical mirrors. Laue diffraction patterns scattered from the sample are collected with an area detector and then analyzed to obtain the local crystal structure, lattice orientation, and strain tensor. These new microdiffraction capabilities have enabled both 2D and 3D structural studies of materials on mesoscopic length-scales of tenths-to-hundreds of microns. For thin samples such as deposited films, 2D structural maps are obtained by step-scanning the area of interest. For example, 2D x-ray microscopy has been applied in studies of the epitaxial growth of oxide films. For bulk samples, a 3D differential-aperture x-ray microscopy technique has been developed that yields the full diffraction information from each submicron volume element. The capabilities of 3D x-ray microscopy are demonstrated here with measurements of grain orientations and grain boundary motion in polycrystalline aluminum during 3D thermal grain growth. X-ray microscopy provides the needed, direct link between the experimentally measured 3D microstructural evolution and the results of theory and modeling of materials processes on mesoscopic length scales.

  19. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  20. Mixed-Mode Fracture and Fatigue Analysis of Cracked 3D Complex Structures using a 3D SGBEM-FEM Alternating Method

    NASA Astrophysics Data System (ADS)

    Bhavanam, Sharada

    The aim of this thesis is to numerically evaluate the mixed-mode Stress Intensity Factors (SIFs) of complex 3D structural geometries with arbitrary 3D cracks using the Symmetric Galerkin Boundary Element Method-Finite Element Method (SGBEM-FEM) Alternating Method. Various structural geometries with different loading scenarios and crack configurations were examined in this thesis to understand the behavior and trends of the mixed-mode SIFs as well as the fatigue life for these complex structural geometries. Although some 3D structures have empirical and numerical solutions that are readily available in the open literature, some do not; therefore this thesis presents the results of fracture and fatigue analyses of these 3D complex structures using the SGBEM-FEM Alternating Method to serve as reference for future studies. Furthermore, there are advantages of using the SGBEM-FEM Alternating Method compared to traditional FEM methods. For example, the fatigue-crack-growth and fatigue life can be better estimated for a structure because different fatigue models (i.e. Walker, Paris, and NASGRO) can be used within the same framework of the SGBEM-FEM Alternating Method. The FEM (un-cracked structure)/BEM(crack model) meshes are modeled independently, which speeds up the computation process and reduces the cost of human labor. A simple coarse mesh can be used for all fracture and fatigue analyses of complex structures. In this thesis, simple coarse meshes were used for 3D complex structures, which were below 5000 elements as compared to traditional FEM, which require meshes where the elements range on the order of ˜250,000 to ˜106 and sometimes even more than that.

  1. Crustal and upper mantle structures beneath Cenozoic volcanoes on the board of China and North Korea.

    NASA Astrophysics Data System (ADS)

    Rhie, J.; Kim, S.

    2015-12-01

    The Cenozoic-to-recent volcanoes on the border of China and North Korea are recognized as continental intraplate volcanoes. Despite of much work, the origin and mechanism of the volcanoes remain as an issue of debate, due to their complex and long-lived volcanic activities and lack of detailed information for the crust and upper mantle structures. In this work, ambient noise analysis is performed to image lithospheric structures beneath the volcanoes and surrounding regions using continuous broadband recordings of two temporary networks (1998-1999 PASSCAL array and a part of the 2009-2011 NECASSArray). To better constrain the entire depths of lithosphere in the estimated 3-D velocity structure, we utilize the spectral auto-correlation (SPAC) method and a Bayesian inversion technique to measure phase velocity dispersion data and to obtain shear-wave velocity structures, respectively. We developed a novel grid-search technique for more stable SPAC measurements, and obtained phase velocity data are compared and combined with group and phase velocity data from the conventional frequency-time analysis. Hierarchical and trans-dimensional techniques are implemented in the Bayesian method to estimate more rigorous models and associated uncertainties. The estimated 3-D model shows slower velocity (~0.3 km/s) at the bottom of lithosphere (>60 km) and less modified thick-crust beneath the volcanoes compared to other regions in the model. This suggests our model favors the theory of magma underplating, crustal assimilation, and less volume of magma supply from upper mantle.

  2. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  3. Computational methods for constructing protein structure models from 3D electron microscopy maps

    PubMed Central

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-01-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3 Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. PMID:23796504

  4. Segmented images and 3D images for studying the anatomical structures in MRIs

    NASA Astrophysics Data System (ADS)

    Lee, Yong Sook; Chung, Min Suk; Cho, Jae Hyun

    2004-05-01

    For identifying the pathological findings in MRIs, the anatomical structures in MRIs should be identified in advance. For studying the anatomical structures in MRIs, an education al tool that includes the horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is necessary. Such an educational tool, however, is hard to obtain. Therefore, in this research, such an educational tool which helps medical students and doctors study the anatomical structures in MRIs was made as follows. A healthy, young Korean male adult with standard body shape was selected. Six hundred thirteen horizontal MRIs of the entire body were scanned and inputted to the personal computer. Sixty anatomical structures in the horizontal MRIs were segmented to make horizontal segmented images. Coronal, sagittal MRIs and coronal, sagittal segmented images were made. 3D images of anatomical structures in the segmented images were reconstructed by surface rendering method. Browsing software of the MRIs, segmented images, and 3D images was composed. This educational tool that includes horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is expected to help medical students and doctors study anatomical structures in MRIs.

  5. 3D flexible NiTi-braided elastomer composites for smart structure applications

    NASA Astrophysics Data System (ADS)

    Heller, L.; Vokoun, D.; Šittner, P.; Finckh, H.

    2012-04-01

    While outstanding functional properties of thin NiTi wires are nowadays well recognized and beneficially utilized in medical NiTi devices, development of 2D/3D wire structures made out of these NiTi wires remains challenging and mostly unexplored. The research is driven by the idea of creating novel 2D/3D smart structures which inherit the functional properties of NiTi wires and actively utilize geometrical deformations within the structure to create new/improved functional properties. Generally, textile technology provides attractive processing methods for manufacturing 2D/3D smart structures made out of NiTi wires. Such structures may be beneficially combined with soft elastomers to create smart deformable composites. Following this route, we carried out experimental work focused on development of 3D flexible NiTi-braided elastomer composites involving their design, laboratory manufacture and thermomechanical testing. We describe the manufacturing technology and structural properties of these composites; and perform thermomechanical tests on the composites, focusing particularly on quasistatic tensile properties, energy absorption, damping and actuation under tensile loading. Functional thermomechanical properties of the composites are discussed with regard to the mechanical properties of the components and architecture of the composites. It is found that the composites indeed inherit all important features of the thermomechanical behavior of NiTi wires but, due to their internal architecture, outperform single NiTi wires in some features such as the magnitude of recoverable strain, superelastic damping capacity and thermally induced actuation strain.

  6. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

    PubMed

    Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

    2016-07-01

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. PMID:27095203

  7. Ellipticity of Rayleigh waves and crustal structure in northern Italy

    NASA Astrophysics Data System (ADS)

    Berbellini, Andrea; Morelli, Andrea; Ferreira, Ana M. G.

    2016-04-01

    Horizontal-to-vertical amplitude ratio of elliptically-polarised ground motion of Rayleigh waves depends on the local crustal structure. Its measurement therefore adds another, seldom used, tool to image shallow earth structure. Frequency-dependent sensitivity kernels are dominated by shear-wave velocity and are rather shallow, so they are a convenient tool to model sedimentary layers that nicely complement surface wave studies. We perform extensive measurements, in the period range between 10 and 110 s, on traces from about 500 globally-distributed earthquakes, occurred in years 2008 ÷ 2014, recorded by 95 stations in northern Italy - - a region including the wide basin of the Po Plain and encircling Alps and northern Apennines. The observations are well correlated with known strucure: high ellipticity correlates well with low seismic velocity (such as in the Po Plain), and low ellipticity corresponds to fast seismic velocity in hard rock environments in correspondence of Alps and Apennines. Comparison between observations and predicted ellipticity from a reference crustal model of the region (Molinari et al., 2015) shows substantial fit. Sensitivity to vS is quite non linear, but inversion is possible and may provide very useful complementary information to, e.g., surface wave phase or group velocity or receiver functions.

  8. 3D tomographic structure of the north andean subduction zone at the Colombia-Ecuador border

    NASA Astrophysics Data System (ADS)

    Garcia Cano, L. C.; Galve, A.; de La Torre, G.; Charvis, P.; Pontoise, B.; Hello, Y.; Anglade, A.; Yates, B. A.

    2007-12-01

    At the latitude of Ecuador - southern Colombia, the Nazca plate converges toward the South American plate along an ~E-W direction at a rate of about 6 cm/yr. Several large subduction earthquakes affected this area during the last century. Near the Ecuador-Colombia border the 500 km long rupture zone of the 1906 event (M = 8.8) was partially reactivated, from south to north, by a sequence of 3 thrust events in 1942 (Mw = 7.8), 1958 (Mw = 7.7) and 1979 (Mw = 8.2). From 1998 to 2005, this zone was the target of five marine geophysical campaigns in order to determine the shallow and deep structure of the margin, its deformation and the possible relation with the rupture zone of the major earthquakes. Bathymetric data, passive and active seismic data were collected off South-Colombia and Ecuador. The data suggest that the interplate earthquakes and the extension of their rupture zone are at least partly controlled by structures on the downgoing and upper plates. To the south the subduction of the buoyant Carnegie Ridge, with a up to 19 km thick crust, is inferred to partially lock the plate interface along central Ecuador. This is illustrated by the rupture zones during the 1942 and 1906 earthquakes that terminated against the subducted northern flank of the ridge. The margin wedge is segmented by transverse crustal faults that correlate with the limits of the earthquake coseismic slip zones at the limit between the 1942 and 1958 rupture zones as well as at the limit between the 1958 and 1979 rupture zones. Furthermore, seaward of the 1958 rupture zone, a 2D profile from the SALIERI experiment (2001) highlights that the margin seems to overthrust a low velocity outer basement high along a splay fault that would decouple the bulk of the margin basement from its frontal part during great earthquake rupture. During, the 3D Esmeraldas experiment, conducted from February to June 2005, 34 3-components portable stations were installed on land and 26 3-components Ocean Bottom

  9. Magnetotelluric images of the crustal structure of Chyulu Hills volcanic field, Kenya

    NASA Astrophysics Data System (ADS)

    Sakkas, V.; Meju, M. A.; Khan, M. A.; Haak, V.; Simpson, F.

    2002-03-01

    affected by volcanism. The low-resistivity anomalies are interpreted as possible magmatic features and may be related to the low-velocity zones recently detected at greater depth in the same geographic locations. The MT results, thus, provide a necessary upper crustal constraint on the anomalous zone in Chyulu Hills, and we suggest that MT is a logical compliment to seismics for the exploration of the deep crust in this volcanic-covered basement terrain. A detailed 3-D field study is recommended to gain a better understanding of the deep structure of the volcanic field.

  10. Seismic source inversion using Green's reciprocity and a 3-D structural model for the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

    We present a feasibility study for seismic source inversions using a 3-D velocity model for the Japanese Islands. The approach involves numerically calculating 3-D Green's tensors, which is made efficient by exploiting Green's reciprocity. The rationale for 3-D seismic source inversion has several aspects. For structurally complex regions, such as the Japan area, it is necessary to account for 3-D Earth heterogeneities to prevent unknown structure polluting source solutions. In addition, earthquake source characterisation can serve as a means to delineate existing faults. Source parameters obtained for more realistic Earth models can then facilitate improvements in seismic tomography and early warning systems, which are particularly important for seismically active areas, such as Japan. We have created a database of numerically computed 3-D Green's reciprocals for a 40°× 40°× 600 km size area around the Japanese Archipelago for >150 broadband stations. For this we used a regional 3-D velocity model, recently obtained from full waveform inversion. The model includes attenuation and radial anisotropy and explains seismic waveform data for periods between 10 - 80 s generally well. The aim is to perform source inversions using the database of 3-D Green's tensors. As preliminary steps, we present initial concepts to address issues that are at the basis of our approach. We first investigate to which extent Green's reciprocity works in a discrete domain. Considering substantial amounts of computed Green's tensors we address storage requirements and file formatting. We discuss the importance of the initial source model, as an intelligent choice can substantially reduce the search volume. Possibilities to perform a Bayesian inversion and ways to move to finite source inversion are also explored.

  11. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  12. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  13. Pore-scale intermittent velocity structure underpinning anomalous transport through 3-D porous media

    NASA Astrophysics Data System (ADS)

    Kang, Peter K.; Anna, Pietro; Nunes, Joao P.; Bijeljic, Branko; Blunt, Martin J.; Juanes, Ruben

    2014-09-01

    We study the nature of non-Fickian particle transport in 3-D porous media by simulating fluid flow in the intricate pore space of real rock. We solve the full Navier-Stokes equations at the same resolution as the 3-D micro-CT (computed tomography) image of the rock sample and simulate particle transport along the streamlines of the velocity field. We find that transport at the pore scale is markedly anomalous: longitudinal spreading is superdiffusive, while transverse spreading is subdiffusive. We demonstrate that this anomalous behavior originates from the intermittent structure of the velocity field at the pore scale, which in turn emanates from the interplay between velocity heterogeneity and velocity correlation. Finally, we propose a continuous time random walk model that honors this intermittent structure at the pore scale and captures the anomalous 3-D transport behavior at the macroscale.

  14. Element-specific X-ray phase tomography of 3D structures at the nanoscale.

    PubMed

    Donnelly, Claire; Guizar-Sicairos, Manuel; Scagnoli, Valerio; Holler, Mirko; Huthwelker, Thomas; Menzel, Andreas; Vartiainen, Ismo; Müller, Elisabeth; Kirk, Eugenie; Gliga, Sebastian; Raabe, Jörg; Heyderman, Laura J

    2015-03-20

    Recent advances in fabrication techniques to create mesoscopic 3D structures have led to significant developments in a variety of fields including biology, photonics, and magnetism. Further progress in these areas benefits from their full quantitative and structural characterization. We present resonant ptychographic tomography, combining quantitative hard x-ray phase imaging and resonant elastic scattering to achieve ab initio element-specific 3D characterization of a cobalt-coated artificial buckyball polymer scaffold at the nanoscale. By performing ptychographic x-ray tomography at and far from the Co K edge, we are able to locate and quantify the Co layer in our sample to a 3D spatial resolution of 25 nm. With a quantitative determination of the electron density we can determine that the Co layer is oxidized, which is confirmed with microfluorescence experiments. PMID:25839287

  15. Advanced resin systems and 3D textile preforms for low cost composite structures

    NASA Technical Reports Server (NTRS)

    Shukla, J. G.; Bayha, T. D.

    1993-01-01

    Advanced resin systems and 3D textile preforms are being evaluated at Lockheed Aeronautical Systems Company (LASC) under NASA's Advanced Composites Technology (ACT) Program. This work is aimed towards the development of low-cost, damage-tolerant composite fuselage structures. Resin systems for resin transfer molding and powder epoxy towpreg materials are being evaluated for processability, performance and cost. Three developmental epoxy resin systems for resin transfer molding (RTM) and three resin systems for powder towpregging are being investigated. Various 3D textile preform architectures using advanced weaving and braiding processes are also being evaluated. Trials are being conducted with powdered towpreg, in 2D weaving and 3D braiding processes for their textile processability and their potential for fabrication in 'net shape' fuselage structures. The progress in advanced resin screening and textile preform development is reviewed here.

  16. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  17. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays. PMID:27285961

  18. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

    Shearography (speckle pattern shearing interferometry) is a non-destructive testing technique that provides full-field surface strain characterization. Although real-life objects especially in aerospace, transport or cultural heritage are not flat (e.g. aircraft leading edges or sculptures), their inspection with shearography is of interest for both hidden defect detection and material characterization. Accurate strain measuring of a highly curved or free form surface needs to be performed by combining inline object shape measuring and processing of shearography data in 3D. Previous research has not provided a general solution. This research is devoted to the practical questions of 3D shape shearography system development for surface strain characterization of curved objects. The complete procedure of calibration and data processing of a 3D shape shearography system with integrated structured light projector is presented. This includes an estimation of the actual shear distance and a sensitivity matrix correction within the system field of view. For the experimental part a 3D shape shearography system prototype was developed. It employs three spatially-distributed shearing cameras, with Michelson interferometers acting as the shearing devices, one illumination laser source and a structured light projector. The developed system performance was evaluated with a previously reported cylinder specimen (length 400 mm, external diameter 190 mmm) loaded by internal pressure. Further steps for the 3D shape shearography prototype and the technique development are also proposed.

  19. Simultaneous determination of hypocenter location and crustal structure in the Virginia seismic region

    SciTech Connect

    Koch, M.; Kalata, J.

    1992-11-10

    Simultaneous inversions for one- (1-D) and three-dimensional (3-D) seismic structure and hypocenters (SSH) for both the central and western Virginia seismic regions are performed, using direct and refracted phases from about 60 earthquakes. Optimal inversion models are computed by employing regularization techniques of Tikhonov and of Backus and Gilbert. Improvements for the residual sum squared, of up to 70% are obtained for the 3-D models and somewhat less for the 1-D models. For the central Virginia seismic region the SSH 1-D velocity models show a strong negative bias in the deduced P{sub n} velocity which could only be alleviated after a ray-tracing travel time correction for the P{sub n} phases due to the east-west downdipping Moho has been applied. A 4{degrees} Moho dip turns out to be optimal for best explaining the observed travel time residuals and returning a realistic P{sub n} velocity of 8.2-8.3 km/s. However, the deduced velocity in the lower crust is only {approximately} 6.35 km/s, which is lower than that predicted from gravity modeling but can be explained in terms of a lower crustal petrology of anorthosite-rich granulite. A more detailed analysis of the lower crust shows that the hypothesized high-velocity layer at the bottom of the crust is not clearly identifiable by the present travel time data and so can neither be corroborated nor refuted. Many of the 1-D crustal results are further substantiated by the 3-D model, which also provides a reduced lower crustal velocity under the Goochland Terrane. Positive velocity anomalies, which are found in the upper and middle crust under the Blue Ridge/Piedmont boundary, correlate qualitatively with the high-density, thrust-faulted slab deduced by Pratt et al. from gravity modeling. The vertical movements of the relocated hypocenters in the central region are of O(2-5 km) and are such as to further widen the seismic gap under the Goochland Terrane. 61 refs., 16 figs, 1 tab.

  20. RNAssess--a web server for quality assessment of RNA 3D structures.

    PubMed

    Lukasiak, Piotr; Antczak, Maciej; Ratajczak, Tomasz; Szachniuk, Marta; Popenda, Mariusz; Adamiak, Ryszard W; Blazewicz, Jacek

    2015-07-01

    Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of 3D models has a fundamental impact on the progress of structural bioinformatics. Here, we present RNAssess server, a novel tool dedicated to visual evaluation of RNA 3D models in the context of the known reference structure for a wide range of accuracy levels (from atomic to the whole molecule perspective). The proposed server is based on the concept of local neighborhood, defined as a set of atoms observed within a sphere localized around a central atom of a particular residue. A distinctive feature of our server is the ability to perform simultaneous visual analysis of the model-reference structure coherence. RNAssess supports the quality assessment through delivering both static and interactive visualizations that allows an easy identification of native-like models and/or chosen structural regions of the analyzed molecule. A combination of results provided by RNAssess allows us to rank analyzed models. RNAssess offers new route to a fast and efficient 3D model evaluation suitable for the RNA-Puzzles challenge. The proposed automated tool is implemented as a free and open to all users web server with an user-friendly interface and can be accessed at: http://rnassess.cs.put.poznan.pl/. PMID:26068469

  1. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-01-01

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions. PMID:25940394

  2. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  3. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  4. A reduced-coordinate approach to modeling RNA 3-D structures

    SciTech Connect

    Tung, Chang-Shung

    1997-09-01

    With the realization of RNA molecules capable of performing very specific functions (e.g., catalytic RNAs and RNAs that bind ligand with affinity and specificity of an anti-body) and contrary to the traditional view that structure of RNA molecules being functionally passive, it has become clear that studying the 3-dimensional (3-D) folding of RNA molecules is a very important task. In the absence of sufficient number of experimentally determined RNA structures available up-to-date, folding of RNA structures computationally provides an alternative approach in studying the 3-D structure of RNA molecules. We have developed a computational approach for folding RNA 3-D structures. The method is conceptually simple and general. It consists of two major components. The first being the arrangement of all helices in space. Once the helices are positioned and oriented in space, structures of the connecting loops are modeled and inserted between the helices. Any number of structural constraints derived either experimentally or theoretically can be used to guide the folding processes. A conformational sampling approach is developed with structural equilibration using the Metropolis Monte Carlo simulation. The lengths of various loop sizes (ranging from 1 base to 7 bases) are calculated based on a set of RNA structures deposited in PDB as well as a set of loop structures constructed using our method. The validity of using the averaged loop lengths of the connecting loops as distance constraints for arranging the helices in space is studied.

  5. VARNET-96: three-dimensional upper crustal velocity structure of SW Ireland

    NASA Astrophysics Data System (ADS)

    Landes, M.; O'Reilly, B. M.; Readman, P. W.; Shannon, P. M.; Prodehl, C.

    2003-05-01

    During the VARNET-96 seismic experiment three seismic refraction/wide-angle reflection profiles were acquired in order to examine the crustal structure in the southwest of Ireland. A total of 170 seismic stations were used on 300 recording sites. The shotpoint geometry was designed to allow for inline and offline fan shot recordings on the three profiles, using a total of 34 shots. Results from 3-D ray-trace and inversion modelling illustrate the pervasive lateral heterogeneity of the crust south of the Shannon Estuary. About 5 km of interpreted Palaeozoic sediment at the south coast was associated with the sedimentary infill of the Munster and South Munster Basins. This sedimentary layer, which thins to approximately 2 km in the northern Munster Basin, is significantly thinner than previously estimated from geological field studies. High-velocity zones beneath Dingle Bay and the Kenmare River region may be associated with the deep traces of the Killarney-Mallow Fault Zone and the Cork-Kenmare line. A zone of high-velocity upper crust (6.4-6.6 km s-1) beneath the South Munster Basin is found in the area between the Kenmare-Killarney and the Leinster Granite gravity lows. The depth to the Moho varies from approximately 28-29 km at the south coast to approximately 32-33 km in the Dingle-Shannon Basin. The interpretation of the 2-D and 3-D velocity models suggests that Variscan deformation is confined to sedimentary and upper crustal structures in the southwest of Ireland.

  6. Modeling the Effects of Crustal Structure on Surface-Wave Phase Delays

    NASA Astrophysics Data System (ADS)

    Liu, K.; Zhou, Y.

    2010-12-01

    In tomographic studies, crustal structure has significant impact on the observed data but it is usually too thin to be resolved using traditional tomographic methods and "crustal corrections" - assuming known crustal structure - are often required in mantle tomographic inversions. Seismic surface waves propagate in the outer shell of the earth and are highly sensitive to crustal structure, therefore they can be potentially used to constrain crustal structure at a global scale. We investigate the limitations of linear perturbation theory in global seismic tomography of crustal structure. We calculate surface-wave phase velocity perturbations caused by Moho boundary variations in spherically symmetrical reference earth models using linear perturbation theory. Our calculations show that linear perturbation theory works well for Love waves over a range of periods from 40 to 200 seconds for perturbations up to 30 km; while for Rayleigh waves, linear perturbation theory breaks down for large perturbations in crustal thickness (~15km). To quantify finite-frequency effects in global crustal models, we simulate global wave propagation in crustal models using the spectral element method (SEM) and make phase delay measurements caused by lateral variations in crustal thickness. The measured delay times are compared with predictions made based upon three different methods associated with crustal tomography: path integrations of local phase delays, ray perturbation theory and finite-frequency theory. We show that finite-frequency effects are dependent upon the length scale of lateral variations in crustal thickness. In addition to forward simulations, we discuss limitations of each method in the inversion of global and regional crustal structure using the synthetic SEM measurements and tradesoffs between velocity and Moho boundary discontinuity perturbations.

  7. About the automated pattern creation of 3D jacquard double needle bed warp knitted structures

    NASA Astrophysics Data System (ADS)

    Renkens, W.; Kyosev, Y.

    2016-07-01

    Three dimensional structures can be produced on jacquard warp knitting machines with double needle bed. This work presents theoretical considerations about the modelling and simulation of these structures. After that a method is described, how to obtain production parameters from the simulation data. The analysis demonstrates, that the automated pattern creation of 3D structures is not always possible and not all mathematical solutions of the problem can be knittable.

  8. Crustal structure north of Falkland Plateau offshore Argentina

    NASA Astrophysics Data System (ADS)

    Becker, Katharina; Schnabel, Michael; Franke, Dieter

    2010-05-01

    The passive continental margin offshore Argentina has been investigated by numerous geophysical surveys conducted by the Federal Institute for Geoscience and Natural Resources. In this study we focus on the area located north of Falkland Plateau. There, the passive margin forms the transition between the sheared margin of the Falkland Plateau and the volcanic passive margin of southern Argentina. This study aims at achieving a more detailed image of the crustal structure along the continent-ocean transition. Also we want to decipher the influence of the plume (Tristan da Cunha) on the evolution of the continental margin. The seismic data were acquired during a marine geophysical survey in 2004 and edited with an improved processing sequence. The imaging involves the application of Prestack Depth Migration, which gives information about depth and interval velocities of the reflectors. In addition we combine our seismic section with information from magnetic and gravimetric measurements. In this study we present preliminary results. A first section gives insight in the structure of the crust along the continent ocean boundary. Landwards there is no clear evidence of extension, which can be inferred from graben structures. In the transition zone the breakup unconformity is tilted seawards. In this part it is covered by a sedimentary drift body, which reaches a maximum thickness of 4km. The drift body can be divided into several units. In the east the oceanic basement is highly dissected by faults. The sedimentary succession overlying the oceanic basement reaches a maximum thickness of 4km. Further processing will reveal more details about the upper crustal structure along the margin. In the future we want to investigate the structure of the lower crust based on refraction seismic measurements.

  9. What spherically symmetric viscosity structure produces the same PGR as a realistic 3D Earth?

    NASA Astrophysics Data System (ADS)

    Paulson, A.; Zhong, S.; Wahr, J.

    2003-04-01

    Observations of isostatic adjustment of the earth's surface due to transient loading provide important constraints on the mantle viscosity structure. However, most studies of this response have assumed a spherically symmetric (1D) earth. This study is motivated by the following question: when a one-dimensional viscosity model is derived from post-glacial rebound (PGR) observations, how does this 1D structure correspond to the three-dimensional structure of the earth? Using the 3D spherical finite element software CitcomSVE [Zhong et al., 2002], we are able to compute the earth's response to realistic glacial loading when the earth has a truly 3D viscosity structure. The loading is provided by the ICE-3G deglaciation history [Tushingham &Peltier, 1991]. The 3D viscosity structure is constructed by first selecting a priori a radial average viscosity (for example, ( 1021 \\: {Pa \\cdot s}) in the upper mantle and (2 × 1021 \\: {Pa \\cdot s}) in the lower mantle). The lateral variations about this radial structure are derived from seismic shear-velocity tomography models by converting velocities to temperature, then temperature to viscosity. The seismic tomography models used are S20RTS [Ritsema et al., 1999] and NA00 [Van der Lee, 2002]. From the computed isostatic response, we measure typical PGR observables: relative sea level change (RSLC) and (dot{J2}). These measurements are then treated as synthetic data, and we search for 1D (radially stratified) viscosity models, forced with the same glaciation history, that will best fit these synthetic PGR observations. We find that for sites near the center of a large glacial load (e.g., southern Hudson Bay), a local average of the 3D viscosity structure provides a reasonable 1D proxy. For sites along the periphery of the glacial load (e.g., Boston), it is much more difficult to find a 1D model that can reproduce the 3D observations. We also approach the problem by running an ensemble of 1D viscosity models, and finding

  10. Crustal Structure of the PARANÁ Basin from Ambient Noise Tomography

    NASA Astrophysics Data System (ADS)

    Collaço, B.; Assumpcao, M.

    2015-12-01

    Conventional seismic tomography tends to have poor resolution in regions of low seismicity where good path coverage is not always possible. Previous studies carried out in South America did not map clearly some areas of the continent, such as the southern part of the Paraná basin, because of insufficient number of crossing paths. To describe the crustal structure of the whole Paraná basin, in addition to data obtained by the analysis of Andean earthquakes, we used dispersion curves from ambient noise correlation between pairs of seismographic stations, a technique known by Ambient Noise Tomography (ANT). The obtained group velocity maps for South America correspond well with the main geological provinces of the continent: low velocities under the Andes and sedimentary basins and high velocities in cratonic regions. Inversion of the group velocities for the Paraná Basin were carried out with the following results: a) crustal thicknesses tend to be 45 km; b) high velocity anomalies for the uppermost mantle, which agree with previous studies consistent with the presence of a cratonic nucleus in the basin, particularly beneath its northern part. However, our surface wave tomography had no resolution to say whether such a nucleus is intact.

  11. Mathematical structure of the three-dimensional (3D) Ising model

    NASA Astrophysics Data System (ADS)

    Zhang, Zhi-Dong

    2013-03-01

    An overview of the mathematical structure of the three-dimensional (3D) Ising model is given from the points of view of topology, algebra, and geometry. By analyzing the relationships among transfer matrices of the 3D Ising model, Reidemeister moves in the knot theory, Yang-Baxter and tetrahedron equations, the following facts are illustrated for the 3D Ising model. 1) The complex quaternion basis constructed for the 3D Ising model naturally represents the rotation in a (3+1)-dimensional space-time as a relativistic quantum statistical mechanics model, which is consistent with the 4-fold integrand of the partition function obtained by taking the time average. 2) A unitary transformation with a matrix that is a spin representation in 2n·l·o-space corresponds to a rotation in 2n·l·o-space, which serves to smooth all the crossings in the transfer matrices and contributes the non-trivial topological part of the partition function of the 3D Ising model. 3) A tetrahedron relationship would ensure the commutativity of the transfer matrices and the integrability of the 3D Ising model, and its existence is guaranteed by the Jordan algebra and the Jordan-von Neumann-Wigner procedures. 4) The unitary transformation for smoothing the crossings in the transfer matrices changes the wave functions by complex phases varphix, varphiy, and varphiz. The relationship with quantum field and gauge theories and the physical significance of the weight factors are discussed in detail. The conjectured exact solution is compared with numerical results, and the singularities at/near infinite temperature are inspected. The analyticity in β = 1/(kBT) of both the hard-core and the Ising models has been proved only for β > 0, not for β = 0. Thus the high-temperature series cannot serve as a standard for judging a putative exact solution of the 3D Ising model.

  12. Modelling and analysing 3D buildings with a primal/dual data structure

    NASA Astrophysics Data System (ADS)

    Boguslawski, Pawel; Gold, Christopher M.; Ledoux, Hugo

    While CityGML permits us to represent 3D city models, its use for applications where spatial analysis and/or real-time modifications are required is limited since at this moment the possibility to store topological relationships between the elements is rather limited and often not exploited. We present in this paper a new topological data structure, the dual half-edge (DHE), which permits us to represent the topology of 3D buildings (including their interiors) and of the surrounding terrain. It is based on the idea of simultaneously storing a graph in 3D space and its dual graph, and to link the two. We propose Euler-type operators for incrementally constructing 3D models (for adding individual edges, faces and volumes to the model while updating the dual structure simultaneously), and we also propose navigation operators to move from a given point to all the connected planes or polyhedra for example. The DHE also permits us to store attributes to any element. We have implemented the DHE and have tested it with different CityGML models. Our technique allows us to handle important query types, for example finding the nearest exterior exit to a given room, as in disaster management planning. As the structure is locally modifiable the model may be adapted whenever a particular pathway is no longer available. The proposed DHE structure adds significant analytic value to the increasingly popular CityGML model.

  13. Proteopedia: A Collaborative, Virtual 3D Web-Resource for Protein and Biomolecule Structure and Function

    ERIC Educational Resources Information Center

    Hodis, Eran; Prilusky, Jaime, Sussman, Joel L.

    2010-01-01

    Protein structures are hard to represent on paper. They are large, complex, and three-dimensional (3D)--four-dimensional if conformational changes count! Unlike most of their substrates, which can easily be drawn out in full chemical formula, drawing every atom in a protein would usually be a mess. Simplifications like showing only the surface of…

  14. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

    PubMed

    Theis, Corinna; Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Gorodkin, Jan

    2013-12-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. PMID:24005040

  15. Ion Beam Etching: Replication of Micro Nano-structured 3D Stencil Masks

    SciTech Connect

    Weber, Patrick; Guibert, Edouard; Mikhailov, Serguei; Bruegger, Juergen; Villanueva, Guillermo

    2009-03-10

    Ion beam LIGA allows the etching of 3D nano-structures by direct writing with a nano-sized beam. However, this is a relatively time consuming process. We propose here another approach for etching structures on large surfaces and faster, compared to the direct writing process. This approach consists of replicating 3D structured masks, by scanning an unfocused ion beam. A polymer substrate is placed behind the mask, as in UV photolithography. But the main advantage is that the 3D structure of the mask can be replicated into the polymer. For that purpose, the masks (developped at LMIS1, EPFL) are made of a silicon nitride membrane 100 nm thick, on which 3D gold structures up to 200 nm thick, are deposited. The 3D Au structures are made with the nanostencil method, based on successive gold deposition. The IMA institute, from HE-Arc, owns a High Voltage Engineering 1.7 MV Tandetron with both solid and gaseous negative ion sources, able to generate ions from almost every chemical element in a broad range of energies comprised between 400 keV and 6.8 MeV. The beam composition and energy are chosen in such a way, that ions lose a significant fraction of their energy when passing through the thickest regions of the mask. Ions passing through thinner regions of the mask loose a smaller fraction of their energy and etch the polymer with larger thicknesses, allowing a replication of the mask into the polymer. For our trials, we have used a carbon beam with an energy of 500 keV. The beam was focussed to a diameter of 5 mm with solid slits, in order to avoid border effects and thus ensure a homogeneous dose distribution on the beam diameter. The feasibility of this technique has been demonstrated, allowing industrial applications for micro-mould fabrication, micro-fluidics and micro-optics.

  16. Prediction of spin-dependent electronic structure in 3d-transition-metal doped antimonene

    NASA Astrophysics Data System (ADS)

    Yang, L. F.; Song, Y.; Mi, W. B.; Wang, X. C.

    2016-07-01

    We investigate the geometric structure and electronic and magnetic properties of 3d-transition-metal atom doped antimonene using spin-polarized first-principles calculations. Strong orbital hybridization exhibits between 3d-transition-metal and Sb atoms, where covalent bonds form in antimonene. A spin-polarized semiconducting state appears in Cr-doped antimonene, while half-metallic states appear by doping Ti, V, and Mn. These findings indicate that once combined with doping states, the bands of antimonene systems offer a variety of features. Specific dopants lead to half-metallic characters with high spin polarization that has potential application in spintronics.

  17. Studies of the 3D Structure of the Nucleon at JLab

    NASA Astrophysics Data System (ADS)

    Avakian, Harut

    2016-08-01

    Studies of the 3D structure of the nucleon encoded in transverse momentum dependent distribution and fragmentation functions of partons and generalized parton distributions are among the key objectives of the JLab 12 GeV upgrade and the electron ion collider. Main challenges in extracting 3D partonic distributions from precision measurements of hard scattering processes include clear understanding of leading twist QCD fundamentals, higher twist effects, and also correlations of hadron production in target and current fragmentation regions. In this contribution we discuss some ongoing studies and future measurements of spin-orbit correlations at Jefferson Lab.

  18. Holographic particle velocimetry - A 3D measurement technique for vortex interactions, coherent structures and turbulence

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

    To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.

  19. Non-contact 3D fingerprint scanner using structured light illumination

    NASA Astrophysics Data System (ADS)

    Troy, Mike; Hassebrook, Laurence; Yalla, Veeraganesh; Daley, Raymond

    2011-03-01

    As crime prevention and national security remain a top priority, requirements for the use of fingerprints for identification continue to grow. While the size of fingerprint databases continues to expand, new technologies that can improve accuracy and ultimately matching performance will become more critical to maintain the effectiveness of the systems. FlashScan3D has developed non-contact, fingerprint scanners based on the principles of Structured Light Illumination (SLI) that capture 3Dimensional data of fingerprints quickly, accurately and independently of an operator. FlashScan3D will present findings from various research projects performed for the US Army and the Department of Homeland Security.

  20. A Patterned 3D Silicon Anode Fabricated by Electrodeposition on a Virus-Structured Current Collector

    SciTech Connect

    Chen, X L; Gerasopoulos, K; Guo, J C; Brown, A; Wang, Chunsheng; Ghodssi, Reza; Culver, J N

    2010-11-09

    Electrochemical methods were developed for the deposition of nanosilicon onto a 3D virus-structured nickel current collector. This nickel current collector is composed of self-assembled nanowire-like rods of genetically modified tobacco mosaic virus (TMV1cys), chemically coated in nickel to create a complex high surface area conductive substrate. The electrochemically depo­sited 3D silicon anodes demonstrate outstanding rate performance, cycling stability, and rate capability. Electrodeposition thus provides a unique means of fabricating silicon anode materials on complex substrates at low cost.

  1. Research of aluminium alloy aerospace structure aperture measurement based on 3D digital speckle correlation method

    NASA Astrophysics Data System (ADS)

    Bai, Lu; Wang, Hongbo; Zhou, Jiangfan; Yang, Rong; Zhang, Hui

    2014-11-01

    In this paper, the aperture change of the aluminium alloy aerospace structure under real load is researched. Static experiments are carried on which is simulated the load environment of flight course. Compared with the traditional methods, through experiments results, it's proved that 3D digital speckle correlation method has good adaptability and precision on testing aperture change, and it can satisfy measurement on non-contact,real-time 3D deformation or stress concentration. The test results of new method is compared with the traditional method.

  2. A New Comprehensive Model for Crustal and Upper Mantle Structure of the European Plate

    NASA Astrophysics Data System (ADS)

    Morelli, A.; Danecek, P.; Molinari, I.; Postpischl, L.; Schivardi, R.; Serretti, P.; Tondi, M. R.

    2009-12-01

    We present a new comprehensive model of crustal and upper mantle structure of the whole European Plate — from the North Atlantic ridge to Urals, and from North Africa to the North Pole — describing seismic speeds (P and S) and density. Our description of crustal structure merges information from previous studies: large-scale compilations, seismic prospection, receiver functions, inversion of surface wave dispersion measurements and Green functions from noise correlation. We use a simple description of crustal structure, with laterally-varying sediment and cristalline layers thickness and seismic parameters. Most original information refers to P-wave speed, from which we derive S speed and density from scaling relations. This a priori crustal model by itself improves the overall fit to observed Bouguer anomaly maps, as derived from GRACE satellite data, over CRUST2.0. The new crustal model is then used as a constraint in the inversion for mantle shear wave speed, based on fitting Love and Rayleigh surface wave dispersion. In the inversion for transversely isotropic mantle structure, we use group speed measurements made on European event-to-station paths, and use a global a priori model (S20RTS) to ensure fair rendition of earth structure at depth and in border areas with little coverage from our data. The new mantle model sensibly improves over global S models in the imaging of shallow asthenospheric (slow) anomalies beneath the Alpine mobile belt, and fast lithospheric signatures under the two main Mediterranean subduction systems (Aegean and Tyrrhenian). We map compressional wave speed inverting ISC travel times (reprocessed by Engdahl et al.) with a non linear inversion scheme making use of finite-difference travel time calculation. The inversion is based on an a priori model obtained by scaling the 3D mantle S-wave speed to P. The new model substantially confirms images of descending lithospheric slabs and back-arc shallow asthenospheric regions, shown in

  3. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  4. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  5. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures.

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  6. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  7. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Cao, Yiping; Xiang, Liqun; Chen, Wenjing

    2002-06-01

    The shoeprint impressions of suspect left at the crime scene can sometimes tell investigators what type of shoes to be looked for. These shoeprint impressions as one of the important evidence are useful in the detection of criminals. In this paper we propose a novel technique for identifying and analyzing the 3D characteristics of shoeprint impressions. We also design 3D shoeprint impression analysis system based on the combination the 3D shape measurement with structured illumination and fringe pattern analysis. We give a detail discussion on the principle and configuration of the system. Laboratory experiments show the technique is efficient in the detection of shoeprint and in the offering the reference for judicial evidence.

  8. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    NASA Astrophysics Data System (ADS)

    Zenou, M.; Sa'Ar, A.; Kotler, Z.

    2015-11-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures.

  9. Crustal Structure of the Middle East from Regional Seismic Studies

    NASA Astrophysics Data System (ADS)

    Gritto, Roland; Sibol, Matthew; Caron, Pierre; Ghalib, Hafidh; Chen, Youlin

    2010-05-01

    We present results of crustal studies obtained with seismic data from the Northern Iraq Seismic Network (NISN). NISN has operated ten broadband stations in north-eastern Iraq since late 2005. This network was supplemented by the five-element broadband Iraq Seismic Array (KSIRS) in 2007. More recently, the former Iraq Seismic Network (ISN), destroyed during the war with Iran, was reestablished with the deployment of six broadband stations throughout Iraq. The aim of the present study is to derive models of the local and regional crustal structure of the Middle East, including Eastern Turkey, Iraq and Iran. To achieve this goal, we derive crustal velocity models using receiver function, surface wave and body wave analyses. These refined velocity models will eventually be used to obtain accurate hypocenter locations and event focal mechanisms. Our analysis of preliminary hypocenter locations produced a clearer picture of the seismicity associated with the tectonics of the region. The largest seismicity rate is confined to the active northern section of the Zagros thrust zone, while it decreases towards the southern end, before the intensity increases in the Bandar Abbas region again. Additionally, the rift zones in the Red Sea and the Gulf of Aden are clearly demarked by high seismicity rates. Surface wave velocity analysis resulted in a clear demarcation of the tectonic features in the region. The Arabian shield, Zagros thrust zone and the Red Sea are apparent through distinct velocity distributions separating them from each other. Furthermore, the shear wave velocity of the crust in North Iraq appears to be 10% higher than that of the Iranian plateau. The velocity anomaly of the Zagros mountains appears to be present into the upper mantle beyond the resolving limit of our model. Analysis of waveform data for obstructed pathways indicates clear propagation paths from the west or south-west across the Arabian shield as well as from the north and east into NISN. Phases

  10. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

    PubMed Central

    2014-01-01

    Background Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required. Description In this paper, we present a web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein–small ligand complexes are statistically overrepresented. This server consists of two main components: “Complex Analyzer”, and “Pattern Viewer”. The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The “Pattern Viewer” provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein–ligand complexes showing similar interactions. Conclusions Users can interactively analyze protein–small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at http://giant.hgc.jp/. PMID:24423161

  11. Ground and Structure Deformation 3d Modelling with a Tin Based Property Model

    NASA Astrophysics Data System (ADS)

    TIAN, T.; Zhang, J.; Jiang, W.

    2013-12-01

    With the development of 3D( three-dimensional) modeling and visualization, more and more 3D tectonics are used to assist the daily work in Engineering Survey, in which the prediction of deformation field in strata and structure induced by underground construction is an essential part. In this research we developed a TIN (Triangulated Irregular Network) based property model for the 3D (three dimensional) visualization of ground deformation filed. By record deformation vector for each nodes, the new model can express the deformation with geometric-deformation-style by drawing each node in its new position and deformation-attribute-distribution-style by drawing each node in the color correspond with its deformation attribute at the same time. Comparing with the volume model based property model, this new property model can provide a more precise geometrical shape for structure objects. Furthermore, by recording only the deformation data of the user-interested 3d surface- such as the ground surface or the underground digging surface, the new property model can save a lot of space, which makes it possible to build the deformation filed model of a much more large scale. To construct the models of deformation filed based on TIN model, the refinement of the network is needed to increase the nodes number, which is necessary to express the deformation filed with a certain resolution. The TIN model refinement is a process of sampling the 3D deformation field values on points on the TIN surface, for which we developed a self-adapting TIN refinement method. By set the parameter of the attribute resolution, this self-adapting method refines the input geometric-expressing TIN model by adding more vertexes and triangles where the 3D deformation filed changing faster. Comparing with the even refinement method, the self-adapting method can generate a refined TIN model with nodes counted less by two thirds. Efficiency Comparison between Self-adapting Refinement Method and Even

  12. Crustal Seismic Structure of Central Alberta from Receiver Function Inversions

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Dokht, R.; Gu, Y. J.; Sacchi, M. D.

    2013-12-01

    It is widely believed that the basement structure of central Alberta represents the tectonic assembly and evolution of several Archean lithospheric fragments. These fragments underwent episodes of rifting, collision, subduction and melting during the Proterozoic, giving rise to a complex network of tectonic domains with considerable differences in the crustal magnetic and seismic signatures. Observational support for these episodes, e.g., the coeval subduction around the Hearne province, has been limited due to the lack of exposed geology and insufficient teleseismic data prior to 2006. Since mid 2007, the establishment of the Canadian Rockies and Alberta Network (CRANE) has greatly improved the broadband seismic data coverage in central and southern Alberta. Based on 5+ years of CRANE data, we systematically analyze crust and shallow mantle shear velocities through simultaneous inversions of low and high frequency receiver functions. P-to-S converted waves from several stations in central Alberta suggest a significant mid crustal low velocity zone (LVZ), where shear velocity could vary by as much as 35 percent in a depth range of 15-35 km. This structure is not required by the receiver functions from stations along the foothills of the Rocky Mountains. While LVZ of notable magnitudes have been suggested previously in an overlapped part of the study region and attributed to the presence of serpentine or intrusive sill, the spatial dimensions of the anomaly reported in the current study is significantly larger: this anomaly spans hundreds of kilometers horizontally and is generally thicker than 10 km. The presence of mid/lower crustal LVZ in central Alberta is supported by recent group velocity maps based on noise correlation tomography, and the southeastward orientation of this LVZ is consistent with the proposed direction of the subducted oceanic microplate beneath the northwestern Hearne province during the Proterozoic. Still, the cause of the LVZ remains

  13. Crustal structure and tectonics of the northern part of the Southern Granulite Terrane, India

    USGS Publications Warehouse

    Rao, V.V.; Sain, K.; Reddy, P.R.; Mooney, W.D.

    2006-01-01

    Deep seismic reflection studies investigating the exposed Archean lower continental crust of the Southern Granulite Terrane, India, yield important constraints on the nature and evolution of the deep crust, including the formation and exhumation of granulites. Seismic reflection images along the Kuppam-Bhavani profile reveal a band of reflections that dip southward from 10.5 to 15.0??s two-way-time (TWT), across a distance of 50??km. The bottom of these reflections beneath the Dharwar craton is interpreted as the Moho. Further south, another reflection band dipping northward is observed. These bands of reflectivity constitute a divergent reflection fabric that converges at the Moho boundary observed at the Mettur shear zone. Reflection fabrics that intersect at a steep angle are interpreted as a collisional signature due to the convergence of crustal blocks, which we infer resulted in crustal thickening and the formation of granulites. Anomalous gravity and magnetic signatures are also observed across the Mettur shear zone. The gravity model derived from the Bouguer gravity data corroborates seismic results. The tectonic regime and seismic reflection profiles are combined in a 3-D representation that illustrates our evidence for paleo-subduction at a collision zone. The structural dissimilarities and geophysical anomalies suggest that the Mettur shear zone is a suture between the Dharwar craton in the north and another crustal block in the south. This study contributes significantly to our understanding of the operation of Archean plate tectonics, here inferred to involve collision and subduction. Furthermore, it provides an important link between the Gondwanaland and global granulite evolution occurring throughout the late Archean. ?? 2006 Elsevier B.V. All rights reserved.

  14. Modeling tumor/polyp/lesion structure in 3D for computer-aided diagnosis in colonoscopy

    NASA Astrophysics Data System (ADS)

    Chen, Chao-I.; Sargent, Dusty; Wang, Yuan-Fang

    2010-02-01

    We describe a software system for building three-dimensional (3D) models from colonoscopic videos. The system is end-to-end in the sense that it takes as input raw image frames-shot during a colon exam-and produces the 3D structure of objects of interest (OOI), such as tumors, polyps, and lesions. We use the structure-from-motion (SfM) approach in computer vision which analyzes an image sequence in which camera's position and aim vary relative to the OOI. The varying pose of the camera relative to the OOI induces the motion-parallax effect which allows 3D depth of the OOI to be inferred. Unlike the traditional SfM system pipeline, our software system contains many check-and-balance mechanisms to ensure robustness, and the analysis from earlier stages of the pipeline is used to guide the later processing stages to better handle challenging medical data. The constructed 3D models allow the pathology (growth and change in both structure and appearance) to be monitored over time.

  15. EK3D: an E. coli K antigen 3-dimensional structure database

    PubMed Central

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host–pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  16. Fabrication of 3D microfluidic structures inside glass by femtosecond laser micromachining

    NASA Astrophysics Data System (ADS)

    Sugioka, Koji; Cheng, Ya

    2014-01-01

    Femtosecond lasers have opened up new avenues in materials processing due to their unique characteristics of ultrashort pulse widths and extremely high peak intensities. One of the most important features of femtosecond laser processing is that a femtosecond laser beam can induce strong absorption in even transparent materials due to nonlinear multiphoton absorption. This makes it possible to directly create three-dimensional (3D) microfluidic structures in glass that are of great use for fabrication of biochips. For fabrication of the 3D microfluidic structures, two technical approaches are being attempted. One of them employs femtosecond laser-induced internal modification of glass followed by wet chemical etching using an acid solution (Femtosecond laser-assisted wet chemical etching), while the other one performs femtosecond laser 3D ablation of the glass in distilled water (liquid-assisted femtosecond laser drilling). This paper provides a review on these two techniques for fabrication of 3D micro and nanofluidic structures in glass based on our development and experimental results.

  17. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  18. Image enhancement and segmentation of fluid-filled structures in 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Chalana, Vikram; Dudycha, Stephen; McMorrow, Gerald

    2003-05-01

    Segmentation of fluid-filled structures, such as the urinary bladder, from three-dimensional ultrasound images is necessary for measuring their volume. This paper describes a system for image enhancement, segmentation and volume measurement of fluid-filled structures on 3D ultrasound images. The system was applied for the measurement of urinary bladder volume. Results show an average error of less than 10% in the estimation of the total bladder volume.

  19. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

    Watanabe, Yosuke; Gong, Jing; Masato, Makino; Kabir, M. Hasnat; Furukawa, Hidemitsu

    2014-04-01

    The 3D printing technology, causing much attention from the beginning of 2013, will be possibly an alternative method to fabricate the biological soft tissues. Recently our group of Yamagata University has developed the world-first 3D Gel Printer to fabricate the complicated gel-materials with high-strength and biocompatibility. However, there are no 3D scanners that collect the data from the internal structure of complicated gel objects such as eye lens. It means that a new system for scanning the internal structure is needed now. In this study, firstly, we have tried to investigate the gel network of synthetic and biological gel with scanning microscopic light scattering (SMILS). We calculated the Young's modulus of synthetic gels with the SMILS and with the tensile test, and precisely compared the results between them. The temperature dependences of the inside structure and the transparency are observed in the pig crystalline lens. The quantitative analysis indicates the importance of the internal structure of real object. Secondary, we show the new system named Gel-scanner that can provide the 2-dimentional data of the internal structure. From examining our findings, the scanning of internal structure will enable us to expect physical properties of the real object. We convince that the gelscanner will play major role in the various fields.

  20. Deep reflection structure imaged by the 2008 3D seismic reflection Survey at the RIDGE- 2000 East Pacific Rise Integrated Studies Site

    NASA Astrophysics Data System (ADS)

    Nedimović, M. R.; Carbotte, S. M.; Mutter, J. C.; Canales, P. J.; Carton, H.; Aghaei, O.; Marjanović, M.; Newman, K. R.; Hu, M.; Stowe, L.

    2008-12-01

    The first multi-source and multi-streamer 3D seismic reflection experiment carried out using academic resources was done aboard the R/V Marcus G. Langseth in Summer 2008 during cruise MGL0812. The targeted area was the RIDGE-2000 Integrated Studies Site at the East Pacific Rise. Our primary 3D survey grid extends from about 9° 57'N to 9° 42'N, with a smaller grid just to the south covering approximately from 9° 40'N to 9° 37.5'N. Additionally, about 1 and 0.5 km wide across-ridge-axis swaths of data were collected at 9° 36'N and 9°30'N respectively, as well as an along-ridge-axis swath about 1 km wide and extending from 10° 05'N to 9° 40'N. We here focus on a preliminary analysis of the reflection structure imaged within the lower crust and uppermost mantle. Moho reflection arrivals are imaged through much of the investigated area. The character of Moho reflection events varies from simple, single reflection wavelet to more complex arrivals indicating spatial changes in structure within the Moho transition zone. Particularly strong Moho reflections are observed in the southern half of the main 3D grid. In places, Moho reflection event appears to extend across the ridge axis potentially suggesting "zero-age" Moho development. Weak Moho arrivals are found at the north end of the main 3D box and within the smaller box to the south. Most notable place lacking Moho reflections is the Lamont seamount area where Moho is not observed on either side of the ridge axis, although the area lacking Moho reflections is wider on the western ridge flank. Further south, along the across-ridge-axis swaths, Moho reflections again become more pronounced. A suit of what mostly appear to be reflection events is recognized between the AMC and Moho. Many of them do not appear to be multiples, and their origin is not well understood. Possible origins for these events include: lower boundary of the AMC, S-converted waves, and lower crustal melt lenses. Along sections of the two 3D

  1. Analysis of the rupture process of the 1995 Kobe earthquake using a 3D velocity structure

    NASA Astrophysics Data System (ADS)

    Guo, Yujia; Koketsu, Kazuki; Ohno, Taichi

    2013-12-01

    A notable feature of the 1995 Kobe (Hyogo-ken Nanbu) earthquake is that violent ground motions occurred in a narrow zone. Previous studies have shown that the origin of such motions can be explained by the 3D velocity structure in this zone. This indicates not only that the 3D velocity structure significantly affects strong ground motions, but also that we should consider its effects in order to determine accurately the rupture process of the earthquake. Therefore, we have performed a joint source inversion of strong-motion, geodetic, and teleseismic data, where 3D Green's functions were calculated for strong-motion and geodetic data in the Osaka basin. Our source model estimates the total seismic moment to be about 2.1 × 1019 N m and the maximum slip reaches 2.9 m near the hypocenter. Although the locations of large slips are similar to those reported by Yoshida et al. (1996), there are quantitative differences between our results and their results due to the differences between the 3D and 1D Green's functions. We have also confirmed that our source model realized a better fit to the strong motion observations, and a similar fit as Yoshida et al. (1996) to the observed static displacements.

  2. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications. PMID:25982877

  3. 3D interactive model of lumbar spinal structures of anesthetic interest.

    PubMed

    Prats-Galino, Alberto; Reina, Miguel A; Mavar Haramija, Marija; Puigdellivol-Sánchez, Anna; Juanes Méndez, Juan A; De Andrés, José A

    2015-03-01

    A 3D model of lumbar structures of anesthetic interest was reconstructed from human magnetic resonance (MR) images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The MR images were analyzed using a specific 3D software platform for biomedical data. Models generated from manually delimited volumes of interest and selected MR images were exported to Virtual Reality Modeling Language format and were presented in a PDF document containing JavaScript-based functions. The 3D file and the corresponding instructions and license files can be downloaded freely at http://diposit.ub.edu/dspace/handle/2445/44844?locale=en. The 3D PDF interactive file includes reconstructions of the L3-L5 vertebrae, intervertebral disks, ligaments, epidural and foraminal fat, dural sac and nerve root cuffs, sensory and motor nerve roots of the cauda equina, and anesthetic approaches (epidural medial, spinal paramedial, and selective nerve root paths); it also includes a predefined sequential educational presentation. Zoom, 360° rotation, selective visualization, and transparency graduation of each structure and clipping functions are available. Familiarization requires no specialized informatics knowledge. The ease with which the document can be used could make it valuable for anatomical and anesthetic teaching and demonstration of patient information. PMID:25352014

  4. Generation of 3-D surface maps in waste storage silos using a structured light source

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  5. Crustal structure of the Columbia Plateau region, Washington

    SciTech Connect

    Rohay, A.C.; Malone, S.D.

    1983-04-01

    Refraction data from blasts recorded in eastern Washington between 1980 and 1983 are used to determine the upper crustal structure of the Columbia Plateau. Fourteen blast sites with over 25 individual shots were recorded on the University of Washington regional seismic network made up of 36 short-period seismograph stations recorded digitally at 100 samples/s. Additional data were obtained from a 12-station dense digital network in the central plateau operated by the Rockwell Hanford Operations Basalt Waste Isolation Project. Major crustal refractors of 5.1 and 6.05 km/s are observed at distances of 15 to 50 km and 50 to 120 km, respectively. A time-term method is used to model layer thicknesses below the stations for each major refractor. A statistical source-receiver separation operation is used to handle the inherent nonindependence of the data. Constraints are used to fix the mean values of the time terms. Ray tracing through two-dimensional velocity structures is used to augment the interpretation of the time-term solutions for areas where the lateral velocity changes are large. Station delays for the 5.1-km/s layer show a good correlation with elevation and surficial geology. The areal extent of the 5.1-km/s layer roughly coincides with the Columbia River basalts. Time terms from the 6.05-km/s layer indicate a nearly uniform depth of 1 to 2 km in the northern plateau. Time terms in the central plateau indicate a depth to the 6.05-km/s layer of over 8 km, and a systematic thinning away from its center. Magnetotelluric studies indicate that the basalts are probably no thicker than 5 km in the central Columbia Plateau region.

  6. The degree of π electron delocalization and the formation of 3D-extensible sandwich structures.

    PubMed

    Wang, Xiang; Wang, Qiang; Yuan, Caixia; Zhao, Xue-Feng; Li, Jia-Jia; Li, Debao; Wu, Yan-Bo; Wang, Xiaotai

    2016-04-28

    DFT B3LYP/6-31G(d) calculations were performed to examine the feasibility of graphene-like C42H18 and starbenzene C6(BeH)6 (SBz) polymers as ligands of 3D-extensible sandwich compounds (3D-ESCs) with uninterrupted sandwich arrays. The results revealed that sandwich compounds with three or more C42H18 ligands were not feasible. The possible reason may be the localization of π electrons on certain C6 hexagons due to π-metal interactions, which makes the whole ligand lose its electronic structure basis (higher degree of π electron delocalization) to maintain the planar structure. For comparison, with the aid of benzene (Bz) molecules, the SBz polymers can be feasible ligands for designing 3D-ESCs because the C-Be interactions in individual SBz are largely ionic, which will deter the π electrons on one C6 ring from connecting to those on neighbouring C6 rings. This means that high degree of π electron delocalization is not necessary for maintaining the planarity of SBz polymers. Such a locally delocalized π electron structure is desirable for the ligands of 3D-ESCs. Remarkably, the formation of a sandwich compound with SBz is thermodynamically more favourable than that found for bis(Bz)chromium. The assembly of 3D-ESCs is largely exothermic, which will facilitate future experimental synthesis. The different variation trends on the HOMO-LUMO gaps in different directions (relative to the sandwich axes) suggest that they can be developed to form directional conductors or semiconductors, which may be useful in the production of electronic devices. PMID:27004750

  7. Optimal Image Stitching for Concrete Bridge Bottom Surfaces Aided by 3d Structure Lines

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

  8. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    NASA Astrophysics Data System (ADS)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  9. Finding the displacement of wood structure in heritage building by 3D laser scanner

    NASA Astrophysics Data System (ADS)

    Lee, M. C.; Tsai, Y. L.; Wang, R. Z.; Lin, M. L.

    2015-08-01

    Heritage buildings are highly prone to long term damage from the microclimate, scourge and vandalism, which can result in damaged materials, structures, painting and cultural heritage items. This study will focus on finding the displacement of wood structural members through the use of a 3D laser scanner and the 4D concept of time. The results will compare the scans from different periods to find the difference (if any) in the structural member position. Wood structures usually consist of numerous wood members connected to form the structure. However, these members can be damaged in various ways such as physical mechanisms, chemical reactions, and biological corrosion. When damage to the wood structure occurs, the structural displacement can be affected, and if affected severely, can lead to a building collapse. Monitoring of the structural displacement is the best way to discover damage immediately and to preserve the heritage building. However, the Cultural Heritage Preservation Law in Taiwan prohibits the installation of monitoring instruments (e.g strain gauge, accelerometer) in historic structures (heritage buildings). Scanning the wood structure with 3D lasers is the most non-intrusive method and quickly achieves displacement through visualization. The displacement scan results can be compared with different periods and different members to analyze the severity of damage. Once the 3D scanner is installed, the whole building is scanned, and point clouds created to build the visual building model. The structural displacement can be checked via the building model and the differences are measured between each member to find the high risk damaged areas or members with large displacement. Early detection of structural damage is the most effective way means of preservation.

  10. Crustal structure of the Middle Urals based on reflection seismic data

    NASA Astrophysics Data System (ADS)

    Juhlin, C.; Friberg, M.; Kashubin, A.; Rybalka, A.; Bliznetsov, M.; Petrov, G.; Perez-Estaun, A.; Steer, D.

    2003-04-01

    EUROPROBE related reflection seismic surveys in the Middle Urals, Russia (latitude 56-62 degrees) since 1993 have led to an increased understanding of the crustal structure and tectonic evolution of this region. A series of six acquisition campaigns along the ESRU profile (Europrobe Seismic Reflection profiling in the Urals) has resulted in an over 400 km long nearly continuous reflection seismic image across the orogen from the foreland basin in the west and extending well into the West Siberian Basin (WSB) in the east. The ESRU profile shows the bivergent nature of the Uralide orogen with east dipping structures generally present in the west and west dipping ones in the east. Below the adjacent basins the lower crustal reflectivity is pronounced and the Moho lies at a depth of 40-45 km. Lower crustal reflectivity below the exposed Uralides is weak, however, a deepening of the Moho by about 5 km is indicated. This is consistent with DSS/refraction seismic data and coincides with a long wavelength negative Bouger gravity anomaly. Much of the ESRU data were acquired along crooked lines and much of the earlier processing used straight CDP lines, requiring care when carrying out geological interpretation. All data along the ESRU profile have now been reprocessed along crooked CDP lines. By utilizing the change in direction of the seismic lines the 3D orientation of some reflection zones can be determined. The new processing shows that many of these reflections strike parallel to the N-S running orogen, however, there are sets of reflections which have a NW strike and a dip to the SW, especially in the lower crust below the WSB. This orientation and the location of the reflections indicate that accretion of crustal material came from the present day northeast in the later stages of the orogen. Two sets of late arriving (20-25 s) reflections are present on the recently acquired ESRU01 data below the foreland basin. One set may be attributed to a 45 degree SW dipping and

  11. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  12. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases. PMID:26231917

  13. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  14. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  15. LigandBox: A database for 3D structures of chemical compounds

    PubMed Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

  16. Sequence-based identification of 3D structural modules in RNA with RMDetect.

    PubMed

    Cruz, José Almeida; Westhof, Eric

    2011-06-01

    Structural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently observed in RNA families throughout the phylogeny. Here we describe a computational tool, RNA three-dimensional (3D) modules detection, or RMDetect, for identifying known 3D structural modules in single and multiple RNA sequences in the absence of any other information. Currently, four modules can be searched for: G-bulge loop, kink-turn, C-loop and tandem-GA loop. In control test sequences we found all of the known modules with a false discovery rate of 0.23. Scanning through 1,444 publicly available alignments, we identified 21 yet unreported modules and 141 known modules. RMDetect can be used to refine RNA 2D structure, assemble RNA 3D models, and search and annotate structured RNAs in genomic data. PMID:21552257

  17. Deep crustal structures of the Cape Fold Belt, South Africa

    NASA Astrophysics Data System (ADS)

    Weckmann, U.; Ritter, O.; Chen, X.; Tietze, K.; de Wit, M.

    2010-12-01

    Magnetotelluric (MT) soundings along a 100 km segment of the Inkaba yeAfrica Agulhas-Karoo transect through the Cape Fold Belt, South Africa, yield its first electrical conductivity image on a crustal scale. The Cape Fold Belt (CFB) plays an important role to understand the inversion tectonic setting within the accretionary history along the paleo-pacific margin of Gondwana. The MT profile crosses the Swartberg and Outeniqua (Langeberg) mountain ranges, as well as the Oudtshoorn Basin and the Kango and Kaaimans tectonic inliers. Two-dimensional (2D) inversion models of the MT data show generally good correlation with surface geology. We resolve the resistive roots of the both mountain ranges, to depths of approximately 5 and 10 km, respectively. By contrast, the adjacent Kango and Kaaimans inliers are imaged as shallow wedges partly overlain by sediments of the Oudtshoorn Basin and the Pletmos Basin, respectively. The Kango fault has a shallow southward dip, in contrast to more sub-vertical structures south of the Oudtshoorn basin. Based on the conductivity section we estimate the thickness of the Oudtshoorn basin to 2-3 km. A massive conductivity anomaly at a depth of 3-4 km is located in a synclinorium between the anticlinoria of Table Mountain Group rocks in the Swartberg and Outeniqua ranges. From the conductivity image alone we can neither confirm nor rule out the existence of a mega-detachment in the middle crust, as previously suggested. However, if the Kango Fault is rooted in a detachment zone, it is at upper crustal levels.

  18. Low-cost structured-light based 3D capture system design

    NASA Astrophysics Data System (ADS)

    Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

    2014-03-01

    Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

  19. Experimentation of structured light and stereo vision for underwater 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Bruno, F.; Bianco, G.; Muzzupappa, M.; Barone, S.; Razionale, A. V.

    Current research on underwater 3D imaging methods is mainly addressing long range applications like seafloor mapping or surveys of archeological sites and shipwrecks. Recently, there is an increasing need for more accessible and precise close-range 3D acquisition technologies in some application fields like, for example, monitoring the growth of coral reefs or reconstructing underwater archaeological pieces that in most cases cannot be recovered from the seabed. This paper presents the first results of a research project that aims to investigate the possibility of using active optical techniques for the whole-field 3D reconstructions in an underwater environment. In this work we have tested an optical technique, frequently used for in air acquisition, based on the projection of structured lighting patterns acquired by a stereo vision system. We describe the experimental setup used for the underwater tests, which were conducted in a water tank with different turbidity conditions. The tests have evidenced that the quality of 3D reconstruction is acceptable even with high turbidity values, despite the heavy presence of scattering and absorption effects.

  20. Multi Length Scale Imaging of Flocculated Estuarine Sediments; Insights into their Complex 3D Structure

    NASA Astrophysics Data System (ADS)

    Wheatland, Jonathan; Bushby, Andy; Droppo, Ian; Carr, Simon; Spencer, Kate

    2015-04-01

    Suspended estuarine sediments form flocs that are compositionally complex, fragile and irregularly shaped. The fate and transport of suspended particulate matter (SPM) is determined by the size, shape, density, porosity and stability of these flocs and prediction of SPM transport requires accurate measurements of these three-dimensional (3D) physical properties. However, the multi-scaled nature of flocs in addition to their fragility makes their characterisation in 3D problematic. Correlative microscopy is a strategy involving the spatial registration of information collected at different scales using several imaging modalities. Previously, conventional optical microscopy (COM) and transmission electron microscopy (TEM) have enabled 2-dimensional (2D) floc characterisation at the gross (> 1 µm) and sub-micron scales respectively. Whilst this has proven insightful there remains a critical spatial and dimensional gap preventing the accurate measurement of geometric properties and an understanding of how structures at different scales are related. Within life sciences volumetric imaging techniques such as 3D micro-computed tomography (3D µCT) and focused ion beam scanning electron microscopy [FIB-SEM (or FIB-tomography)] have been combined to characterise materials at the centimetre to micron scale. Combining these techniques with TEM enables an advanced correlative study, allowing material properties across multiple spatial and dimensional scales to be visualised. The aims of this study are; 1) to formulate an advanced correlative imaging strategy combining 3D µCT, FIB-tomography and TEM; 2) to acquire 3D datasets; 3) to produce a model allowing their co-visualisation; 4) to interpret 3D floc structure. To reduce the chance of structural alterations during analysis samples were first 'fixed' in 2.5% glutaraldehyde/2% formaldehyde before being embedding in Durcupan resin. Intermediate steps were implemented to improve contrast and remove pore water, achieved by the

  1. Investigation of upper crustal structure beneath eastern Java

    NASA Astrophysics Data System (ADS)

    Martha, Agustya Adi; Widiyantoro, Sri; Cummnins, Phil; Saygin, Erdinc; Masturyono

    2016-05-01

    The complexity of geology structure in eastern Java causes this region has many potential resources as much as the disasters. Therefore, the East Java province represents an interesting area to be explored, especially regarding its upper crustal structure. To investigate this structure, we employ the Ambient Noise Tomography (ANT) method. We have used seismic waveform data from 25 Meteorological, Climatological and Geophysical Agency (BMKG) stationary seismographic stations and 26 portable seismographs installed for 2 to 8 weeks. Inter-station cross-correlation produces more than 800 Rayleigh wave components, which depict the structure beneath eastern Java. Based on the checkerboard resolution test, we found that the optimal grid size is 0.25ox0.25o. Our inversion results for the periods of 1 to 10 s indicate a good agreement with geological and Bouguer anomaly maps. Rembang high depression, most of the southern mountains zone, the northern part of Rembang zone and the central part of the Madura Island, the area of high gravity anomaly and areas dominated with igneous rocks are associated with high velocity zones. On the other hand, Kendeng zone and most of the basin in the Rembang zone are associated with low velocity zones.

  2. Determination and validation of mTOR kinase-domain 3D structure by homology modeling

    PubMed Central

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site. PMID:26257525

  3. Utilizing in-situ resources and 3D printing structures for a manned Mars mission

    NASA Astrophysics Data System (ADS)

    Kading, Benjamin; Straub, Jeremy

    2015-02-01

    This paper presents a manned Mars mission, which is based on the use of in-situ resources for the fabrication of structures. First, it provides an overview of the two-phase mission. In phase one, robotic construction units prepare a functional base for phase-two human habitation. Then, it describes a set of prospective structures that can be created utilizing additive manufacturing (commonly known as 3D printing) techniques and in situ materials. Next, the technological advancements required to allow this type of mission are considered and their feasibility is discussed. Specific focus is given to the topics of basalt 3D printing and the maintenance of the pressure environment. The process of the construction of the base is also discussed. Finally the proposed approach is analyzed through comparison to prior missions, before concluding.

  4. Topology optimization of 3D structures with design-dependent loads

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Liu, Shu-Tian; Zhang, Xiong

    2010-10-01

    Topology optimization of continuum structures with design-dependent loads has long been a challenge. In this paper, the topology optimization of 3D structures subjected to design-dependent loads is investigated. A boundary search scheme is proposed for 3D problems, by means of which the load surface can be identified effectively and efficiently, and the difficulties arising in other approaches can be overcome. The load surfaces are made up of the boundaries of finite elements and the loads can be directly applied to corresponding element nodes, which leads to great convenience in the application of this method. Finally, the effectiveness and efficiency of the proposed method is validated by several numerical examples.

  5. 3D structural analysis of proteins using electrostatic surfaces based on image segmentation

    PubMed Central

    Vlachakis, Dimitrios; Champeris Tsaniras, Spyridon; Tsiliki, Georgia; Megalooikonomou, Vasileios; Kossida, Sophia

    2016-01-01

    Herein, we present a novel strategy to analyse and characterize proteins using protein molecular electro-static surfaces. Our approach starts by calculating a series of distinct molecular surfaces for each protein that are subsequently flattened out, thus reducing 3D information noise. RGB images are appropriately scaled by means of standard image processing techniques whilst retaining the weight information of each protein’s molecular electrostatic surface. Then homogeneous areas in the protein surface are estimated based on unsupervised clustering of the 3D images, while performing similarity searches. This is a computationally fast approach, which efficiently highlights interesting structural areas among a group of proteins. Multiple protein electrostatic surfaces can be combined together and in conjunction with their processed images, they can provide the starting material for protein structural similarity and molecular docking experiments.

  6. Crustal structure, seismicity and seismotectonics of the Trentino region (Southern Alps, Italy)

    NASA Astrophysics Data System (ADS)

    Viganò, Alfio; Scafidi, Davide; Martin, Silvana; Spallarossa, Daniele; Froner, Luca; Groaz, Oscar

    2013-04-01

    The Trentino region is located at the junction between the central and eastern Southern Alps (Italy), at the intersection between the Giudicarie, Schio-Vicenza and Valsugana fault systems. This area is characterized by relevant lithological and structural lateral heterogeneities, both at the crustal and lithospheric scales. A low-to-moderate seismicity is located in the upper crust, where faults are seismically active under a dominant compressive with variable strike-slip component regime. Here we study the crustal structure of this portion of the Southern Alps (Adria plate) from interpretation of local earthquake tomography images, in relation with distribution of relocated seismicity and regional tectonic patterns. Local earthquake tomography derives from a set of 476 selected earthquakes in the period 1994-2007, with local magnitudes comprised between 0.8 and 5.3. Hypocenter distribution, and number and quality of manually-repicked phases (6322 P and 5483 S) ensure optimal seismic ray coverage. Original recordings are principally from the Provincia Autonoma di Trento (PAT), that manages the Trentino seismic network since 1981, and from other networks (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - INOGS; Istituto Nazionale di Geofisica e Vulcanologia - INGV; others available via the European Integrated Data Archive). The code HYPOELLIPSE is used to perform initial earthquake relocations. The code VELEST is then used to calculate a new minimum 1-D velocity model, as input for tomography. The 3-D tomographic inversion (V P and V P-V S ratio) is obtained via the code SIMULPS, with the implementation of an accurate shooting ray-tracer. The crustal volume is discretized in order to have a regular grid with a homogenous horizontal spatial resolution of 7.5 km. The resolution in depth varies according to the obtained minimum 1-D velocity model. Reliability and accuracy of results are estimated by analyzing the Resolution Diagonal Elements of the

  7. Computer modeling of 3D structures of cytochrome P450s.

    PubMed

    Chang, Y T; Stiffelman, O B; Loew, G H

    1996-01-01

    The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified. PMID:9010606

  8. 3D reconstruction of internal structure of animal body using near-infrared light

    NASA Astrophysics Data System (ADS)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  9. A theoretical study of the structure and stability of borohydride on 3d transition metals

    NASA Astrophysics Data System (ADS)

    Arevalo, Ryan Lacdao; Escaño, Mary Clare Sison; Gyenge, Elod; Kasai, Hideaki

    2012-12-01

    The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s-dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.

  10. Assessment of the isostatic state and the load distribution of the European Molasse basin by means of lithospheric-scale 3D structural and 3D gravity modelling

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2015-07-01

    The European Molasse basin is a foreland basin situated at the northern front of the European Alps and has formed as a consequence of the Euro-Adriatic continental collision since the Tertiary. Today, it is underlain by Mesozoic sedimentary successions on top of a Paleozoic crust. To investigate the deep structure, the isostatic state, as well as the load distribution in the basin and the adjacent Alpine area, we constructed a lithospheric-scale 3D structural model by implementing available surface, well and seismic data. Subsequently, the structure of the model was constrained by means of 3D gravity modelling. Complementary, the isostatic state has been assessed based on the calculation of the 3D load distribution. Our results show that the Molasse basin is not in isostatic equilibrium and that the gravity field of the area is strongly controlled by the configuration of the crystalline crust. Furthermore, we show that the area is influenced by significant lateral load variations down to a depth of -150 km, which are considerably larger than commonly assumed for this level. Furthermore, our results allow a first-order assessment of the minimum compensating horizontal stress required to prevent gravitational collapse.

  11. Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

    NASA Astrophysics Data System (ADS)

    Qin, W.; Yang, L.

    2004-05-01

    Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study

  12. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  13. The seismogenic zone of the continental crust in Northwest Iberia and its relation to crustal structure

    NASA Astrophysics Data System (ADS)

    Llana-Fúnez, Sergio; López-Fernández, Carlos

    2015-08-01

    The distribution of seismicity at the western end of the Cantabrian mountain range (NW Iberia), reflecting current crustal dynamics, is investigated integrating seismically active structures, long-term structures, and the topographic features at the surface. The thickness of the seismogenic zone within the continental crust is established in 20 km. Two crustal domains can be distinguished in the study area in terms of the seismicity pattern, the style of Alpine structures and the relief. The presence of crustal fluids arises as a very likely contributing factor to the excessive thickness of the seismogenic zone in the study area. More importantly, a switch in tectonic style at the transition between crustal domains in coincidence with the lateral termination of orogenic frontal thrusts is envisaged as involving sufficient stress heterogeneity and amplification to explain the current concentration and characteristic pattern of historical seismicity in the region. Overall, the distribution of seismicity in the crust is sensitive to the type and style of crustal structures.

  14. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

    PubMed

    Zhou, Changjun; Hou, Caixia; Zhang, Qiang; Wei, Xiaopeng

    2013-09-01

    The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences. PMID:23824509

  15. Segmentation of bone structures in 3D CT images based on continuous max-flow optimization

    NASA Astrophysics Data System (ADS)

    Pérez-Carrasco, J. A.; Acha-Piñero, B.; Serrano, C.

    2015-03-01

    In this paper an algorithm to carry out the automatic segmentation of bone structures in 3D CT images has been implemented. Automatic segmentation of bone structures is of special interest for radiologists and surgeons to analyze bone diseases or to plan some surgical interventions. This task is very complicated as bones usually present intensities overlapping with those of surrounding tissues. This overlapping is mainly due to the composition of bones and to the presence of some diseases such as Osteoarthritis, Osteoporosis, etc. Moreover, segmentation of bone structures is a very time-consuming task due to the 3D essence of the bones. Usually, this segmentation is implemented manually or with algorithms using simple techniques such as thresholding and thus providing bad results. In this paper gray information and 3D statistical information have been combined to be used as input to a continuous max-flow algorithm. Twenty CT images have been tested and different coefficients have been computed to assess the performance of our implementation. Dice and Sensitivity values above 0.91 and 0.97 respectively were obtained. A comparison with Level Sets and thresholding techniques has been carried out and our results outperformed them in terms of accuracy.

  16. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

    PubMed Central

    Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2012-01-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  17. Integration of nano-scale components and supports in micromachined 3D silicon structures

    NASA Astrophysics Data System (ADS)

    Song, J.; Azimi, S.; Y Dang, Z.; Breese, M. B. H.

    2014-04-01

    We have developed a process for the three-dimensional (3D) machining of p-type silicon on a micro- and nano-scale using high-energy ion beam irradiation with one or more energies and fluences, followed by electrochemical anodization in hydrofluoric acid. We present a study of the dependence of our fabricated structures on irradiating ion energies, fluences, geometries and wafer resistivity. All these factors determine whether the micro- and nano-scale features are properly connected to the supports in the 3D silicon structures. If wrongly chosen, any of these factors may cause a breakage at the connection through localized over-etching. Under optimum irradiation and anodization conditions, free-standing patterned membranes can be fabricated with feature dimensions of 100 nm over areas of many square millimeters. This investigation is based on silicon structures but is relevant to any electro-assisted etching process for 3D fabrication, paving the way for achieving free-standing silicon photonics, mechanical resonators and micro-/nano-electromechanical systems.

  18. 3D Axon structure extraction and analysis in confocal fluorescence microscopy images.

    PubMed

    Zhang, Yong; Zhou, Xiaobo; Lu, Ju; Lichtman, Jeff; Adjeroh, Donald; Wong, Stephen T C

    2008-08-01

    The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects. PMID:18336075

  19. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    NASA Astrophysics Data System (ADS)

    Aldana-Iuit, Javier; Martinez-Perez, M. Elena; Espinosa-Romero, Arturo; Diaz-Uribe, Rufino

    2010-05-01

    3D reconstruction of blood vessels is a powerful visualization tool for physicians, since it allows them to refer to qualitative representation of their subject of study. In this paper we propose a 3D reconstruction method of retinal vessels from fundus images. The reconstruction method propose herein uses images of the same retinal structure in epipolar geometry. Images are preprocessed by RISA system for segmenting blood vessels and obtaining feature points for correspondences. The correspondence points process is solved using correlation. The LMedS analysis and Graph Transformation Matching algorithm are used for outliers suppression. Camera projection matrices are computed with the normalized eight point algorithm. Finally, we retrieve 3D position of the retinal tree points by linear triangulation. In order to increase the power of visualization, 3D tree skeletons are represented by surfaces via generalized cylinders whose radius correspond to morphological measurements obtained by RISA. In this paper the complete calibration process including the fundus camera and the optical properties of the eye, the so called camera-eye system is proposed. On one hand, the internal parameters of the fundus camera are obtained by classical algorithms using a reference pattern. On the other hand, we minimize the undesirable efects of the aberrations induced by the eyeball optical system assuming that contact enlarging lens corrects astigmatism, spherical and coma aberrations are reduced changing the aperture size and eye refractive errors are suppressed adjusting camera focus during image acquisition. Evaluation of two self-calibration proposals and results of 3D blood vessel surface reconstruction are presented.

  20. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    SciTech Connect

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; Loye, Hans-Conrad zur

    2012-11-15

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi{sub 2}O{sub 2}(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P2{sub 1} (a=9.6479(9) A, b=4.2349(4) A, c=11.9615(11) A, {beta}=109.587(1) Degree-Sign ), which contains Bi{sub 2}O{sub 2} chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P2{sub 1} (a=19.0855(7) A, b=13.7706(5) A, c=19.2429(7) A, {beta}=90.701(1) Degree-Sign ) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi{sup 3+}, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer. - Graphical Abstract: Structures of two new, polar, 3D Bismuth(III)-based coordination polymers: Bi{sub 2}O{sub 2}(pydc) (compound 1), and Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (compound 2). Highlights: Black-Right-Pointing-Pointer New, polar, 3D Bismuth(III)-based coordination polymers. Black-Right-Pointing-Pointer First polar bismuth-based coordination polymers synthesized via a 'hybrid' strategy. Black-Right-Pointing-Pointer Combination of stereochemically-active lone pairs and unsymmetrical or chiral ligands. Black-Right-Pointing-Pointer Synthesis of class C-SHG materials based on Kurtz-Perry categories.

  1. Crustal structure beneath the eastern Swiss Alps derived from seismic refraction data

    NASA Astrophysics Data System (ADS)

    Ye, S.; Ansorge, J.; Kissling, E.; Mueller, St.

    1995-02-01

    incomplete images of the shallow heterogeneous 3-D structure.

  2. The crustal structure of Beira High, Central Mozambique

    NASA Astrophysics Data System (ADS)

    Olaf Müller, Christian; Franke, Dieter; Heyde, Ingo; Schreckenberger, Bernd; Jokat, Wilfried

    2015-04-01

    the western part of Beira High with a velocity of 7.2-7.4 km/s and 3 km thickness is found. Below the shelf our results indicate evidences for an increased volcanism during the initial break-up. The location of the continent-ocean boundary as well as the geometry of the break-up depend strongly on the tectonic classification of Beira High. Future work will provide further constraints by amplitude modelling, a 3D gravity model of Beira High and by means of interpretation of the magnetic anomalies.

  3. 3-D Radar Imaging Reveals Deep Structures and Buried Craters Within the Martian Polar Caps

    NASA Astrophysics Data System (ADS)

    Putzig, N. E.; Foss, F. J., II; Campbell, B. A.; Phillips, R. J.; Smith, I. B.

    2015-12-01

    We use Shallow Radar (SHARAD) observations on thousands of orbital passes by the Mars Reconnaissance Orbiter to produce fully imaged 3-D data volumes encompassing both polar ice caps of Mars. Greatly clarifying the view of subsurface features, a completed volume for Planum Boreum provides new constraints on the nature and timing of emplacement of the northern polar deposits and their relationship to climate. The standard method of mapping subsurface features with single-pass 2-D radargrams has been very fruitful (see Brothers et al. 2015, JGR 120 in press, and references therein), but a full assessment of internal structures has been hindered by interfering off-nadir echoes from spiral troughs and other variable topography prevalent on both caps. By assembling the SHARAD radargrams into a volume and applying a 3-D imaging process (migration) borrowed from seismic processing techniques, we enhance the signal-to-noise ratio while repositioning the echoes to their proper locations, thereby unraveling the interference. As part of the process, we correct ionospheric distortions and delays of the radar echoes (Campbell et al. 2014, IEEE GRSL 11 #3). Interfaces painstakingly mapped in radargrams (e.g., the basal-unit surface, a buried chasma) are clearly visible in the 3-D volume, and new features are revealed. Structures may now be mapped through trough-rich regions, including a widespread sequence that provides corroborative evidence of recent ice ages (Smith et al. 2015, LPSC XLVI #2574). Distinctive radar signatures associated with known, partially buried craters also occur elsewhere in the volume but without surface expression. Presumably, these are fully buried craters that may provide a new means to estimate the age of the deposits. Preliminary work for Planum Australe demonstrates that the 3-D processing currently underway will illuminate deep structures that are broadly obfuscated in 2-D radargrams by a shallow scatterer (Campbell et al. 2015, LPSC XLVI #2366).

  4. Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.

    PubMed

    Mrozek, Dariusz; Brożek, Miłosz; Małysiak-Mrozek, Bożena

    2014-02-01

    Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT ("GPU-CASSERT") parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm. PMID:24481593

  5. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

    PubMed Central

    Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong

    2016-01-01

    Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. PMID:27240697

  6. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  7. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    PubMed Central

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  8. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    NASA Astrophysics Data System (ADS)

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-09-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  9. Crustal structure beneath the Paleozoic Parnaíba Basin revealed by airborne gravity and magnetic data, Brazil

    USGS Publications Warehouse

    de Castroa, David L.; Fuck, Reinhardt A.; Phillips, Jeffrey D. Phillips; Vidotti, Roberta M.; Bezerra, Francisco H.R.; Dantas, Elton L.

    2014-01-01

    The Parnaíba Basin is a large Paleozoic syneclise in northeastern Brazil underlain by Precambrian crystalline basement, which comprises a complex lithostructural and tectonic framework formed during the Neoproterozoic–Eopaleozoic Brasiliano–Pan African orogenic collage. A sag basin up to 3.5 km thick and 1000 km long formed after the collage. The lithologic composition, structure, and role in the basin evolution of the underlying basement are the focus of this study. Airborne gravity and magnetic data were modeled to reveal the general crustal structure underneath the Parnaíba Basin. Results indicate that gravity and magnetic signatures delineate the main boundaries and structural trends of three cratonic areas and surrounding Neoproterozoic fold belts in the basement. Triangular-shaped basement inliers are geophysically defined in the central region of this continental-scale Neoproterozoic convergence zone. A 3-D gravity inversion constrained by seismological data reveals that basement inliers exhibit a 36–40.5 km deep crustal root, with borders defined by a high-density and thinner crust. Forward modeling of gravity and magnetic data indicates that lateral boundaries between crustal units are limited by Brasiliano shear zones, representing lithospheric sutures of the Amazonian and São Francisco Cratons, Tocantins Province and Parnaíba Block. In addition, coincident residual gravity, residual magnetic, and pseudo-gravity lows indicate two complex systems of Eopaleozoic rifts related to the initial phase of the sag deposition, which follow basement trends in several directions.

  10. Controls on the Flow Regime and Thermal Structure of the Subduction Zone Mantle Wedge: A Systematic 2-D and 3-D Investigation

    NASA Astrophysics Data System (ADS)

    Le Voci, Giuseppe; Davies, Rhodri; Goes, Saskia; Kramer, Stephan; Wilson, Cian

    2014-05-01

    Arc volcanism at subduction zones is likely regulated by the mantle wedge's flow regime and thermal structure and, hence, numerous studies have attempted to quantify the principal controls on mantle wedge conditions. Here, we build on these previous studies by undertaking the first systematic 2-D and 3-D numerical investigation, across a wide parameter-space, into how hydration and thermal buoyancy influence the wedge's flow regime and associated thermal structure, above a kinematically driven subducting plate. We find that small-scale convection (SSC), resulting from Rayleigh-Taylor instabilities, or drips, off the base of the overriding lithosphere, is a typical occurrence, if: (i) viscosities are < 5×1018 Pa s; and (ii) hydrous weakening of wedge rheology extends at least 100-150 km from the trench. In 2-D models, instabilities generally take the form of 'drips'. Although along-strike averages of wedge velocities and temperature in 3-D structure are consistent with those in 2-D, fluctuations are larger in 3-D. Furthermore, in 3-D, two separate, but interacting, longitudinal Richter roll systems form (with their axes aligned perpendicular to the trench), the first below the arc region and the second below the back-arc region. These instabilities result in transient and spatial temperature fluctuations of 100-150K, which are sufficient to influence melting, the stability of hydrous minerals and the dehydration of crustal material. Furthermore, they are efficient at eroding the overriding lithosphere, particularly in 3-D and, thus, provide a means to explain observations of high heat flow and thin back-arc lithosphere at many subduction zones, if back-arc mantle is hydrated.

  11. Combination of photogrammetric and geoelectric methods to assess 3d structures associated to natural hazards

    NASA Astrophysics Data System (ADS)

    Fargier, Yannick; Dore, Ludovic; Antoine, Raphael; Palma Lopes, Sérgio; Fauchard, Cyrille

    2016-04-01

    The extraction of subsurface materials is a key element for the economy of a nation. However, natural degradation of underground quarries is a major issue from an economic and public safety point of view. Consequently, the quarries stakeholders require relevant tools to define hazards associated to these structures. Safety assessment methods of underground quarries are recent and mainly based on rock physical properties. This kind of method leads to a certain homogeneity assumption of pillar internal properties that can cause an underestimation of the risk. Electrical Resistivity Imaging (ERI) is a widely used method that possesses two advantages to overcome this limitation. The first is to provide a qualitative understanding for the detection and monitoring of anomalies in the pillar body (e.g. faults). The second is to provide a quantitative description of the electrical resistivity distribution inside the pillar. This quantitative description can be interpreted with constitutive laws to help decision support (water content decreases the mechanical resistance of a chalk). However, conventional 2D and 3D Imaging techniques are usually applied to flat surface surveys or to surfaces with moderate topography. A 3D inversion of more complex media (case of the pillar) requires a full consideration of the geometry that was never taken into account before. The Photogrammetric technique presents a cost effective solution to obtain an accurate description of the external geometry of a complex media. However, this method has never been fully coupled with a geophysical method to enhance/improve the inversion process. Consequently we developed a complete procedure showing that photogrammetric and ERI tools can be efficiently combined to assess a complex 3D structure. This procedure includes in a first part a photogrammetric survey, a processing stage with an open source software and a post-processing stage finalizing a 3D surface model. The second part necessitates the

  12. 3D measurement method based on combined temporal encoding structured light

    NASA Astrophysics Data System (ADS)

    Yu, Xiaoyang; Wang, Yang; Yu, Shuang; Cheng, Hao; Sun, Xiaoming; Yu, Shuchun; Chen, Deyun

    2013-10-01

    Three-dimensional (3D) vision measurement technology based on encoding structured light plays an important role and has become the main development trend in the field of 3D non-contact measurement. However, how to synthetically improve measurement speed, accuracy and sampling density is still a difficult problem. Thus in the present work, a novel 3D measurement method based on temporal encoding structured light by combining trapezoidal phase-shifting pattern and cyclic code pattern is proposed. Due to trapezoidal phase-shifting has the advantages of high sampling density and high-speed, the proposed method can maintain these advantages by using cyclic code to expand the range of trapezoidal phase-shifting. In addition, the correction scheme is designed to solve the problem of cycle dislocation. Finally, simulation experimental platform is built with 3ds max and MATLAB. Experimental analyses and results show that, the maximal error is less than 3 mm in the range from 400 mm to 1100 mm, cycle dislocation correction has a good effect.

  13. Characterization of ABS specimens produced via the 3D printing technology for drone structural components

    NASA Astrophysics Data System (ADS)

    Ferro, Carlo Giovanni; Brischetto, Salvatore; Torre, Roberto; Maggiore, Paolo

    2016-07-01

    The Fused Deposition Modelling (FDM) technology is widely used in rapid prototyping. 3D printers for home desktop applications are usually employed to make non-structural objects. When the mechanical stresses are not excessive, this technology can also be successfully employed to produce structural objects, not only in prototyping stage but also in the realization of series pieces. The innovative idea of the present work is the application of this technology, implemented in a desktop 3D printer, to the realization of components for aeronautical use, especially for unmanned aerial systems. For this purpose, the paper is devoted to the statistical study of the performance of a desktop 3D printer to understand how the process performs and which are the boundary limits of acceptance. Mechanical and geometrical properties of ABS (Acrylonitrile Butadiene Styrene) specimens, such as tensile strength and stiffness, have been evaluated. ASTM638 type specimens have been used. A capability analysis has been applied for both mechanical and dimensional performances. Statistically stable limits have been determined using experimentally collected data.

  14. An unprecedented 3D POM-Ag architecture with intertwined and homological helical structures.

    PubMed

    Sha, Jing-Quan; Li, Meng-Ting; Sun, Jing-Wen; Zhang, Yu-Nan; Yan, Peng-Fei; Li, Guang-Ming

    2013-06-01

    A new hybrid compound, Na[Ag6(pyttz)2(H2O)][PMo12O40] (pyttz = 3-(pyrid-3-yl)-5-(1H-1,2,4-triazol-3-yl)-1,2,4-triazolyl), has been hydrothermally synthesized and structurally characterized by routine techniques. X-ray diffraction analysis reveals that the title compound is constructed by the 2D Ag-pyttz coordination polymer and 3D Ag-POM architecture with helix. A fascinating structural feature is the assembling fashion of the right- and left-helical chain, namely, the helical chains with different orientations are intertwined with each other forming intertwined double helical layers along the c-axis, and the identical left- or right-handed helical chains are fused together in a hand-by-hand mode generating another homological helical layer along the a-axis. As a result, these helical layers intersect each other obtaining an unprecedented 3D POM-Ag inorganic architecture. Note that the 3D framework with a helix constructed by POMs and metal ions has never been observed up to date. Additionally, its photocatalytic degradation of RhB was also investigated. PMID:23558903

  15. Density structure and geometry of the Costa Rican subduction zone from 3-D gravity modeling and local earthquake data

    NASA Astrophysics Data System (ADS)

    Lücke, O. H.; Arroyo, I. G.

    2015-10-01

    The eastern part of the oceanic Cocos Plate presents a heterogeneous crustal structure due to diverse origins and ages as well as plate-hot spot interactions which originated the Cocos Ridge, a structure that converges with the Caribbean Plate in southeastern Costa Rica. The complex structure of the oceanic plate directly influences the dynamics and geometry of the subduction zone along the Middle American Trench. In this paper an integrated interpretation of the slab geometry in Costa Rica is presented based on 3-D density modeling of combined satellite and surface gravity data, constrained by available geophysical and geological data and seismological information obtained from local networks. The results show the continuation of steep subduction geometry from the Nicaraguan margin into northwestern Costa Rica, followed by a moderate dipping slab under the Central Cordillera toward the end of the Central American Volcanic Arc. Contrary to commonly assumed, to the southeast end of the volcanic arc, our preferred model shows a steep, coherent slab that extends up to the landward projection of the Panama Fracture Zone. Overall, a gradual change in the depth of the intraplate seismicity is observed, reaching 220 km in the northwestern part, and becoming progressively shallower toward the southeast, where it reaches a maximum depth of 75 km. The changes in the terminal depth of the observed seismicity correlate with the increased density in the modeled slab. The absence of intermediate depth (> 75 km) intraplate seismicity in the southeastern section and the higher densities for the subducted slab in this area, support a model in which dehydration reactions in the subducted slab cease at a shallower depth, originating an anhydrous and thus aseismic slab.

  16. Direct observation in 3d of structural crossover in binary hard sphere mixtures

    NASA Astrophysics Data System (ADS)

    Statt, Antonia; Pinchaipat, Rattachai; Turci, Francesco; Evans, Robert; Royall, C. Patrick

    2016-04-01

    For binary fluid mixtures of spherical particles in which the two species are sufficiently different in size, the dominant wavelength of oscillations of the pair correlation functions is predicted to change from roughly the diameter of the large species to that of the small species along a sharp crossover line in the phase diagram [C. Grodon et al., J. Chem. Phys. 121, 7869 (2004)]. Using particle-resolved colloid experiments in 3d we demonstrate that crossover exists and that its location in the phase diagram is in quantitative agreement with the results of both theory and our Monte-Carlo simulations. In contrast with previous work [J. Baumgartl et al., Phys. Rev. Lett. 98, 198303 (2007)], where a correspondence was drawn between crossover and percolation of both species, in our 3d study we find that structural crossover is unrelated to percolation.

  17. Micro-CT for the quantification of 3D voids within damaged structures

    SciTech Connect

    Patterson, Brian M; Hamilton, Christopher E; Cerreta, Ellen K; Dennis - Koller, Darcie; Bronkhorst, C. A.; Hansen, B. L.

    2011-01-26

    Micro X-ray Computed Tomography (MXCT) is widely used in the materials community to examine the internal structure of materials for voids and cracks due to damage or casting, or other defects. Most research in this area focuses on the qualitative aspect of the image, simply answering; Are there voids present? Here we present an ongoing study of the quantified incipient spall voids in Cu with different grain sizes, using a gas gun with various velocities. Data analysis packages for MXCT are just now becoming able to dimensionally measure and produce statistics on the voids-present. In order to make the size of the features in the 3D image quantifiable, the question, how many radiographs are required to render the object dimensionally accurate in 3D, must be answered. A series of data sets has been coUected, varying the number of radiographs collected in order to determine the appropriate number required.

  18. Shape optimization of 3D continuum structures via force approximation techniques

    NASA Technical Reports Server (NTRS)

    Vanderplaats, Garret N.; Kodiyalam, Srinivas

    1988-01-01

    The existing need to develop methods whereby the shape design efficiency can be improved through the use of high quality approximation methods is addressed. An efficient approximation method for stress constraints in 3D shape design problems is proposed based on expanding the nodal forces in Taylor series with respect to shape variations. The significance of this new method is shown through elementary beam theory calculations and via numerical computations using 3D solid finite elements. Numerical examples including the classical cantilever beam structure and realistic automotive parts like the engine connecting rod are designed for optimum shape using the proposed method. The numerical results obtained from these methods are compared with other published results, to assess the efficiency and the convergence rate of the proposed method.

  19. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Technical Reports Server (NTRS)

    Nandhakumar, N.; Smith, Philip W.

    1993-01-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

  20. Crustal structure off Norway, 62° to 70° north

    NASA Astrophysics Data System (ADS)

    Planke, Sverre; Skogseid, Jakob; Eldholm, Olav

    1991-04-01

    Extensive geophysical surveys have been undertaken on the volcanic passive continental margin offshore Norway between 62° and 70°N during the last 25 years. Three main margin segments have been identified, the Lofoten-Vesteralen Margin, the Vøring Margin and the Møre Margin. The main features of the margins are prominent marginal highs, including seaward dipping reflector sequences and an up to 22 km thick volcanic and transitional crust, prominent escarpments (the Vøring Plateau Escarpment and the Faeroe-Shetland Escarpment), and up to 12 km deep post-Jurassic sedimentary basins east of the escarpments. Velocity-depth solutions from about 250 sonobuoys, expanding spread profiles and refraction profiles have been compiled and contoured. Isovelocity horizon contour maps and velocity transects outline a crust which broadly thickens from an oceanic crust with a normal oceanic-type velocity structure to a ca. 35 km thick continental crust with a continental velocity structure, beneath the Norwegian coast. Anomalous features include local crustal thickening below the Møre and Vering marginal highs, and high-velocity bodies in the lower crust in the extension of the Precambrian Lofoten-Vesterålen archipelago. The free-air SEASAT-derived gravity anomalies show a good correlation with the high-velocity bodies, and show prominent NE-trending highs from the Rockall Plateau/Porcupine Plateau region, over the Møre, Vøring and Lofoten-Vesterålen margins, to the southwestern Barents Sea.

  1. Geophysical characteristics and crustal structure of greenstone terranes: Canadian Shield

    NASA Technical Reports Server (NTRS)

    Thomas, M. D.; Losier, L.; Thurston, P. C.; Gupta, V. K.; Gibb, R. A.; Grieve, R. A. F.

    1986-01-01

    Geophysical studies in the Canadian Shield have provided some insights into the tectonic setting of greenstone belts. Greenstone belts are not rooted in deep crustal structures. Geophysical techniques consistently indicate that greenstones are restricted to the uppermost 10 km or so of crust and are underlain by geophysically normal crust. Gravity models suggest that granitic elements are similarly restricted, although magnetic modelling suggests possible downward extension to the intermediate discontinuity around approx. 18 km. Seismic evidence demonstrates that steeply-dipping structure, which can be associated with the belts in the upper crust, is not present in the lower crust. Horizontal intermediate discontinuities mapped under adjacent greenstone and granitic components are not noticeably disrupted in the boundary zone. Geophysical evidence points to the presence of discontinuities between greenhouse-granite and adjacent metasedimentary erranes. Measured stratigraphic thicknesses of greenstone belts are often twice or more the vertical thicknesses determined from gravity modelling. Explantations advanced for the discrepancy include stratigraphy repeated by thrust faulting and/or listric normal faulting, mechanisms which are consistent with certain aspects of conceptual models of greenstone development. Where repetition is not a factor the gravity evidence points to removal of the root zones of greenstone belts. For one region, this has been attributed to magmatic stopping during resurgent caldera activity.

  2. The crustal structure of the southern Argentine margin

    NASA Astrophysics Data System (ADS)

    Becker, Katharina; Franke, Dieter; Schnabel, Michael; Schreckenberger, Bernd; Heyde, Ingo; Krawczyk, Charlotte M.

    2012-06-01

    Multichannel reflection seismic profiles, combined with gravimetric and magnetic data provide insight into the crustal structure of the southernmost Argentine margin, at the transition from a rifted to a transform margin and outline the extent of the North Falkland Graben. Based on these data, we establish a regional stratigraphic model for the post-rift sediments, comprising six marker horizons with a new formation in the Barremian/Lower Cretaceous. Our observations support that a N-S trending subsidiary branch of the North Falkland Graben continues along the continental shelf and slope to the Argentine basin. During the rift phase, a wide shelf area was affected by the E-W extension, subsequently forming the North Falkland Graben and the subsidiary branch along which finally breakup occurred. We propose the division of the margin in two segments: a N-S trending rifted margin and an E-W trending transform margin. This is further underpinned by crustal scale gravity modelling. Three different tectono-dynamic processes shaped the study area. (1) The Triassic/Early Jurassic extensional phase resulting in the formation of the North Falkland Graben and additional narrower rift grabens ended synchronously with the breakup of the South Atlantic in the early Valanginian. (2) Extensional phase related to the opening of the South Atlantic. (3) The transform margin was active in the study area from about Hauterivian times and activity lasted until late Cretaceous/early Cenozoic. Both, the rifted margin and the transform margin are magma-poor. Very limited structures may have a volcanic origin but are suggested to be post-rift. The oceanic crust was found to be unusually thin, indicating a deficit in magma supply during formation. These findings in combination with the proposed breakup age in the early Valanginian that considerably predates the formation of the Paraná-Etendeka continental flood basalt provinces in Brazil and Namibia question the influence of the Tristan da

  3. Reconstruction of 3D structure using stochastic methods: morphology and transport properties

    NASA Astrophysics Data System (ADS)

    Karsanina, Marina; Gerke, Kirill; Čapek, Pavel; Vasilyev, Roman; Korost, Dmitry; Skvortsova, Elena

    2013-04-01

    One of the main factors defining numerous flow phenomena in rocks, soils and other porous media, including fluid and solute movements, is pore structure, e.g., pore sizes and their connectivity. Numerous numerical methods were developed to quantify single and multi-phase flow in such media on microscale. Among most popular ones are: 1) a wide range of finite difference/element/volume solutions of Navier-Stokes equations and its simplifications; 2) lattice-Boltzmann method; 3) pore-network models, among others. Each method has some advantages and shortcomings, so that different research teams usually utilize more than one, depending on the study case. Recent progress in 3D imaging of internal structure, e.g., X-ray tomography, FIB-SEM and confocal microscopy, made it possible to obtain digitized input pore parameters for such models, however, a trade-off between resolution and sample size is usually unavoidable. There are situations then only standard two-dimensional information of porous structure is known due to tomography high cost or resolution limitations. However, physical modeling on microscale requires 3D information. There are three main approaches to reconstruct (using 2D cut(s) or some other limited information/properties) porous media: 1) statistical methods (correlation functions and simulated annealing, multi-point statistics, entropy methods), 2) sequential methods (sphere or other granular packs) and 3) morphological methods. Stochastic reconstructions using correlation functions possess some important advantage - they provide a statistical description of the structure, which is known to have relationships with all physical properties. In addition, this method is more flexible for other applications to characterize porous media. Taking different 3D scans of natural and artificial porous materials (sandstones, soils, shales, ceramics) we choose some 2D cut/s as sources of input correlation functions. Based on different types of correlation functions

  4. Loading mode dependent effective properties of octet-truss lattice structures using 3D-printing

    NASA Astrophysics Data System (ADS)

    Challapalli, Adithya

    Cellular materials, often called lattice materials, are increasingly receiving attention for their ultralight structures with high specific strength, excellent impact absorption, acoustic insulation, heat dissipation media and compact heat exchangers. In alignment with emerging additive manufacturing (AM) technology, realization of the structural applications of the lattice materials appears to be becoming faster. Considering the direction dependent material properties of the products with AM, by directionally dependent printing resolution, effective moduli of lattice structures appear to be directionally dependent. In this paper, a constitutive model of a lattice structure, which is an octet-truss with a base material having an orthotropic material property considering AM is developed. In a case study, polyjet based 3D printing material having an orthotropic property with a 9% difference in the principal direction provides difference in the axial and shear moduli in the octet-truss by 2.3 and 4.6%. Experimental validation for the effective properties of a 3D printed octet-truss is done for uniaxial tension and compression test. The theoretical value based on the micro-buckling of truss member are used to estimate the failure strength. Modulus value appears a little overestimate compared with the experiment. Finite element (FE) simulations for uniaxial compression and tension of octettruss lattice materials are conducted. New effective properties for the octet-truss lattice structure are developed considering the observed behavior of the octet-truss structure under macroscopic compression and tension trough simulations.

  5. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

    PubMed Central

    Gouet, Patrice; Robert, Xavier; Courcelle, Emmanuel

    2003-01-01

    The fortran program ESPript was created in 1993, to display on a PostScript figure multiple sequence alignments adorned with secondary structure elements. A web server was made available in 1999 and ESPript has been linked to three major web tools: ProDom which identifies protein domains, PredictProtein which predicts secondary structure elements and NPS@ which runs sequence alignment programs. A web server named ENDscript was created in 2002 to facilitate the generation of ESPript figures containing a large amount of information. ENDscript uses programs such as BLAST, Clustal and PHYLODENDRON to work on protein sequences and such as DSSP, CNS and MOLSCRIPT to work on protein coordinates. It enables the creation, from a single Protein Data Bank identifier, of a multiple sequence alignment figure adorned with secondary structure elements of each sequence of known 3D structure. Similar 3D structures are superimposed in turn with the program PROFIT and a final figure is drawn with BOBSCRIPT, which shows sequence and structure conservation along the Cα trace of the query. ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript. PMID:12824317

  6. The "lnc" between 3D chromatin structure and X chromosome inactivation.

    PubMed

    Pandya-Jones, Amy; Plath, Kathrin

    2016-08-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilitates the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  7. A 3D moisture-stress FEM analysis for time dependent problems in timber structures

    NASA Astrophysics Data System (ADS)

    Fortino, Stefania; Mirianon, Florian; Toratti, Tomi

    2009-11-01

    This paper presents a 3D moisture-stress numerical analysis for timber structures under variable humidity and load conditions. An orthotropic viscoelastic-mechanosorptive material model is specialized on the basis of previous models. Both the constitutive model and the equations needed to describe the moisture flow across the structure are implemented into user subroutines of the Abaqus finite element code and a coupled moisture-stress analysis is performed for several types of mechanical loads and moisture changes. The presented computational approach is validated by analyzing some wood tests described in the literature and comparing the computational results with the reported experimental data.

  8. The “lnc” between 3D Chromatin Structure and X Chromosome Inactivation

    PubMed Central

    Pandya-Jones, Amy; Plath, Kathrin

    2016-01-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilities the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  9. 3-D Structure of the Moho Interface beneath South Korea from Regional Seismic Observations

    NASA Astrophysics Data System (ADS)

    Gritto, R.; Siegel, J.; Chan, W. C.

    2007-12-01

    The current project is concerned with the collection and processing of seismic waveform data to perform 3-D tomographic inversions and produce high-resolution 3-D crustal P- and S-wave velocity models for the South Korean peninsula. At present, we have analyzed and archived Korean Meteorological Administration (KMA) waveform data from 2001 through 2006 and mapped of the Moho discontinuity below South Korea. Phase arrival information from both, velocity and accelerometer sensors were collected. The analysis included 226 events throughout the region producing a total of 6,275 phase picks including Pg, Pn, Sg/Lg, and Sn phases. A total of 3,550 P-wave and 2,725 S-wave phases were identified. Using the combination of all available velocity and accelerometer data it was possible to estimate depth locations for 198 KMA events. The hypocenters were subsequently used to derive travel-time distance curves to appraise the quality of the travel-time picks. Static corrections were calculated for each seismic station within the KMA network to remove the effects of local inhomogeneities in the vicinity of each station. After applying static corrections to the observed travel-times, refracted P-wave phases along the Moho boundary were selected from the dataset to estimate the depth and topography of the Moho discontinuity beneath South Korea. In total, 526 Pn phases were collected from the KMA data with hypocentral distances from 130 km to over 650 km. The resulting Moho topography reveals a slightly undulating interface with a large-scale dip from north (31 km) to south (38 km) and a depth range from 32 km in the east to 39 km in the south-west. On a smaller scale, a more pronounced depression is evident in the south- central part of the mapped area, which opens to the south. The presented results are corroborated by other studies which mapped the Moho interface using surface-wave dispersion and receiver-function analysis. The present study is complementary to these earlier

  10. Crustal Structure of the PARANÁ Basin from Ambient Noise Tomography

    NASA Astrophysics Data System (ADS)

    Collaço, B.; Assumpcao, M.; Rosa, M. L.; Sanchez, G.

    2013-12-01

    Previous surface-wave tomography in South America (SA) (e.g., Feng et al., 2004; 2007) mapped the main large-scale features of the continent, such as the high lithospheric velocities in cratonic areas and low velocities in the Patagonian province. However, more detailed features such as the Paraná Basin, have not been mapped with good resolution because of poor path coverage, i.e. classic surface- wave tomography has low resolution in low-seismicity areas, like Brazil and the Eastern Argentina. Crustal structure in Southern Brazil is poorly known. Most paths used by Feng et al. (2007) in this region are roughly parallel, which prevents good spatial resolution in tomographic inversions. This work is part of a major project that will increase knowledge of crustal structure in Southern Brazil and Eastern Argentina and is being carried out by IAG-USP (Brazil) in collaboration with UNLP and INPRES (Argentina). To improve resolution for the Paraná Basin we used inter-station dispersion curves derived from correlation of ambient noise for new stations deployed with the implementation of the Brazilian Seismic Network (Pirchiner et al. 2011). This technique, known as ambient noise tomography (ANT), was first applied by Shapiro et al. (2005) and is now expanding rapidly, especially in areas with high density of seismic stations (e.g. Bensen et al. 2007, Lin et al. 2008, Moschetti et al. 2010). ANT is a well-established method to estimate short period (< 20s) and intermediate periods (20 - 50s) surface wave speeds both in regional or continental scales (Lin et al. 2008). ANT data processing in this work was similar to the one described by Bensen et al. 2007, in four major steps with addition of a data inversion step. Group velocities between pairs of stations were derived from correlation of two years of ambient noise in the period range 5 to 60 s. The dispersion curves measurements were made using a modified version of PGSWMFA (PGplot Surface Wave Multiple Filter Analysis

  11. Multi-dimensional Crustal and Lithospheric Structure of the Atlas Mountains of Morocco by Magnetotelluric Imaging

    NASA Astrophysics Data System (ADS)

    Kiyan, D.; Jones, A. G.; Fullea, J.; Ledo, J.; Siniscalchi, A.; Romano, G.

    2014-12-01

    The PICASSO (Program to Investigate Convective Alboran Sea System Overturn) project and the concomitant TopoMed (Plate re-organization in the western Mediterranean: Lithospheric causes and topographic consequences - an ESF EUROSCORES TOPO-EUROPE project) project were designed to collect high resolution, multi-disciplinary lithospheric scale data in order to understand the tectonic evolution and lithospheric structure of the western Mediterranean. The over-arching objectives of the magnetotelluric (MT) component of the projects are (i) to provide new electrical conductivity constraints on the crustal and lithospheric structure of the Atlas Mountains, and (ii) to test the hypotheses for explaining the purported lithospheric cavity beneath the Middle and High Atlas inferred from potential-field lithospheric modeling. We present the results of an MT experiment we carried out in Morocco along two profiles: an approximately N-S oriented profile crossing the Middle Atlas, the High Atlas and the eastern Anti-Atlas to the east (called the MEK profile, for Meknes) and NE-SW oriented profile through western High Atlas to the west (called the MAR profile, for Marrakech). Our results are derived from three-dimensional (3-D) MT inversion of the MT data set employing the parallel version of Modular system for Electromagnetic inversion (ModEM) code. The distinct conductivity differences between the Middle-High Atlas (conductive) and the Anti-Atlas (resistive) correlates with the South Atlas Front fault, the depth extent of which appears to be limited to the uppermost mantle (approx. 60 km). In all inverse solutions, the crust and the upper mantle show resistive signatures (approx. 1,000 Ωm) beneath the Anti-Atlas, which is the part of stable West African Craton. Partial melt and/or exotic fluids enriched in volatiles produced by the melt can account for the high middle to lower crustal and uppermost mantle conductivity in the Folded Middle Atlas, the High Moulouya Plain and the

  12. 3D Geo-Structures Visualization Education Project (3dgeostructuresvis.ucdavis.edu)

    NASA Astrophysics Data System (ADS)

    Billen, M. I.

    2014-12-01

    Students of field-based geology must master a suite of challenging skills from recognizing rocks, to measuring orientations of features in the field, to finding oneself (and the outcrop) on a map and placing structural information on maps. Students must then synthesize this information to derive meaning from the observations and ultimately to determine the three-dimensional (3D) shape of the deformed structures and their kinematic history. Synthesizing this kind of information requires sophisticated visualizations skills in order to extrapolate observations into the subsurface or missing (eroded) material. The good news is that students can learn 3D visualization skills through practice, and virtual tools can help provide some of that practice. Here I present a suite of learning modules focused at developing students' ability to imagine (visualize) complex 3D structures and their exposure through digital topographic surfaces. Using the software 3DVisualizer, developed by KeckCAVES (keckcaves.org) we have developed visualizations of common geologic structures (e.g., syncline, dipping fold) in which the rock is represented by originally flat-lying layers of sediment, each with a different color, which have been subsequently deformed. The exercises build up in complexity, first focusing on understanding the structure in 3D (penetrative understanding), and then moving to the exposure of the structure at a topographic surface. Individual layers can be rendered as a transparent feature to explore how the layer extends above and below the topographic surface (e.g., to follow an eroded fold limb across a valley). The exercises are provided using either movies of the visualization (which can also be used for examples during lectures), or the data and software can be downloaded to allow for more self-driven exploration and learning. These virtual field models and exercises can be used as "practice runs" before going into the field, as make-up assignments, as a field

  13. Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-N-Acetylhexosaminidase

    PubMed Central

    Hossain, Md. Anowar

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom. PMID:25165734

  14. Learning the 3-D structure of objects from 2-D views depends on shape, not format

    PubMed Central

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-01-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  15. Learning the 3-D structure of objects from 2-D views depends on shape, not format.

    PubMed

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-05-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  16. Crustal structure of central Lake Baikal: Insights into intracontinental rifting

    USGS Publications Warehouse

    ten Brink, U.S.; Taylor, M.H.

    2002-01-01

    The Cenozoic rift system of Baikal, located in the interior of the largest continental mass on Earth, is thought to represent a potential analog of the early stage of breakup of supercontinents. We present a detailed P wave velocity structure of the crust and sediments beneath the Central Basin, the deepest basin in the Baikal rift system. The structure is characterized by a Moho depth of 39-42.5 km; an 8-km-thick, laterally continuous high-velocity (7.05-7.4 km/s) lower crust, normal upper mantle velocity (8 km/s), a sedimentary section reaching maximum depths of 9 km, and a gradual increase of sediment velocity with depth. We interpret the high-velocity lower crust to be part of the Siberian Platform that was not thinned or altered significantly during rifting. In comparison to published results from the Siberian Platform, Moho under the basin is elevated by <3 km. On the basis of these results we propose that the basin was formed by upper crustal extension, possibly reactivating structures in an ancient fold-and-thrust belt. The extent and location of upper mantle extension are not revealed by our data, and it may be offset from the rift. We believe that the Baikal rift structure is similar in many respects to the Mesozoic Atlantic rift system, the precursor to the formation of the North Atlantic Ocean. We also propose that the Central Baikal rift evolved by episodic fault propagation and basin enlargement, rather than by two-stage rift evolution as is commonly assumed.

  17. Crustal structure of an intraplate thrust belt: The Iberian Chain revealed by wide-angle seismic, magnetotelluric soundings and gravity data

    NASA Astrophysics Data System (ADS)

    Seillé, Hoël; Salas, Ramon; Pous, Jaume; Guimerà, Joan; Gallart, Josep; Torne, Montserrat; Romero-Ruiz, Ivan; Diaz, Jordi; Ruiz, Mario; Carbonell, Ramon; Mas, Ramón

    2015-11-01

    The Iberian Chain is a Cenozoic intraplate thrust belt located within the Iberian plate. Unlike other belts in the Iberia Peninsula, the scarcity of geophysical studies in this area results in a number of unknowns about its crustal structure. The Iberian Chain crust was investigated by means of a NE-SW refraction/wide-angle reflection seismic transect and two magnetotelluric profiles across the chain, oriented along the same direction. The seismic profile was designed to sample the crust by means of three shots designed to obtain a reversed profile. The resulting velocity-depth model shows a moderate thickening of the crust toward the central part of the profile, where crustal thickness reaches values above 40 km, thinning toward de SW Tajo and NE Ebro foreland basins. The crustal thickening is concentrated in the upper crust. The seismic results are in overall agreement with regional trends of Bouguer gravity anomaly and the main features of the seismic model were reproduced by gravity modeling. The magnetotelluric data consist of 39 sites grouped into two profiles, with periods ranging from 0.01 s to 1000 s. Dimensionality analyses show significant 3D effects in the resistivity structure and therefore we carried out a joint 3D inversion of the full impedance tensor and magnetic transfer functions. The Mesozoic and Cenozoic basins along the Chain are well characterized by shallow high conductive zones and low velocities. Elongated conductors reaching mid-crustal depths evidence the presence of major faults dominating the crustal structure. The results from the interpretation of these complementary geophysical data sets provided the first images of the crustal structure of the Iberian Chain. They are consistent with a Cenozoic shortening responsible of the upper crust thickening as well as of the uplift of the Iberian Chain and the generation of its present day topography.

  18. The crustal structure of south central Mongolia using receiver functions

    NASA Astrophysics Data System (ADS)

    He, Jing; Wu, Qingju; Sandvol, Eric; Ni, James; Gallegos, Andrea; Gao, Mengtan; Ulziibat, Munkhuu; Demberel, Sodnomsambuu

    2016-06-01

    The crustal thickness H and average crustal velocity ratio k (Vp/Vs) beneath south central Mongolia are investigated using the H-k stacking method based on teleseismic radial receiver functions. Our primary results reveal that the local crustal thickness varies from 38 to 46 km with an average value of 43 km. Thicker crust is found beneath the western Hentey Mountains, while thinner crust is located in the southern area of the Zuunbayan fault zone. The Bouguer gravity anomalies exhibit a strong correlation with the overall crustal thickness pattern throughout most of our study regime. Moreover, a new approach which integrates the Bouguer anomaly gradient and the receiver function-derived crustal thickness is adopted to calculate the density of the lower crust underneath central Mongolia. Fairly dense lower crust of approximately 3000 kg/m3 is found in the Middle Gobi Desert. The measured crustal Vp/Vs ratio ranges from 1.68 to 1.83 with an average value of 1.74. Low Vp/Vs ratio is found beneath the western Hentey Mountains. In general, low Vp/Vs ratios correlate well with regions of quartz-rich crust and high heat flow. High Vp/Vs ratios occur in the Middle Gobi volcanic regions and the Mesozoic Southern Gobi Basin.

  19. Color influence on accuracy of 3D scanners based on structured light

    NASA Astrophysics Data System (ADS)

    Voisin, Sophie; Page, David L.; Foufou, Sebti; Truchetet, Frédéric; Abidi, Mongi A.

    2006-02-01

    The characterization of commercial 3D scanners allows acquiring precise and useful data. The accuracy of range and, more recently, color for 3D scanners is usually studied separately, but when the 3D scanner is based on structured light with a color coding pattern, color influence on range accuracy should be investigated. The commercial product that we have tested has the particularity that it can acquire data under ambient light instead of a controlled environment as it is with most available scanners. Therefore, based on related work in the literature and on experiments we have done on a variety of standard illuminants, we have designed an interesting setup to control illuminant interference. Basically, the setup consists of acquiring the well-known Macbeth ColorChecker under a controlled environment and also ambient daylight. The results have shown variations with respect to the color. We have performed several statistical studies to show how the range results evolve with respect to the RGB and the HSV channels. In addition, a systematic noise error has also been identified. This noise depends on the object color. A subset of colors shows strong noise errors while other colors have minimal or even no systematic error under the same illuminant.

  20. PACS-based interface for 3D anatomical structure visualization and surgical planning

    NASA Astrophysics Data System (ADS)

    Koehl, Christophe; Soler, Luc; Marescaux, Jacques

    2002-05-01

    The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

  1. Modeling the Impact of Drizzle and 3D Cloud Structure on Remote Sensing of Effective Radius

    NASA Technical Reports Server (NTRS)

    Platnick, Steven; Zinner, Tobias; Ackerman, S.

    2008-01-01

    Remote sensing of cloud particle size with passive sensors like MODIS is an important tool for cloud microphysical studies. As a measure of the radiatively relevant droplet size, effective radius can be retrieved with different combinations of visible through shortwave infrared channels. MODIS observations sometimes show significantly larger effective radii in marine boundary layer cloud fields derived from the 1.6 and 2.1 pm channel observations than for 3.7 pm retrievals. Possible explanations range from 3D radiative transport effects and sub-pixel cloud inhomogeneity to the impact of drizzle formation on the droplet distribution. To investigate the potential influence of these factors, we use LES boundary layer cloud simulations in combination with 3D Monte Carlo simulations of MODIS observations. LES simulations of warm cloud spectral microphysics for cases of marine stratus and broken stratocumulus, each for two different values of cloud condensation nuclei density, produce cloud structures comprising droplet size distributions with and without drizzle size drops. In this study, synthetic MODIS observations generated from 3D radiative transport simulations that consider the full droplet size distribution will be generated for each scene. The operational MODIS effective radius retrievals will then be applied to the simulated reflectances and the results compared with the LES microphysics.

  2. Micro-structured materials and mechanical cues in 3D collagen gels.

    PubMed

    Phillips, James B; Brown, Robert

    2011-01-01

    Collagen gels provide a versatile and widely used substrate for three-dimensional (3D) cell culture. Here we describe how cell-seeded Type-I collagen gels can be adapted to provide powerful 3D models to support a wide range of research applications where cell/substrate alignment, density, stiffness/compliance, and strain are critical factors. In their fully hydrated form, rectangular collagen gels can be tethered such that endogenous forces generated as resident cells attach to and remodel the fibrillar collagen network can align the substrate in a controllable, predictable, and quantifiable manner. By removing water from collagen gels (plastic compression), their density increases towards that of body tissues, facilitating the engineering of a range of biomimetic constructs with controllable mechanical properties. This dense collagen can be used in combination with other components to achieve a range of functional properties from controlled perfusion, or tensile/compressive strength to new micro-structures. Detailed methodology is provided for the assembly of a range of 3D collagen materials including tethered aligned hydrogels and plastic compressed constructs. A range of techniques for analysing cell behaviour within these models, including microscopy and molecular analyses are described. These systems therefore provide a highly controllable mechanical and chemical micro-environment for investigating a wide range of cellular responses. PMID:21042973

  3. Integration of 3D Structure from Disparity into Biological Motion Perception Independent of Depth Awareness

    PubMed Central

    Wang, Ying; Jiang, Yi

    2014-01-01

    Images projected onto the retinas of our two eyes come from slightly different directions in the real world, constituting binocular disparity that serves as an important source for depth perception - the ability to see the world in three dimensions. It remains unclear whether the integration of disparity cues into visual perception depends on the conscious representation of stereoscopic depth. Here we report evidence that, even without inducing discernible perceptual representations, the disparity-defined depth information could still modulate the visual processing of 3D objects in depth-irrelevant aspects. Specifically, observers who could not discriminate disparity-defined in-depth facing orientations of biological motions (i.e., approaching vs. receding) due to an excessive perceptual bias nevertheless exhibited a robust perceptual asymmetry in response to the indistinguishable facing orientations, similar to those who could consciously discriminate such 3D information. These results clearly demonstrate that the visual processing of biological motion engages the disparity cues independent of observers’ depth awareness. The extraction and utilization of binocular depth signals thus can be dissociable from the conscious representation of 3D structure in high-level visual perception. PMID:24586622

  4. Algorithms for extraction of structural attitudes from 3D outcrop models

    NASA Astrophysics Data System (ADS)

    Duelis Viana, Camila; Endlein, Arthur; Ademar da Cruz Campanha, Ginaldo; Henrique Grohmann, Carlos

    2016-05-01

    The acquisition of geological attitudes on rock cuts using traditional field compass survey can be a time consuming, dangerous, or even impossible task depending on the conditions and location of outcrops. The importance of this type of data in rock-mass classifications and structural geology has led to the development of new techniques, in which the application of photogrammetric 3D digital models has had an increasing use. In this paper we present two algorithms for extraction of attitudes of geological discontinuities from virtual outcrop models: ply2atti and scanline, implemented with the Python programming language. The ply2atti algorithm allows for the virtual sampling of planar discontinuities appearing on the 3D model as individual exposed surfaces, while the scanline algorithm allows the sampling of discontinuities (surfaces and traces) along a virtual scanline. Application to digital models of a simplified test setup and a rock cut demonstrated a good correlation between the surveys undertaken using traditional field compass reading and virtual sampling on 3D digital models.

  5. Tensor decomposition in electronic structure calculations on 3D Cartesian grids

    SciTech Connect

    Khoromskij, B.N. Khoromskaia, V.; Chinnamsetty, S.R.; Flad, H.-J.

    2009-09-01

    In this paper, we investigate a novel approach based on the combination of Tucker-type and canonical tensor decomposition techniques for the efficient numerical approximation of functions and operators in electronic structure calculations. In particular, we study applicability of tensor approximations for the numerical solution of Hartree-Fock and Kohn-Sham equations on 3D Cartesian grids. We show that the orthogonal Tucker-type tensor approximation of electron density and Hartree potential of simple molecules leads to low tensor rank representations. This enables an efficient tensor-product convolution scheme for the computation of the Hartree potential using a collocation-type approximation via piecewise constant basis functions on a uniform nxnxn grid. Combined with the Richardson extrapolation, our approach exhibits O(h{sup 3}) convergence in the grid-size h=O(n{sup -1}). Moreover, this requires O(3rn+r{sup 3}) storage, where r denotes the Tucker rank of the electron density with r=O(logn), almost uniformly in n. For example, calculations of the Coulomb matrix and the Hartree-Fock energy for the CH{sub 4} molecule, with a pseudopotential on the C atom, achieved accuracies of the order of 10{sup -6} hartree with a grid-size n of several hundreds. Since the tensor-product convolution in 3D is performed via 1D convolution transforms, our scheme markedly outperforms the 3D-FFT in both the computing time and storage requirements.

  6. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

    PubMed

    Tokheim, Collin; Bhattacharya, Rohit; Niknafs, Noushin; Gygax, Derek M; Kim, Rick; Ryan, Michael; Masica, David L; Karchin, Rachel

    2016-07-01

    The impact of somatic missense mutation on cancer etiology and progression is often difficult to interpret. One common approach for assessing the contribution of missense mutations in carcinogenesis is to identify genes mutated with statistically nonrandom frequencies. Even given the large number of sequenced cancer samples currently available, this approach remains underpowered to detect drivers, particularly in less studied cancer types. Alternative statistical and bioinformatic approaches are needed. One approach to increase power is to focus on localized regions of increased missense mutation density or hotspot regions, rather than a whole gene or protein domain. Detecting missense mutation hotspot regions in three-dimensional (3D) protein structure may also be beneficial because linear sequence alone does not fully describe the biologically relevant organization of codons. Here, we present a novel and statistically rigorous algorithm for detecting missense mutation hotspot regions in 3D protein structures. We analyzed approximately 3 × 10(5) mutations from The Cancer Genome Atlas (TCGA) and identified 216 tumor-type-specific hotspot regions. In addition to experimentally determined protein structures, we considered high-quality structural models, which increase genomic coverage from approximately 5,000 to more than 15,000 genes. We provide new evidence that 3D mutation analysis has unique advantages. It enables discovery of hotspot regions in many more genes than previously shown and increases sensitivity to hotspot regions in tumor suppressor genes (TSG). Although hotspot regions have long been known to exist in both TSGs and oncogenes, we provide the first report that they have different characteristic properties in the two types of driver genes. We show how cancer researchers can use our results to link 3D protein structure and the biologic functions of missense mutations in cancer, and to generate testable hypotheses about driver mechanisms. Our results

  7. Influence of pre-existing salt structures in the 3D pattern of multilayer folding

    NASA Astrophysics Data System (ADS)

    Fernandez, Naiara; Kaus, Boris J. P.; Collignon, Marine

    2014-05-01

    Upward movement of the Precambrian Hormuz salt in the Fars region of the Zagros is supposed to have started as early as Late Cretaceous. The Late Cretaceous - Tertiary deformation events that lead to the folding of the sedimentary cover in this area would have therefore, enhance the upward salt movement by squeezing the pre-existing salt structures. How these salt diapirs evolve under such compressive events has already been previously addressed using analogue models (e.g. Callot et al. 2012). The same authors observed that pre-existing salt structures control the size and geometry of folds in sandbox models. Our previous work has shown that 3D folding instability gives rise to a wide variety of fold shapes (e.g. from dome shape structures to long en echelon or straight anticlines), resulting of the interactions between growing fold segments. The three dimensional growth of these folds, the wavelength and the lateral propagation, is itself controlled by physical parameters. However, the existence of initial weak zones such as pre-existing salt plugs within the sedimentary cover can affect the development of such folds by localizing part of the deformation. In this study we have used numerical modeling to investigate how the fold pattern in 3D multilayer folding is affected by pre-existing salt structures. High-resolution 3D folding simulations (with and without pre-existing salt structures) were performed with the parallel code LaMEM. Cylindrically shaped diapirs with different diameters and heights have been added to a multilayer folding setup. The use of a finite element based landscape evolution model (both erosion and sedimentation) allows for initially buried salt diapirs to be exposed at the surface during folding evolution. Acknowledgements Funding was provided by the European Research Council under the European Community's Seventh Framework program (FP7/2007-2013) ERC Grant agreement #258830. 3D simulations are performed in the IBM Blue Gene/Q JUQUEEN

  8. 3-D velocity structure around tehri region of the garhwal lesser himalaya: constraints on geometry of the underthrusting indian plate

    NASA Astrophysics Data System (ADS)

    Kanaujia, Jyotima; Kumar, Ashwani; Gupta, S. C.

    2016-02-01

    We investigate the upper crustal velocity structure beneath the Tehri region of the Garhwal Himalaya. The investigated region is situated within the 700-km-long central seismic gap of the Himalaya that has experienced three gap-filling earthquakes since 1991 including the recent 2015 Nepal earthquake (Mw 7.8). The local tomographic inversion is based on a dataset of 1365 events collected from January 2008 to December 2012 by a 12-station local network that covers an area of about 100 × 80 km around Tehri Dam. We perform a simultaneous inversion for P- and S-wave velocity anomalies. Tomograms are interpreted in the backdrop of the regional geological and tectonic framework of the region. The spatial distribution of relocated events from the 3- D velocity model has shed new light on the pattern of seismicity in the vicinity of the Main Central thrust (MCT), and has elucidated the structure of the underthrusting Indian plate. Our model exhibits a significant negative velocity anomaly up to ˜5 per cent beneath the central part of the Garhwal Inner Lesser Himalaya, and a P-wave low velocity anomaly near the Chamoli region. The seismicity zone around the Chamoli region may be attributed to the presence of fluid filled rocks. Furthermore, an area with˜3-4 per cent positive velocity anomaly is delineated to the northwest of the Uttarkashi thrust in the vicinity of the MCT. Significant findings of the study include: a flat-ramp-flat type sub-surface geometry of the underthrusting Indian plate below the Garhwal Himalaya, high velocity images representing the trend and configuration of Delhi-Haridwar-ridge below the Sub Himalaya and Lesser Himalaya, and a seismically active zone representing geometrical asperity on the basement thrust in the vicinity of the MCT.

  9. Experimental Investigation of the Near Wall Flow Structure of a Low Reynolds Number 3-D Turbulent Boundary Layer

    NASA Technical Reports Server (NTRS)

    Fleming, J. L.; Simpson, R. L.

    1997-01-01

    Laser Doppler velocimetry (LDV) measurements and hydrogen bubble flow visualization techniques were used to examine the near-wall flow structure of 2D and 3D turbulent boundary layers (TBLs) over a range of low Reynolds numbers. The goals of this research were (1) an increased understanding of the flow physics in the near wall region of turbulent boundary layers,(2) to observe and quantify differences between 2D and 3D TBL flow structures, and (3) to document Reynolds number effects for 3D TBLs. The LDV data have provided results detailing the turbulence structure of the 2D and 3D TBLs. These results include mean Reynolds stress distributions, flow skewing results, and U and V spectra. Effects of Reynolds number for the 3D flow were also examined. Comparison to results with the same 3D flow geometry but at a significantly higher Reynolds number provided unique insight into the structure of 3D TBLs. While the 3D mean and fluctuating velocities were found to be highly dependent on Reynolds number, a previously defined shear stress parameter was discovered to be invariant with Reynolds number. The hydrogen bubble technique was used as a flow visualization tool to examine the near-wall flow structure of 2D and 3D TBLs. Both the quantitative and qualitative results displayed larger turbulent fluctuations with more highly concentrated vorticity regions for the 2D flow.

  10. Crustal structure between Lake Mead, Nevada, and Mono Lake, California

    USGS Publications Warehouse

    Johnson, Lane R.

    1964-01-01

    Interpretation of a reversed seismic-refraction profile between Lake Mead, Nevada, and Mono Lake, California, indicates velocities of 6.15 km/sec for the upper layer of the crust, 7.10 km/sec for an intermediate layer, and 7.80 km/sec for the uppermost mantle. Phases interpreted to be reflections from the top of the intermediate layer and the Mohorovicic discontinuity were used with the refraction data to calculate depths. The depth to the Moho increases from about 30 km near Lake Mead to about 40 km near Mono Lake. Variations in arrival times provide evidence for fairly sharp flexures in the Moho. Offsets in the Moho of 4 km at one point and 2 1/2 km at another correspond to large faults at the surface, and it is suggested that fracture zones in the upper crust may displace the Moho and extend into the upper mantle. The phase P appears to be an extension of the reflection from the top of the intermediate layer beyond the critical angle. Bouguer gravity, computed for the seismic model of the crust, is in good agreement with the measured Bouguer gravity. Thus a model of the crustal structure is presented which is consistent with three semi-independent sources of geophysical data: seismic-refraction, seismic-reflection, and gravity.

  11. Structural and property studies on metal–organic compounds with 3-D supramolecular network

    SciTech Connect

    Zhang, Qi-Ying; Ma, Ke-Fang; Xiao, Hong-Ping; Li, Xin-Hua; Shi, Qian

    2014-07-01

    Two carboxylato-bridged allomeric compounds, ([Cu{sub 2}(dbsa){sub 2}(hmt) (H{sub 2}O){sub 4}]{sub 1/2}·2H{sub 2}O){sub n} (1), ([Ni(dbsa)(H{sub 2}O){sub 2}]{sub 1/2}[Ni(dbsa)(hmt)(H{sub 2}O){sub 2}]{sub 1/2}·2H{sub 2}O){sub n} (2) (H{sub 2}dbsa=meso-2,3-dibromosuccinic acid, hmt=hexamethylenetetramine) have been synthesized and characterized by X-ray structral analyses. The metal ions have two kinds of coordination fashion in one unit, and bridged by carboxylate and hmt ligands along with weak interactions existing in the solid structure, forming a 3-D supramolecular network. Variable-temperature magnetic property studies reveal the existence of antiferromagnetic interactions in 1 and 2 with g=2.2, J{sub 1}=−3.5 cm{sup −1}, J{sub 2}=−2.8 cm{sup −1} for 1, and g=2.1, J=−3.5 cm{sup −1} for 2. - Graphical abstract: Variable-temperature magnetic property studies of two 3-D supramolecular compounds reveal the existence of antiferromagnetic interactions between the metal ions, through the effective super-exchange media. - Highlights: • Two 3-D allomeric Cu(II) and Ni(II) metal–organic compounds have been prepared. • The 3-D networks were constructed by coordination bonds, weak interactions and hydrogen bond interactions. • There are antiferromagnetic super-exchange interactions between the metal ions.

  12. The 3D geological model of the Eastern Romania tectonics and structure

    NASA Astrophysics Data System (ADS)

    Necula, Nicusor; Sorin Baciu, Dorin; Niculita, Mihai; Dumitriu, Tony-Cristian

    2016-04-01

    3D geologic modelling is a modern tool which allow the conceptualization of geologic relations in an interactive environment, strengthening the ability to understand and present tectonic and structural geologic models. We integrated the data available in the literature (wells, maps, cross-sections) for the geological structure of the Eastern Romania, comprising the Eastern Carpathians Orogen and its foreland. The subducting East European plate generated the Eastern Carphatians thrusts. Under the Eastern Carpathians, beside East European plate, the Tornquist-Teysseire zone is caught. East European Craton (Proterozoic), Scythian Platform (Paleozoic), North Dobrogean Orogen (Paleozoic) and Moesian Platform (Paleozoic), all neighbor Tornquist-Teysseire zone (Paleozoic), playing the role of foreland for the Eastern Carpathian Orogen. The Eastern Carphatians Orogen has two flysch belts, the Inner Carpathian called Dacides formed in Cretacic deformations and the Outer Carpathian called Moldavides and formed in Late Badenian to Sarmatian deformations. The modelling was performed in Midland Valley's Move software. The boundaries of all the structural units presented above were modelled, together with the faults which are represented on the various osurces used. The created 3D geological model is seen as a tool to better understand and represent the tectonic and structural model of the Eastern ROmania and will also allow a better quantification of the relations between geology and landforms in Eastern Romania.

  13. 3-D seismic improves structural mapping of a gas storage reservoir (Paris basin)

    SciTech Connect

    Huguet, F. ); Pinson, C. )

    1993-09-01

    In the Paris basin, anticlinal structures with closure of no more than 80 m and surface area of a few km[sup 2] are used for underground gas storage. At Soings-en-Sologne, a three-dimensional (3-D) survey (13 km[sup 2]) was carried out over such a structure to establish its exact geometry and to detail its fault network. Various reflectors were picked automatically on the migrated data: the top of the Kimmeridgian, the top of the Bathoinian and the base of the Hettangian close to the top of the reservoir. The isochron maps were converted into depth using data from 12 wells. Horizon attributes (amplitude, dip, and azimuth) were used to reconstruct the fault's pattern with much greater accuracy than that supplied by interpretation from previous two-dimensional seismic. The Triassic and the Jurassic are affected by two systems of conjugate faults (N10-N110, inherited from the Hercynian basement and N30-N120). Alternating clay and limestone are the cause of numerous structural disharmonies, particularly on both sides of the Bathonian. Ridges associated with N30-N120 faults suggest compressive movements contemporaneous with the tertiary events. The northern structure in Soings-en-Sologne thus appear to be the result of polyphased tectonics. Its closure (25 m), which is associated either with dips or faults, is described in detail by 3-D seismic, permitting more accurate forecast of the volume available for gas storage.

  14. Error analysis for creating 3D face templates based on cylindrical quad-tree structure

    NASA Astrophysics Data System (ADS)

    Gutfeter, Weronika

    2015-09-01

    Development of new biometric algorithms is parallel to advances in technology of sensing devices. Some of the limitations of the current face recognition systems may be eliminated by integrating 3D sensors into these systems. Depth sensing devices can capture a spatial structure of the face in addition to the texture and color. This kind of data is yet usually very voluminous and requires large amount of computer resources for being processed (face scans obtained with typical depth cameras contain more than 150 000 points per face). That is why defining efficient data structures for processing spatial images is crucial for further development of 3D face recognition methods. The concept described in this work fulfills the aforementioned demands. Modification of the quad-tree structure was chosen because it can be easily transformed into less dimensional data structures and maintains spatial relations between data points. We are able to interpret data stored in the tree as a pyramid of features which allow us to analyze face images using coarse-to-fine strategy, often exploited in biometric recognition systems.

  15. Comparative 3D Genome Structure Analysis of the Fission and the Budding Yeast

    PubMed Central

    Gong, Ke; Tjong, Harianto; Zhou, Xianghong Jasmine; Alber, Frank

    2015-01-01

    We studied the 3D structural organization of the fission yeast genome, which emerges from the tethering of heterochromatic regions in otherwise randomly configured chromosomes represented as flexible polymer chains in an nuclear environment. This model is sufficient to explain in a statistical manner many experimentally determined distinctive features of the fission yeast genome, including chromatin interaction patterns from Hi-C experiments and the co-locations of functionally related and co-expressed genes, such as genes expressed by Pol-III. Our findings demonstrate that some previously described structure-function correlations can be explained as a consequence of random chromatin collisions driven by a few geometric constraints (mainly due to centromere-SPB and telomere-NE tethering) combined with the specific gene locations in the chromosome sequence. We also performed a comparative analysis between the fission and budding yeast genome structures, for which we previously detected a similar organizing principle. However, due to the different chromosome sizes and numbers, substantial differences are observed in the 3D structural genome organization between the two species, most notably in the nuclear locations of orthologous genes, and the extent of nuclear territories for genes and chromosomes. However, despite those differences, remarkably, functional similarities are maintained, which is evident when comparing spatial clustering of functionally related genes in both yeasts. Functionally related genes show a similar spatial clustering behavior in both yeasts, even though their nuclear locations are largely different between the yeast species. PMID:25799503

  16. Linear-Time Protein 3-D Structure Searching with Insertions and Deletions

    NASA Astrophysics Data System (ADS)

    Shibuya, Tetsuo; Jansson, Jesper; Sadakane, Kunihiko

    It becomes more and more important to search for similar structures from molecular 3-D structure databases in the structural biology of the post genomic era. Two molecules are said to be similar if the RMSD (root mean square deviation) of the two molecules is less than or equal to some given constant bound. In this paper, we consider an important, fundamental problem of finding all the similar substructures from 3-D structure databases of chain molecules (such as proteins), with consideration of indels (i.e., insertions and deletions). The problem has been believed to be very difficult, but its computational difficulty has not been well known. In this paper, we first show that the same problem in arbitrary dimension is NP-hard. Moreover, we also propose a new algorithm that dramatically improves the average-case time complexity for the problem, in case the number of indels k is bounded by some constant. Our algorithm solves the above problem in average O(N) time, while the time complexity of the best known algorithm was O(Nm k + 1), for a query of size m and a database of size N.

  17. Crustal structure of Europe, Greenland, and North Atlantics: Synthesis and analysis

    NASA Astrophysics Data System (ADS)

    Artemieva, I. M.; Thybo, H.

    2012-04-01

    We use a new regional crustal database to compare regional and global crustal models for the area 70W-62E, 30N-85N; this region encompasses all of Europe from Svalbard in the north to the Mediterranean in the south and the Ural mountains in the east, as well as Iceland, Greenland, and the North Atlantic region including the Baffin Bay and the Labrador sea. Our new crustal database is compilation "from scratch" of all available seismic data for the region, acquired and interpreted from the late 1960-ies until present. The new database is based on ca. 200 seismic surveys reported in ca. 400 publications and includes the results of seismic reflection, refraction and receiver functions studies, but excludes unreliable constraints, such as based on seismic interpolations, gravity modelling, or tectonic similarities. The new regional crustal model comprises detailed and reliable information on the seismic structure of the crust for most of the tectonic structures of the region and allows for examination of spatial correlations with tectonic and geological structures. We show that several widely accepted hypotheses about crustal structure of the continents are not supported by regional seismic data. In particular, the Archean crust of the East European craton, which is 40-45 km thick (locally >50 km) and has a thick (10-25 km thick) high-velocity lower crust, is similar to the Proterozoic crust both in thickness and in structure. Regional seismic data also disagree with the global averages for structure of the continental crust of different tectonic types: there is not a single tectonic structure in the region that matches global averages neither in the crustal thickness nor in the average crustal Vp velocity. As a result, the regional crustal model averaged on 2x2 deg or 5x5 deg grid is also in striking contrast with global crustal models CRUST2.0 and CRUST5.1. Significant differences between regional and global models in the crustal velocities and thickness of

  18. Traversing and labeling interconnected vascular tree structures from 3D medical images

    NASA Astrophysics Data System (ADS)

    O'Dell, Walter G.; Govindarajan, Sindhuja Tirumalai; Salgia, Ankit; Hegde, Satyanarayan; Prabhakaran, Sreekala; Finol, Ender A.; White, R. James

    2014-03-01

    Purpose: Detailed characterization of pulmonary vascular anatomy has important applications for the diagnosis and management of a variety of vascular diseases. Prior efforts have emphasized using vessel segmentation to gather information on the number or branches, number of bifurcations, and branch length and volume, but accurate traversal of the vessel tree to identify and repair erroneous interconnections between adjacent branches and neighboring tree structures has not been carefully considered. In this study, we endeavor to develop and implement a successful approach to distinguishing and characterizing individual vascular trees from among a complex intermingling of trees. Methods: We developed strategies and parameters in which the algorithm identifies and repairs false branch inter-tree and intra-tree connections to traverse complicated vessel trees. A series of two-dimensional (2D) virtual datasets with a variety of interconnections were constructed for development, testing, and validation. To demonstrate the approach, a series of real 3D computed tomography (CT) lung datasets were obtained, including that of an anthropomorphic chest phantom; an adult human chest CT; a pediatric patient chest CT; and a micro-CT of an excised rat lung preparation. Results: Our method was correct in all 2D virtual test datasets. For each real 3D CT dataset, the resulting simulated vessel tree structures faithfully depicted the vessel tree structures tha