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Sample records for 3d crustal structure

  1. NACr14: A 3D model for the crustal structure of the North American Continent

    NASA Astrophysics Data System (ADS)

    Tesauro, Magdala; Kaban, Mikhail K.; Mooney, Walter D.; Cloetingh, Sierd

    2014-09-01

    Based on the large number of crustal seismic experiments carried out in the last decades we create NACr14, a 3D crustal model of the North American continent at a resolution of 1° × 1°. We present maps of thickness and average velocities of the main layers that comprise the North American crystalline crust, obtained from the most recent seismic crustal models within the USGS crustal structure database. However, the crustal data are unevenly distributed and in some cases discrepancies exist between published models. In order to construct a consistent 3D crustal model with three layers in the crystalline crust, we refrained from a direct interpolation of the crustal seismic parameters in the database. Instead, we implemented the following sequence of steps: 1. Definition of the geometry of the main tectonic provinces of North America; 2. Selection and evaluation of the reliability of seismic crustal models in the database; 3. Estimation of the P-wave seismic velocity and thickness of the upper, middle and lower crust for each tectonic province; 4. Estimation of the interpolated Pn velocity distribution. The resulting average velocity of the crystalline crust is mostly consistent with that of the seismic points. The main variations of the structure of the crystalline crust of North America displayed in the model can be related to its tectonic evolution. The model, available in a digital form, can be used in various geophysical applications, such as the correction for the crustal effects in gravity and seismic tomography and models of dynamic topography, in order to detect heterogeneities characterizing the underlying upper mantle.

  2. 3D crustal and lithospheric structure of the Pyrenean orogenic wedge

    NASA Astrophysics Data System (ADS)

    Theunissen, Thomas; Chevrot, Sébastien; Sylvander, Matthieu; Monteiller, Vadim; Villasenor, Antonio; Benahmed, Sébastien; Calvet, Marie

    2013-04-01

    The Pyrenean orogenic wedge is the consequence of the collision between the Iberian microplate and the southwesternmost part of the Eurasian plate from 55 to 25 Ma (Eocene to Oligocene). The shortening began since Late Cretaceous, about 100 My ago, leading to about 75 km from the west to 125 km to the east of continental crustal shortening. Before this period of time, the region was characterized by a sedimentary basin associated with a very important thinning that later controlled the deformation during the shortening process. Mantle outcrops are therefore present along and north of the North Pyrenean Fault with a scattered localization to the west toward the Mauleon basin. Today, the horizontal deformation rate is very low and the recent seismicity, mainly normal faulting mechanisms, is certainly caused by coupling between erosion and isostatic readjustments. Images from seismic reflection, gravity modeling, local and teleseismic seismic waves inversions and magnetotellurics inversions are in agreement with the subduction of Iberia beneath Aquitania. The 3D crustal structure reveals the presence of an important thickening of the continental crust associated with the subduction of the Iberian lower crust through the north beneath Aquitania at the favor of a detachment. Lateral variations of the geometry (including that of the Moho) and the wave propagation properties are important. In order to better analyze waveforms from local, regional or teleseismic earthquakes and to better constrain the geodynamical evolution of the Pyrenean chain over the time, PYROPE and TOPO-IBERIA projects were born. Two temporary seismic arrays (using broadband seismometers), on the French and Spanish sides, have been deployed between 2010 and 2013. We present here preliminary results on 3D crustal structures (approximately in the window 40° N-45° N and -4° E and 5° E) from arrival-times of about 20000 earthquakes recorded at about 200 seismic stations between 1978 and 2012

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. Crustal density structure in northwestern South America derived from analysis and 3-D modeling of gravity and seismicity data

    NASA Astrophysics Data System (ADS)

    Sanchez-Rojas, J.; Palma, M.

    2014-11-01

    This paper presents a three-dimensional (3-D) interpretation of new gravity and seismicity datasets for northern South America. A 3-D forward density model was constructed on the basis of deep wide-angle seismic refraction sections, Moho depth from receiver functions, and surface geology. Density values were estimated from published borehole data for sediments by using empirical velocity-density functions and considering mineralogical-chemical composition variations under typical pressure-temperature conditions for upper and lower crustal rocks. The modeled 3-D density structure was kept as simple as possible. The continental and oceanic plates were formed by two sedimentary bodies, one crustal body, and one mantle lithosphere body overlying a sub-lithospheric mantle. The Caribbean plate was modeled with an atypical crustal thickness of ~ 18 km (including sediments). The geometry of the Caribbean plate was modeled using a combination of gravity modeling and analyses of the seismicity and focal-mechanism solutions. Intermediate seismicity and the orientation of the T-axes appeared aligned along the predicted position of the slab. As a result, the estimated slab dip angle under Maracaibo and the Mérida Andes was ~ 15° and increases up to ~ 20° after 100 km depth. The model shows two orientations in the slab strike: ~ N150°E ± 5 in western Colombia and southward underneath the Maracaibo block. The modeling results suggest that the northern South American upper and lower crusts are relatively light and the density of the Caribbean crust is typical for an oceanic crust.

  9. 3-D seismic tomographic modelling of the crustal structure of northwestern Svalbard based on deep seismic soundings

    NASA Astrophysics Data System (ADS)

    Czuba, Wojciech

    2016-11-01

    Wide angle refraction and reflection measurements were carried out in the passive continental margin zone of the northwestern Svalbard during several expeditions in 1978-1999. Data from a set of 2-D archival and modern seismic profiles recorded in-line and off-line, and from an additional permanent seismic station, were altogether used for seismic modelling of the crustal structure of the study area. Seismic arrivals (airgun and chemical explosive sources) were recorded by land (onshore) seismic stations, ocean bottom seismometers (OBS), and ocean bottom hydrophone stations (OBH). Good quality refracted and reflected P waves have provided an excellent data base for a seismic modelling. Chemical explosive sources were recorded even up to 300 km distances. The 3-D tomographic inversion method was applied. The results are comparable to the earlier 2-D modelling. Additional off-line information allowed to develop a 3-D image of the crustal structure. The continental crust thins to the west and north. A minimum depth of about 6 km to the Moho interface was determined east of the Molloy Deep and in the Knipovich Ridge. The Moho discontinuity deepens down to about 30 km below the continental crust of Spitsbergen.

  10. 3-D seismic tomographic modelling of the crustal structure of northwestern Svalbard based on deep seismic soundings

    NASA Astrophysics Data System (ADS)

    Czuba, Wojciech

    2017-01-01

    Wide angle refraction and reflection measurements were carried out in the passive continental margin zone of the northwestern Svalbard during several expeditions in 1978-1999. Data from a set of 2-D archival and modern seismic profiles recorded in-line and off-line, and from an additional permanent seismic station, were altogether used for seismic modelling of the crustal structure of the study area. Seismic arrivals (airgun and chemical explosive sources) were recorded by land (onshore) seismic stations, ocean bottom seismometers (OBS), and ocean bottom hydrophone stations (OBH). Good quality refracted and reflected P waves have provided an excellent data base for a seismic modelling. Chemical explosive sources were recorded even up to 300 km distances. The 3-D tomographic inversion method was applied. The results are comparable to the earlier 2-D modelling. Additional off-line information allowed to develop a 3-D image of the crustal structure. The continental crust thins to the west and north. A minimum depth of about 6 km to the Moho interface was determined east of the Molloy Deep and in the Knipovich Ridge. The Moho discontinuity deepens down to about 30 km below the continental crust of Spitsbergen.

  11. 3D crustal structure of the Alpine belt and foreland basins as imaged by ambient-noise surface wave

    NASA Astrophysics Data System (ADS)

    Molinari, Irene; Morelli, Andrea; Cardi, Riccardo; Boschi, Lapo; Poli, Piero; Kissling, Edi

    2016-04-01

    We derive a 3-D crustal structure (S wave velocity) underneath northern Italy and the wider Alpine region, from an extensive data set of measurements of Rayleigh-wave phase- and group-velocities from ambient noise correlation among all seismographic stations available to date in the region, via a constrained tomographic inversion made to honor detailed active source reflection/refraction profiles and other geological information. We first derive a regional-scale surface wave tomography from ambient-noise-based phase- and group- surface wave velocity observations (Verbeke et al., 2012). Our regional 3D model (Molinari et al., 2015) shows the low velocity area beneath the Po Plain and the Molasse basin; the contrast between the low-velocity crust of the Adriatic domain and the high-velocity crust of the Tyrrhenian domain is clearly seen, as well as an almost uniform crystalline crust beneath the Alpine belt. However, higher frequency data can be exploited to achieve higher resolution images of the Po Plain and Alpine foreland 3D crustal structure. We collected and analyze one year of noise records (2011) of ~100 North Italy seismic broadband stations, we derive the Green functions between each couple of stations and we measure the phase- and group-Rayleigh wave velocity. We conduct a suite of linear least squares inversion of both phase- and group-velocity data, resulting in 2-D maps of Rayleigh-wave phase and group velocity at periods between 3 and 40s with a resolution of 0.1x0.1 degrees. The maps are then inverted to get the 3D structure with unprecedented details. We present here our results, we compare them with other studies, and we discuss geological/geodynamical implications. We believe that such a model stands for the most up-to-date seismological information on the crustal structure of the Alpine belt and foreland basins, and it can represent a reliable reference for further, more detailed, studies to come, based on the high seismograph station density

  12. 3-D crustal and uppermost mantle structure beneath NE China revealed by ambient noise adjoint tomography

    NASA Astrophysics Data System (ADS)

    Liu, Yaning; Niu, Fenglin; Chen, Min; Yang, Wencai

    2017-03-01

    We construct a new 3-D shear wave speed model of the crust and the uppermost mantle beneath Northeast China using the ambient noise adjoint tomography method. Without intermediate steps of measuring phase dispersion, the adjoint tomography inverts for shear wave speeds of the crust and uppermost mantle directly from 6-40 s waveforms of Empirical Green's functions (EGFs) of Rayleigh waves, which are derived from interferometry of two years of ambient noise data recorded by the 127 Northeast China Extended Seismic Array stations. With an initial 3-D model derived from traditional asymptotic surface wave tomography method, adjoint tomography refines the 3-D model by iteratively minimizing the frequency-dependent traveltime misfits between EGFs and synthetic Green's functions measured in four period bands: 6-15 s, 10-20 s, 15-30 s, and 20-40 s. Our new model shows shear wave speed anomalies that are spatially correlated with known tectonic units such as the Great Xing'an range and the Changbaishan mountain range. The new model also reveals low wave speed conduits in the mid-lower crust and the uppermost mantle with a wave speed reduction indicative of partial melting beneath the Halaha, Xilinhot-Abaga, and Jingpohu volcanic complexes, suggesting that the Cenozoic volcanism in the area has a deep origin. Overall, the adjoint tomographic images show more vertically continuous velocity anomalies with larger amplitudes due to the consideration of the finite frequency and 3-D effects.

  13. 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

  14. Upper Crustal Structure above Off-axis Magma Lenses at RIDGE-2000 East Pacific Rise Integrated Study Site from 3D Multichannel Seismic Reflection Data

    NASA Astrophysics Data System (ADS)

    Han, S.; Carbotte, S. M.; Carton, H. D.; Newman, K. R.; Canales, J.; Nedimovic, M. R.

    2010-12-01

    The 2008 multi-streamer 3D seismic reflection experiment conducted aboard the R/V Marcus Langseth at the RIDGE-2000 East Pacific Rise Integrated Study Site reveals prominent near-axis crustal reflectors on both the east and west flanks of the ridge crest which are interpreted as off-axis melt lenses (OAML) injected at mid-crustal levels. These OAML are probable sites of off-axis volcanism and provide potential heat sources for localized hydrothermal circulation on the ridge flanks, which we speculate may affect off-axis upper crustal structure. To investigate the effect of OAML on the upper crustal structure, we choose two across-axis lines above a prominent OAML on the east flank of the ridge that is present in the southernmost part of our study area: Line 1428P across the middle part of the OAML near 9° 38’N and Line 1476P across the northern end of this OAML near 9° 39’N. Initial analysis includes 2D processing to produce seismic reflection images for each line and 1D travel time modeling on CMP super gathers to characterize Layer 2A and upper Layer 2B velocity structure. Comparison of seismic reflection images and upper crustal velocity structure for the two lines shows a decrease in Layer 2A thickness by 150m and a decrease in the uppermost 2B velocity by 10-20% above the central portion of OAML. We attribute these local anomalies to alteration associated with off-axis hydrothermal circulation driven by the OAML where enhanced precipitation of alteration minerals may seal porosity within lowermost Layer 2A, converting it to lower velocity uppermost Layer 2B. To further constrain the velocity structure of Layer 2A and Layer 2B, we conduct 2D P-wave tomography with downward continued shot gathers along the studied lines (Harding et al, 2007). The downward continued shot gathers simulate seismic sources and receivers located near the seafloor, and therefore provide travel time information from near-offset refractions that are normally obscured by the

  15. 3D crustal velocity structure beneath the broadband seismic array in the Gyeongju area of Korea by receiver function analyses

    NASA Astrophysics Data System (ADS)

    Lee, Dong Hun; Lee, Jung Mo; Cho, Hyun-Moo; Kang, Tae-Seob

    2016-10-01

    A temporary seismic array was in operation between October 2010 and March 2013 in the Gyeongju area of Korea. Teleseismic records of the seismic array appropriate for receiver function analysis were collected, and selected seismograms were split into five groups based on epicenters-the Banda-Molucca, Sumatra, Iran, Aleutian, and Vanuatu groups. 1D velocity structures beneath each seismic station were estimated by inverting the stacked receiver functions for possible groups. The inversion was done by applying a genetic algorithm, whereas surface wave dispersion data were used as constraints to avoid non-uniqueness in the inversion. The composite velocity structure was constructed by averaging the velocity structures weighted by the number of receiver functions used in stacking. The uncertainty analysis for the velocity structures showed that the average of 95% confidence intervals was ± 0.1 km/s. The 3D velocity structure was modeled through interpolation of 1D composite velocity structures. Moho depths were determined in each composite velocity structure based on the AK135-F S-wave velocity model, and the depths were similar to the H-κ analysis results. The deepest Moho depth in the study area was found to be 31.9 km, and the shallowest, was 25.9 km. The Moho discontinuity dips in a southwestward direction beneath the area. A low velocity layer was also detected between 4 and 14 km depth. Adakitic intrusions and/or a high geothermal gradient appear to be the causes of this low velocity layer. The 3D velocity structure can be used to reliably assess seismic hazards in this area.

  16. 3-D crustal structure along the North Anatolian Fault Zone in north-central Anatolia revealed by local earthquake tomography

    NASA Astrophysics Data System (ADS)

    Yolsal-Ćevikbilen, Seda; Biryol, C. Berk; Beck, Susan; Zandt, George; Taymaz, Tuncay; Adıyaman, Hande E.; Özacar, A. Arda

    2012-03-01

    3-D P-wave velocity structure and Vp/Vs variations in the crust along the North Anatolian Fault Zone (NAFZ) in north-central Anatolia were investigated by the inversion of local P- and S-wave traveltimes, to gain a better understanding of the seismological characteristics of the region. The 3-D local earthquake tomography inversions included 5444 P- and 3200 S-wave readings obtained from 168 well-located earthquakes between 2006 January and 2008 May. Dense ray coverage yields good resolution, particularly in the central part of the study area. The 3-D Vp and Vp/Vs tomographic images reveal clear correlations with both the surface geology and significant tectonic units in the region. We observed the lower limit of the seismogenic zone for north-central Anatolia at 15 km depth. Final earthquake locations display a distributed pattern throughout the study area, with most of the earthquakes occurring on the major splays of the NAFZ, rather than its master strand. We identify three major high-velocity blocks in the mid-crust separated by the İzmir-Ankara-Erzincan Suture and interpret these blocks to be continental basement fragments that were accreted onto the margin following the closure of Neo-Tethyan Ocean. These basement blocks may have in part influenced the rupture propagations of the historical 1939, 1942 and 1943 earthquakes. In addition, large variations in the Vp/Vs ratio in the mid-crust were observed and have been correlated with the varying fluid contents of the existing lithologies and related tectonic structures.

  17. Rift processes and crustal structure of the Amundsen Sea Embayment, West Antarctica, from 3D potential field modelling

    NASA Astrophysics Data System (ADS)

    Kalberg, Thomas; Gohl, Karsten; Eagles, Graeme; Spiegel, Cornelia

    2015-12-01

    The Amundsen Sea Embayment of West Antarctica is of particular interest as it provides critical geological boundary conditions in better understanding the dynamic behavior of the West Antarctic Ice Sheet, which is undergoing rapid ice loss in the Amundsen Sea sector. One of the highly debated hypothesis is whether this region has been affected by the West Antarctic Rift System, which is one of the largest in the world and the dominating tectonic feature in West Antarctica. Previous geophysical studies suggested an eastward continuation of this rift system into the Amundsen Sea Embayment. This geophysical study of the Amundsen Sea Embayment presents a compilation of data collected during two RV Polarstern expeditions in the Amundsen Sea Embayment of West Antarctica in 2006 and 2010. Bathymetry and satellite-derived gravity data of the Amundsen Sea Embayment complete the dataset. Our 3-D gravity and magnetic models of the lithospheric architecture and development of this Pacific margin improve previous interpretations from 2-D models of the region. The crust-mantle boundary beneath the continental rise and shelf is between 14 and 29 km deep. The imaged basement structure can be related to rift basins within the Amundsen Sea Embayment, some of which can be interpreted as products of the Cretaceous rift and break-up phase and some as products of later propagation of the West Antarctic Rift System into the region. An estimate of the flexural rigidity of the lithosphere reveals a thin elastic thickness in the eastern embayment which increases towards the west. The results are comparable to estimates in other rift systems such as the Basin and Range province or the East African Rift. Based on these results, we infer an arm of the West Antarctic Rift System is superposed on a distributed Cretaceous rift province in the Amundsen Sea Embayment. Finally, the embayment was affected by magmatism from discrete sources along the Pacific margin of West Antarctica in the Cenozoic.

  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. Crustal and upper mantle 3D shear wave velocity structure of the High Lava Plains, Oregon, determined from ambient noise tomography

    NASA Astrophysics Data System (ADS)

    Hanson-Hedgecock, S.; Wagner, L.; Fouch, M. J.; James, D. E.

    2011-12-01

    We present the results of inversions for 3D shear velocity structure of the crust and uppermost mantle beneath the High Lava Plains, Oregon using data from ~300 broadband stations of the High Lava Plains seismic experiment and the EarthScope/USArray Transportable Array (TA). The High Lava Plains (HLP) is a WNW progressive silicic volcanism, initiated ~14.5 Ma near the Owyhee Plateau and is currently active at the Newberry caldera. The Yellowstone Snake River Plain (YSRP) volcanic track is temporally contemporaneous with the HLP, but trends to the northeast, parallel to North American plate motion. The cause of volcanism along the HLP is debated and has been variously attributed to Basin and Range extension, back-arc extension, rollback of the subducting Juan de Fuca plate, and an intra-continental hotspot/plume source. Additionally the relationship between the HLP, YSRP, and Columbia River Basalts (CRB), the three major post-17Ma intracontinental volcanic provinces of the Pacific Northwest, is not well understood. The 3D shear velocity structure of the crust and uppermost mantle to ~65km depth is determined from fundamental mode Rayleigh wave ambient noise phase velocity maps at periods up to 40s. The use of ambient noise tomography with the dense station spacing of the combined High Lava Plains seismic experiment and the EarthScope/USArray Transportable Array (TA) datasets allows the shallow structure of the High Lava Plains to be imaged in finer detail than previous ANT studies that focused on the entire western United States. In the crust, low velocities in central Oregon are observed in association with the Brothers Fault Zone, Jordan and Diamond Craters and Steens Mountain regions in addition to the strong low velocity zone associated with the Cascades to the west. To the east of the HLP, low velocities are observed to about 10km depth in the western SRP. In the eastern SRP we observe a shallow veneer of low velocities underlain by a ~10km thick high velocity

  20. 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.

  1. 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

  2. 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

  3. The deep crustal structure of the mafic-ultramafic Seiland Igneous Province of Norway from 3-D gravity modelling and geological implications

    NASA Astrophysics Data System (ADS)

    Pastore, Zeudia; Fichler, Christine; McEnroe, Suzanne A.

    2016-12-01

    The Seiland Igneous Province (SIP) is the largest complex of mafic and ultramafic intrusions in northern Fennoscandia intruded at ca. 580-560 Ma. The depth extent and the deep structure of the SIP are mainly unknown apart from three profiles modelled by gravity and refraction seismic data. Utilizing 3-D gravity modelling, a complex model of the deep subsurface structure of the SIP has been developed. The structure is presented in a multiprofile model ranging from the surface to the Moho. The mafic/ultramafic rocks of the SIP are modelled with densities of 3100 and 3300 kg m-3, the surrounding rocks by densities of 2700 and 2900 kg m-3 for upper and lower crust, respectively. This density model explains the pronounced positive Bouguer gravity anomaly of up to 100 mGal above background. Its minimum volume is estimated from the subsurface model to 17 000 km3 and as such we revise downwards the earlier estimations of 25 000 km3. The new subsurface model suggests that most of the SIP has a thickness between 2 and 4 km. An area with roots in an annular pattern is found and two deep-reaching roots have been identified located below the islands of Seiland and Sørøy. The depth of these roots is estimated to approximatively 9 km. The SIP is presently interpreted to be in the Caledonian Kalak Nappe Complex and the roots depth constrains its minimum thickness which is larger than earlier estimated. Furthermore, the rather undisturbed shape of the annular root pattern indicates that the SIP has not been subjected to strong tectonic reworking during the Caledonian orogeny.

  4. 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.

  5. Crustal Seismicity and 3-D Velocity Structure in the Principal Cordillera of Central Chile (33- 34.5 S, 69.5-71 W): Implications on Andean Geodynamic and Seismic Hazard

    NASA Astrophysics Data System (ADS)

    Pardo, M.; Monfret, T.; Vera, E.; Yañez, G.; Eisenberg, A.

    2007-12-01

    Based on data from a dense local temporary seismological network, crustal seismicity is characterized, and a 3- D body wave velocity structure is obtained by tomographic inversion down to the subducted slab. In the framework of Fondecyt 1050758, GeoAzur-IRD and ACT-18 projects, 35 broadband and short period instruments, were deployed in the studied zone for 135 days recording in continuous mode. At this zone the Andean active volcanism reappears after a gap of volcanic activity since late Miocene occurring north of 33 S due to the Central Chile flat slab subduction zone. Crustal seismicity in the depth range 0-30 km is well correlated with known geological faults that become now important in the assessment of the regional seismic hazard. This seismicity also clusters around the giant porphyry cooper deposits in the region (Rio Blanco, El Teniente), and are neither related to mine-blasts nor induced by mining activity. Moreover, the local 3-D velocity structure shows that the zone surrounding each deposit is characterized by high Vp/Vs greater than 1.8, which may indicate fluid phases located in the weakest and more fractured zone of the crust. The body wave velocity pattern shown at depth by the local tomography indicates channels of high Vp/Vs connecting the subducted slab with the surface at places where active volcanism is present, suggesting upward migration of hydrous or melted rocks. This pattern agrees with the one observed with a previous regional tomography that includes this zone, while this Vp/Vs pattern tends to be horizontal at the flat slab zone. At depths of 20-25 km, a layer of high Vp/Vs is observed beneath the Andes Cordillera that could be associated to changes in the rheological properties between the upper and lower crust, or to accumulation of magma. The average stress tensor, derived from focal mechanisms, indicate that the Andean zone is under compression in the plate convergence direction.

  6. GIA-Induced 3-D Crustal Velocities Predicted Using a New Generation of Viscoelastic Earth Models

    NASA Astrophysics Data System (ADS)

    Mitrovica, J. X.; Latychev, K.; Tamisiea, M. E.; Tromp, J.; Milne, G. A.

    2004-05-01

    In recent work we have described a new finite-volume, time-domain numerical scheme for predicting the response of a complex (Maxwell) viscoelastic Earth model to arbitrary surface mass loads. The method permits the incorporation of 3-D variations in mantle viscoelastic structure including, for example, heterogeneities in elastic plate strength and mantle viscosity. To address these complexities numerically, we have developed our code for a distributed (parallel) computer environment such as a Beowulf PC cluster. In this talk we apply the numerical formulation to compute a suite of predictions of present-day 3-D crustal deformation rates driven by the glacial isostatic adjustment process (GIA). These predictions are generated using an input global ice model and an ocean load computed using a solution to the governing `sea-level equation'. The latter is obtained in a numerical calculation that utilizes the same space-time discretization as in the main solver. Our goal is to assess the sensitivity of previous predictions of GIA-induced 3-D crustal rates based on spherically symmetric Earth models to the introduction of: (1) elastic plate thickness variations within oceanic regions and across the ocean-continent interface; and (2) variations in mantle viscosity inferred, indirectly, from a tomographic model of seismic velocity heterogeneity.

  7. A new model of the Arctic crustal thickness from 3D gravity inversion

    NASA Astrophysics Data System (ADS)

    Lebedeva-Ivanova, N. N.; Gaina, C.; Minakov, A.; Kashubin, S.

    2015-12-01

    The remarkable increase of new data collections and compilations for the Arctic region during the last decade motivate for a re-evaluation of our knowledge about the crustal structure and the tectonic evolution of the Arctic basins. 3D forward and inverse gravity modelling methods in the spectral domain (Minakov et al. 2012); lithosphere thermal gravity anomaly correction (Alvey et al., 2008); a vertical density variation for the sedimentary layer and lateral crustal variation density are integrated in the algorithm for derive the crustal thickness of the High Arctic region. Recently updated grids of bathymetry (Jakobsson et al., 2012), gravity anomaly (Gaina et al, 2011) and dynamic topography (Spasojevic & Gurnis, 2012) were used as input data for the algorithm. TeMAr sedimentary thickness grid (Petrov et al., 2015) was modified according to the most recent published seismic data, and was re-gridded and utilized as input data. Other input parameters for the algorithm were calibrated using seismic crustal scale profiles. Derived crustal thickness and Moho depth grids cover the area northward from 66° N and fit within a few kilometres with seismic crustal models for the most parts of the High Arctic region. Greater misfit in Moho depth between our results and seismic study (Chain & Lebedeva-Ivanova, 2015) under the northern Canada Basin suggest exceptional property of crust or/and mantel in this part of the Basin. Assumed mantle density of 3.25 kg/cm3provide the best fit for the region; it may indicate pervasive subcontinental lithospheric mantle (Goldstein et al., 2008) under the whole Arctic region. New results show a possible crustal connection between the Alpha and the Lomonosov ridges near the Canadian margin. The deepest Moho depth of c.34 km for Alpha-Mendeleev Ridge System is observed under the southern Mendeleev Ridge. The derived crustal thickness and Moho depth show a substantial improvement from the publicly available grids (CRUST1 (Laske et al., 2013

  8. Seismic body-wave interferometry using noise autocorrelations for crustal structure and a tutorial on 3D seismic processing and imaging using Madagascar

    NASA Astrophysics Data System (ADS)

    Olejnik, Peter

    Seismic body-wave interferometry is applied to selected seismic stations from the USArray Earthscope Transportable Array (TA) by autocorrelating ambient seismic noise recordings to construct effective zero-offset reflection seismograms. The robustness of the auto-correlations of noise traces is first tested on a TA station in Nevada where body-wave reflections similar to those found in an earlier study are identified. This approach is then applied to several TA stations in the central U.S., and the results are compared with synthetic data. Different stacking time periods are then examined to find the shortest time intervals that provide stable correlation stacks. A tutorial on 3D seismic processing and imaging using the Madagascar open-source software package is next presented for educational purposes. The 3D Teapot Dome seismic data set is examined to illustrate the processing and imaging steps. A number of processing steps are applied to the data set, including amplitude gaining, muting, deconvolution, static corrections, velocity analysis, normal moveout (NMO) correction, and stacking. Post-stack time and depth migrations are then performed on the stacked data along with post-migration f-x deconvolution.

  9. 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.

  10. 3D structured illumination microscopy

    NASA Astrophysics Data System (ADS)

    Dougherty, William M.; Goodwin, Paul C.

    2011-03-01

    Three-dimensional structured illumination microscopy achieves double the lateral and axial resolution of wide-field microscopy, using conventional fluorescent dyes, proteins and sample preparation techniques. A three-dimensional interference-fringe pattern excites the fluorescence, filling in the "missing cone" of the wide field optical transfer function, thereby enabling axial (z) discrimination. The pattern acts as a spatial carrier frequency that mixes with the higher spatial frequency components of the image, which usually succumb to the diffraction limit. The fluorescence image encodes the high frequency content as a down-mixed, moiré-like pattern. A series of images is required, wherein the 3D pattern is shifted and rotated, providing down-mixed data for a system of linear equations. Super-resolution is obtained by solving these equations. The speed with which the image series can be obtained can be a problem for the microscopy of living cells. Challenges include pattern-switching speeds, optical efficiency, wavefront quality and fringe contrast, fringe pitch optimization, and polarization issues. We will review some recent developments in 3D-SIM hardware with the goal of super-resolved z-stacks of motile cells.

  11. Analysis and Simulation of 3D Scattering due to Heterogeneous Crustal Structure and Surface Topography on Regional Phases; Magnitude and Discrimination

    DTIC Science & Technology

    2009-07-07

    inversion technique that is based on different weights for relatively high frequency waveform modeling of Pnl and relatively long period surface waves (Tan...et al., 2006). Pnl and surface waves are also allowed to shift in time to take into account of uncertainties in velocity structure. Joint...inversion of Pnl and surface waves provides better constraints on focal depth as well as source mechanisms. The pure strike-slip mechanism of the earthquake

  12. Venezuela Basin crustal structure

    NASA Astrophysics Data System (ADS)

    Diebold, J. B.; Stoffa, P. L.; Buhl, P.; Truchan, M.

    1981-09-01

    Velocity-depth profiles derived from six two-ship expanding spread experiments, in combination with other geophysical data, define the characteristics of two distinct types of Venezuela Basin crust and the boundary between them. Each two-ship common midpoint reflection/refraction profile is automatically transformed into the τ-p plane, `picked' and interpreted to provide V(Z) functions with appropriate confidence bounds. The results, together with gravity, magnetic, and near-vertical incidence reflection data, reveal a 50,000 km2 triangle of Venezuela Basin crust which resembles normal oceanic crust in a magnetic quiet zone. North and west of this triangle lies the previously defined, thick `Caribbean' crust, having two distinct layers above the M discontinuity. Acoustic basement there appears unusually smooth due to extensive basaltic sills and flows which were cored at Deep Sea Drilling Project sites 146/149(sills), and 150 (flows); also, depths to mantle are greater than normal. Interpretations of near-vertical and wide-angle reflection data show that the extra crustal thickness is due not only to the emplacement of the flows but also to the crust below being somewhat thicker than normal. The boundary between the two crustal areas has a NE-SW trend which parallels the dominant structural and magnetic lineations.This boundary coincides in position, though not in trend, with the previously defined `central Venezuela Basin fault zone'. Further study is required to determine whether this boundary is of tectonic origin or if it represents a change in style of crustal production.

  13. From data to a 3D model: a new method to build a crustal model, applied to Asia

    NASA Astrophysics Data System (ADS)

    Stolk, W.; Kaban, M.; Beekman, F.; Tesauro, M.; Cloetingh, S.

    2012-04-01

    Crustal heterogeneities tend to mask underlying upper mantle heterogeneities. Accurate knowledge of the crustal structure is essential in order to investigate the underlying structures. However, current global crustal models, such as the still widely used Crust 2.0 show large differences with data. Additionally, it is often unclear how these models are created. It is therefore necessary to go back to the data and start a new model from scratch, clearly describing the process from data to model. The inhomogeneous spread of data in the research area provides the researcher with many challenges. In order to obtain a robust 3D model, creative data analysis is required. We have applied our new methodology to estimate the depth to Moho and crustal velocities in Asia, based on seismic data. For the depth to Moho estimation we exploit knowledge of sediments and topography to apply a 'remove-compute-restore' technique, widely used in e.g. gravity field analysis. First the so called adjusted topography is removed from the data, followed by interpolation of the residuals using ordinary kriging and finally the adjusted topography is restored to the model. The crustal velocity structure is estimated by locally fitting velocity depth curves to the available data. Both methods allow us to assess the uncertainty of the model. This can help indicate areas where extra data is required to better constrain our crustal model.

  14. High-resolution imaging of crustal melts using 3D full-waveform seismic inversion

    NASA Astrophysics Data System (ADS)

    Warner, M.; Morgan, J. V.

    2013-12-01

    A newly practical seismic imaging technique, 3D full-waveform inversion (FWI), now has the ability to image zones of melt and melt pathways throughout the crust with a better resolution than any other geophysical method. 3D FWI has recently changed practice within the petroleum industry where it is used to obtain high-resolution high-fidelity models of physical properties in the sub-surface that are both interpreted directly and used to improve the migration of deeper reflections. This technology has been spectacularly successful in improving the imaging of reservoirs beneath shallow heterogeneities produced by, for example, gas clouds, buried fluvial channels, carbonate reefs and salt bodies. During FWI, the sub-surface model is recovered principally by using the low-frequency transmitted, refracted portion of the wavefield which is most sensitive to the macro-velocity structure. In the petroleum industry, these inversions are now routinely performed using long-offset surface-streamer and ocean-bottom data to maximum source-receiver offsets of about 15 km, leading to a maximum penetration depth of around 5 km. Using longer offsets, it is possible to extend this technology to image deeper crustal targets. Localised zones of partial melt produce large changes in p-wave and s-wave properties that are restricted in their spatial extent, and that therefore form ideal targets for 3D FWI. We have performed a suite of tests to explore the use of 3D FWI in imaging melt distribution beneath the active volcano of Montserrat. We built a model of the subsurface using a 3D travel-time tomographic model obtained from the SEA CALIPSO experiment. We added two magma chambers in accordance with a model obtained using surface-elevation changes and geochemical data. We used a wide-angle, wide-azimuth acquisition geometry to generate a fully-elastic synthetic seismic dataset, added noise, and inverted the windowed transmitted arrivals only. We used an elastic code for the forward

  15. 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.

  16. Self assembled structures for 3D integration

    NASA Astrophysics Data System (ADS)

    Rao, Madhav

    Three dimensional (3D) micro-scale structures attached to a silicon substrate have various applications in microelectronics. However, formation of 3D structures using conventional micro-fabrication techniques are not efficient and require precise control of processing parameters. Self assembly is a method for creating 3D structures that takes advantage of surface area minimization phenomena. Solder based self assembly (SBSA), the subject of this dissertation, uses solder as a facilitator in the formation of 3D structures from 2D patterns. Etching a sacrificial layer underneath a portion of the 2D pattern allows the solder reflow step to pull those areas out of the substrate plane resulting in a folded 3D structure. Initial studies using the SBSA method demonstrated low yields in the formation of five different polyhedra. The failures in folding were primarily attributed to nonuniform solder deposition on the underlying metal pads. The dip soldering method was analyzed and subsequently refined. A modified dip soldering process provided improved yield among the polyhedra. Solder bridging referred as joining of solder deposited on different metal patterns in an entity influenced the folding mechanism. In general, design parameters such as small gap-spacings and thick metal pads were found to favor solder bridging for all patterns studied. Two types of soldering: face and edge soldering were analyzed. Face soldering refers to the application of solder on the entire metal face. Edge soldering indicates application of solder only on the edges of the metal face. Mechanical grinding showed that face soldered SBSA structures were void free and robust in nature. In addition, the face soldered 3D structures provide a consistent heat resistant solder standoff height that serve as attachments in the integration of dissimilar electronic technologies. Face soldered 3D structures were developed on the underlying conducting channel to determine the thermo-electric reliability of

  17. 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

  18. 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.

  19. Crustal deformation dynamics and stress evolution during seamount subduction: High-resolution 3-D numerical modeling

    NASA Astrophysics Data System (ADS)

    Ruh, Jonas B.; Sallarès, Valentí; Ranero, César R.; Gerya, Taras

    2016-09-01

    Seamounts or submarine volcanoes frequently collide with the overriding crust along presently active subduction zones locally modifying stress and permanent deformation patterns. Dynamics of this process is not fully understood, and several end-member scenarios of seamount-crust interaction are proposed. Here we use high-resolution 3-D numerical models to investigate evolution of crustal deformation and stress distribution within the upper plate induced by the underthrusting of subducting seamounts. The dynamical effects of the upper plate strength, subduction interface strength, and strain weakening of the crust are investigated. Experiment results demonstrate that characteristic crustal fracturing patterns formed in response to different seamount-crust interaction scenarios. Indenting seamounts strongly deform the overriding plate along a corridor as wide as the underthrusting seamount by constantly shifting subvertical shear zones rooted at the seamount extensions. A reentrant develops during initial seamount collision. A topographic bulge atop the seamount and lateral ridges emerge from further seamount subduction. Obtained stress pattern shows areas of large overpressure above the rearward and large underpressure above the trenchward flank of the seamount. Results of numerical experiments are consistent with seismic reflection images and seismic velocity models of the upper plate in areas of seamount subduction along the Middle America Trench and give important insights into the long-lasting question, whether subducting seamounts and rough seafloor act as barriers or asperities for megathrust earthquakes.

  20. 3D geological modeling of the Trujillo block: Insights for crustal escape models of the Venezuelan Andes

    NASA Astrophysics Data System (ADS)

    Dhont, Damien; Monod, Bernard; Hervouët, Yves; Backé, Guillaume; Klarica, Stéphanie; Choy, José E.

    2012-11-01

    The Venezuelan Andes form a N50°E-trending mountain belt extending from the Colombian border in the SW to the Caribbean Sea in the NE. The belt began to rise since the Middle Miocene in response to the E-W collision between the Maracaibo block to the NW and the Guyana shield belonging to South America to the SE. This oblique collision led to strain partitioning with (1) shortening along opposite-vergent thrust fronts, (2) right-lateral slip along the Boconó fault crossing the belt more or less along-strike and (3) crustal escape of the Trujillo block moving towards the NE in between the Boconó fault and the N-S-striking left-lateral Valera fault. The geology of the Venezuelan Andes is well described at the surface, but its structure at depth remains hypothetic. We investigated the deep geometry of the Mérida Andes by a 3D model newly developed from geological and geophysical data. The 3D fault model is restricted to the crust and is mainly based on the surface data of outcropping fault traces. The final model reveals the orogenic float concept where the mountain belt is decoupled from its underlying lithosphere over a horizontal décollement located either at the upper/lower crust boundary. The reconstruction of the Boconó and Valera faults results in a 3D shape of the Trujillo block, which floats over a mid-crustal décollement horizon emerging at the Boconó-Valera triple junction. Motion of the Trujillo block is accompanied by a widespread extension towards the NE accommodated by normal faults with listric geometries such as for the Motatan, Momboy and Tuñame faults. Extension is explained by the gravitational spreading of the upper crust during the escape process.

  1. 3D Structures of Responsive Nanocompartmentalized Microgels.

    PubMed

    Gelissen, Arjan P H; Oppermann, Alex; Caumanns, Tobias; Hebbeker, Pascal; Turnhoff, Sarah K; Tiwari, Rahul; Eisold, Sabine; Simon, Ulrich; Lu, Yan; Mayer, Joachim; Richtering, Walter; Walther, Andreas; Wöll, Dominik

    2016-11-09

    Compartmentalization in soft matter is important for segregating and coordinating chemical reactions, sequestering (re)active components, and integrating multifunctionality. Advances depend crucially on quantitative 3D visualization in situ with high spatiotemporal resolution. Here, we show the direct visualization of different compartments within adaptive microgels using a combination of in situ electron and super-resolved fluorescence microscopy. We unravel new levels of structural details and address the challenge of reconstructing 3D information from 2D projections for nonuniform soft matter as opposed to monodisperse proteins. Moreover, we visualize the thermally induced shrinkage of responsive core-shell microgels live in water. This strategy opens doors for systematic in situ studies of soft matter systems and their application as smart materials.

  2. Inferential modeling of 3D chromatin structure.

    PubMed

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-04-30

    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.

  3. GPS Measurements of Crustal Motion Indicate 3D GIA Models are Needed to Understand Antarctic Ice Mass Change

    NASA Astrophysics Data System (ADS)

    Konfal, S. A.; Wilson, T. J.; Bevis, M. G.; Kendrick, E. C.; Dalziel, I. W. D.; Smalley, R., Jr.; Willis, M. J.; Heeszel, D.; Wiens, D. A.

    2014-12-01

    Continuous GPS measurements of bedrock crustal motions in response to GIA in Antarctica have been acquired by the Antarctic Network (ANET) component of the Polar Earth Observing Network (POLENET). Patterns of vertical crustal displacements are commonly considered the key fingerprints of GIA, with maximum uplift marking the position of former ice load centers. However, efforts to develop more realistic 3D earth models have shown that the horizontal motion pattern is a more important signature of GIA on a laterally varying earth. Here we provide the first measurements substantiating predictions of a reversal of horizontal motions across an extreme gradient in crustal thickness and mantle viscosity crossing Antarctica. GPS results document motion toward, rather than away from the sites of major ice mass loss in West Antarctica. When compared in a common reference frame, observed crustal motions are not in agreement with predictions from models of GIA. A gradient in crustal velocities, faster toward West Antarctica, is spatially coincident with the rheological boundary mapped from seismic tomographic results. This suggests that horizontal crustal motions are strongly influenced by laterally-varying earth properties, and demonstrates that only 3D earth models can produce reliable predictions of GIA for Antarctica.

  4. Automated modeling of RNA 3D structure.

    PubMed

    Rother, Kristian; Rother, Magdalena; Skiba, Pawel; Bujnicki, Janusz M

    2014-01-01

    This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.

  5. 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

  6. 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.

  7. 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

  8. Microfabricating 3D Structures by Laser Origami

    DTIC Science & Technology

    2011-11-09

    technique generates 3D microstructures by controlled out-of- plane folding of 2D patterns through a variety of laser-based digital fabrication...processes. Digital microfabrication techniques such as laser direct-write (LDW) offer a viable alternative for generating 3D self-folding designs. These...folding at the microscale where manual or mechanized actuation of the smaller struc- tures is not practical. LDW techniques allow micromachining and

  9. 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

  10. 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.

  11. 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

    2016-07-08

    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/.

  12. 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

  13. Three-dimensional (3D) printing of mouse primary hepatocytes to generate 3D hepatic structure

    PubMed Central

    Kim, Yohan; Kang, Kyojin; Jeong, Jaemin; Paik, Seung Sam; Kim, Ji Sook; Park, Su A; Kim, Wan Doo; Park, Jisun

    2017-01-01

    Purpose The major problem in producing artificial livers is that primary hepatocytes cannot be cultured for many days. Recently, 3-dimensional (3D) printing technology draws attention and this technology regarded as a useful tool for current cell biology. By using the 3D bio-printing, these problems can be resolved. Methods To generate 3D bio-printed structures (25 mm × 25 mm), cells-alginate constructs were fabricated by 3D bio-printing system. Mouse primary hepatocytes were isolated from the livers of 6–8 weeks old mice by a 2-step collagenase method. Samples of 4 × 107 hepatocytes with 80%–90% viability were printed with 3% alginate solution, and cultured with well-defined culture medium for primary hepatocytes. To confirm functional ability of hepatocytes cultured on 3D alginate scaffold, we conducted quantitative real-time polymerase chain reaction and immunofluorescence with hepatic marker genes. Results Isolated primary hepatocytes were printed with alginate. The 3D printed hepatocytes remained alive for 14 days. Gene expression levels of Albumin, HNF-4α and Foxa3 were gradually increased in the 3D structures. Immunofluorescence analysis showed that the primary hepatocytes produced hepatic-specific proteins over the same period of time. Conclusion Our research indicates that 3D bio-printing technique can be used for long-term culture of primary hepatocytes. It can therefore be used for drug screening and as a potential method of producing artificial livers. PMID:28203553

  14. RNA Structure: Advances and Assessment of 3D Structure Prediction.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2017-03-30

    Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  15. 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

  16. Quantitative 3D structured illumination microscopy of nuclear structures.

    PubMed

    Kraus, Felix; Miron, Ezequiel; Demmerle, Justin; Chitiashvili, Tsotne; Budco, Alexei; Alle, Quentin; Matsuda, Atsushi; Leonhardt, Heinrich; Schermelleh, Lothar; Markaki, Yolanda

    2017-05-01

    3D structured illumination microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale. This protocol fills an unmet need for the application of 3D-SIM to the technically challenging nuclear environment, and subsequent quantitative analysis of 3D nuclear structures and epigenetic modifications. In addition, it establishes practical guidelines and open-source solutions using ImageJ/Fiji and the TANGO plugin for high-quality and routinely comparable data generation in immunostaining experiments that apply across model systems. From sample preparation through image analysis, the protocol can be executed within one week.

  17. 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

  18. 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.

  19. Electromagnetic 2D/3D Particle-in-Cell simulations of the solar wind interaction with lunar crustal anomalies.

    NASA Astrophysics Data System (ADS)

    Deca, Jan; Lapenta, Giovanni; Lembège, Bertrand; Divin, Andrey; Markidis, Stefano; Amaya, Jorge

    2013-04-01

    We present the first 2D/3D fully kinetic Particle-in-Cell simulations of the solar wind interaction with lunar crustal magnetic anomalies. The simulations are performed using the implicit electromagnetic Particle-in-Cell code iPIC3D [Markidis, Lapenta & Rizwan-uddin, 2010]. Multiscale physics is resolved for all plasma components (heavy ions, protons and electrons) in the code, recently updated with a set of open boundary conditions designed for solar wind-body interactions. We use a dipole to model the crustal anomaly. The dipole center is located outside the computational domain and the boundary representing the lunar surface is modeled as a particle-absorbing plane. Photo-emission from the lunar surface is at this point not included, but will be in future work. We study the behaviour of the dipole model with variable surface magnetic field strength under changing solar wind conditions and confirm that lunar crustal magnetic fields may indeed be strong enough to stand off the solar wind and form a mini-magnetosphere, as suggested by MHD simulations [Harnett & Winglee, 2000, 2002, 2003] and spacecraft observations [Kurata et al., 2005; Halekas et al., 2008; Wieser et al., 2010]. 3D-PIC simulations reveal to be very helpful to analyze the diversion/braking of the particle flux and the characteristics of the resulting particles accumulation. The particle flux to the surface is significantly reduced at the magnetic anomaly, surrounded by a region of enhanced density due to the magnetic mirror effect. Finally we will present preliminary results on the interaction of the solar wind with weaker magnetic anomalies in which highly non-adiabatic interactions are expected.

  20. 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

  1. MSV3d: database of human MisSense Variants mapped to 3D protein structure.

    PubMed

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

  2. Three-dimensional crustal structure beneath the TOR array and effects on teleseismic wavefronts

    NASA Astrophysics Data System (ADS)

    Arlitt, R.; Kissling, E.; Ansorge, J.; TOR Working Group

    1999-12-01

    The temporary seismic station array (TOR) was designed to study the lithosphere-asthenosphere system across the northwestern part of the Trans-European Suture Zone (TESZ) by teleseismic tomography. Teleseismic wavefronts, when propagating through complex crustal structure, undergo severe distortion that may result in travel time residual anomalies of significant amplitude. The inversion of teleseismic travel time residuals for deep structures without accounting for such crustal-related anomalies may erroneously map these travel time anomalies into features at greater depth. In this study we apply a three-dimensional (3-D) technique to estimate effects of a priori known 3-D crustal structure on travel times of teleseismic waves observed at the TOR seismic array across the TESZ to correct for these effects in future tomographic studies. A uniform 3-D crustal model is developed by use of published two-dimensional crustal models from previous active seismic surveys. The parameterization of this 3-D crustal model is designed to adequately represent those crustal structures that mostly influence the propagation of teleseismic wavefronts. The 3-D model includes lateral variation in velocity structure, Moho topography, and large and deep sedimentary basins. The teleseismic forward problem for this local 3-D model is solved by calculation of travel times to the base of the model using a standard whole Earth model and by subsequent propagation of spherical wavefronts using finite difference methods. Travel time calculations for an event near Japan reveal significant lateral variations in the range between -0.3 s and +0.5 s due to crustal structures. Being able to obtain the full travel time field at the surface of the model has the additional advantage of improving the identification and timing of seismic phases observed at the TOR seismic array.

  3. 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.

  4. Combining controlled-source seismology and local earthquake tomography to derive a 3-D crustal model of the western Alpine region

    NASA Astrophysics Data System (ADS)

    Wagner, Michael; Kissling, Edi; Husen, Stephan

    2012-09-01

    We present a newly developed approach of combining controlled-source seismology (CSS) and local earthquake tomography (LET) data to obtain a new 3-D crustal model of the western Alpine region. Our approach combines either data by taking into account the strengths of the individual seismic methods. Our western Alpine 3-D model is primarily based on a well-defined Moho, constrained by CSS and LET data, and includes smooth lateral variations in seismic velocities mainly constrained by LET data, but locally also by CSS data. The consistent combination of results from the two different seismic methods is feasible due to LET Moho elements, as defined by characteristic P-wave velocities and their uncertainty estimates. These uncertainty estimates are based on values of the diagonal element of the resolution matrix, absolute P-wave velocities that are typical for crust and mantle and a specific velocity gradient across the Moho discontinuity. Finally, our definition of LET Moho elements and their uncertainties is validated by comparisons of highest quality Moho results from both methods coinciding in 353 localities. Our model clearly shows three Moho surfaces, being Europe, Adria and Liguria as well as major tectonic structures like suture zones and the high-velocity Ivrea body. In general, it is in a good agreement with previous studies. The biggest differences occur along plate boundaries, where the strong lateral velocity variations are best resolved by LET. Due to the larger number of available Moho reflector elements a more accurate definition of plate boundaries at Moho level is possible and, therefore, new insights in deep lithosphere structures of the Alpine collision zone can be expected. Furthermore, our new 3-D crustal model directly includes a 3-D migrated image of the Ivrea body.

  5. Crustal structure in Eurasia: An overview

    NASA Astrophysics Data System (ADS)

    Thybo, H.; Artemieva, I. M.

    2015-12-01

    We present a compilation of Moho topography and crustal structure the area encompassing most of Europe, Greenland, Siberia, the North Atlantic Ocean and the Arctic shelves (EUNAseis and SibCrust models, Tectonophysics 2013). Our new, high resolution, continent-scale crustal model is based solely on seismic profiles and RF models published since 1960, which makes it applicable to potential field modelling. The database represents a major improvement in coverage and resolution with a sample interval of 50 km or less. It includes information on the depth to Moho, thickness and average P-wave velocity of five crustal layers (sediments, and upper, middle, lower, and lowermost crust) and Pn velocity. For each of the crustal parameters included in the compilation, we discuss uncertainties associated with theoretical limitations, regional data quality, and arising from interpolation. We provide an extensive summary of the tectonic and geodynamic evolution of the region and discuss the origin of crustal heterogeneity and processes of crustal evolution in the Precambrian cratons of Europe and Siberia, and major Phanerozoic basins, orogens, and rift zones. We conclude that for all tectonic settings there are significant variations in depth to Moho and crustal structure, essentially controlled by the age of the last major tectono-thermal event. We demonstrate that generally-adopted global averages of crustal parameters are incorrect for any particular tectonic setting in Europe and in Siberia, and conclude that we cannot define a "typical cratonic" crust. We show that relative thickness of the upper-middle crystalline crust (Vp<6.8 km/s) and the lower (Vp>6.8 km/s) crust is indicative of the crustal origin, i.e. oceanic, transitional, platform, or extended crust. Continental rifting generally thins the upper-middle crust without changing the average Vp. Thinning of the lower crust during rifting is less significant and generally occurs without significant change in lower

  6. The 3D Structure of the Proton

    NASA Astrophysics Data System (ADS)

    Kaiser, Ralf

    2012-09-01

    When Rutherford, Geiger and Marsden discovered the atomic nucleus in 1909 in Manchester, they at the same time also laid the foundations for the most successful method to study the structure of nuclei and nucleons. They found a point-like scattering centre inside the atom and identified it with the atomic nucleus and the theoretical description of this process has been known as Rutherford scattering ever since. The deviation between the theoretical description for a point-like scattering centre and experimental data has since been used to reveal information about the structure of the nucleus as well as the nucleon. There has been a continuous development from Hofstadters experiments in the 1950s, over the SLAC experiments in the 60s and 70s to the the HERA experiments at DESY and the experimental programme at Jeffersonlab. In this paper I am presenting the most recent results in Deeply Virtual Compton Scattering from the Hermes experiment at DESY, taken with a high density unpolarised target and a recoil detector in 2006/7.

  7. 3D finite amplitude folding: Implications for stress evolution during crustal and lithospheric deformation

    NASA Astrophysics Data System (ADS)

    Kaus, Boris J. P.; Schmalholz, Stefan M.

    2006-07-01

    Compression of the lithosphere, sedimentary sequences or quartz veins may result in a folding instability. We perform numerical simulations of viscous single-layer folding to study this instability in 3D. It is demonstrated that linear theories correctly describe the instability for small amplitudes. At larger amplitudes, however, the theory breaks down. For these stages we present a new nonlinear amplification equation. Numerical simulations of folding of an initially horizontal layer, perturbed with random noise, demonstrate that in most cases fold axes form perpendicular to the main shortening direction. Aspect ratios of folds are finite and the patterns are relatively insensitive to the applied background shortening directions. Furthermore, the 3D folding instability reduces the averaged differential stress within the folded (``strong'') layer, in agreement with 2D results. This implies that the Christmas-tree approach to represent the strength of the crust and lithosphere may be invalid if folding occurs during the deformation.

  8. 3D Finite Amplitude Folding: Implications for the Stress Evolution During Crustal and Lithospheric Deformation

    NASA Astrophysics Data System (ADS)

    Kaus, B.; Schmalholz, S.

    2006-12-01

    Compression of the lithosphere, sedimentary sequences or quartz veins may all result in a folding instability, provided that the effective viscosity contrast between "strong" and "weak" layers is sufficiently large. Whereas this process is relatively well understood in 2D, little is known about the finite amplitude instability in 3D. We perform 3D numerical simulations of viscous single-layer folding to study the growth of the fold amplitude during progressive shortening for different amounts of shortening in the two horizontal directions. We demonstrate that existing, linear theories correctly describe the behavior of the instability for small amplitudes. For larger amplitudes, however, numerical results strongly deviate from the linear theory. Therefore, we present a new nonlinear amplification equation that successfully describes folding up to finite amplitudes. Numerical simulations of folding of an initially horizontal layer, perturbed with random noise, demonstrate that in most cases fold axes form perpendicular to the main shortening direction. Aspect ratios of folds are finite and the patterns are relatively insensitive to the applied background shortening directions. Furthermore, the 3D folding instability reduces the averaged differential stress within the folded ("strong") layer, in agreement with 2D results. This implies that the Christmas-tree approach to represent the strength of the crust and lithosphere may be invalid if folding occurs during the deformation.

  9. 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.

  10. 3D Animations for Exploring Nucleon Structure

    NASA Astrophysics Data System (ADS)

    Gorman, Waverly; Burkardt, Matthias

    2016-09-01

    Over the last few years many intuitive pictures have been developed for the interpretation of electron hadron scattering experiments, such as a mechanism for transverse single-spin asymmetries in semi-inclusive deep-inelastic scattering experiments. While Dr. Burkardt's pictures have been helpful for many researchers in the field, they are still difficult to visualize for broader audiences since they rely mostly on 2-dimensional static images. In order to make more accessible for a broader audience what can be learned from Jefferson Lab experiments, we have started to work on developing 3-dimensional animations for these processes. The goal is to enable the viewer to repeatedly look at the same microscopic mechanism for a specific reaction, with the viewpoint of the observer changing. This should help an audience that is not so familiar with these reactions to better understand what can be learned from various experiments at Jefferson Lab aimed at exploring the nucleon structure. Jefferson Lab Minority/Female Undergraduate Research Assistantship.

  11. Preliminary investigations on 3D PIC simulation of DPHC structure using NEPTUNE3D code

    NASA Astrophysics Data System (ADS)

    Zhao, Hailong; Dong, Ye; Zhou, Haijing; Zou, Wenkang; Wang, Qiang

    2016-10-01

    Cubic region (34cm × 34cm × 18cm) including the double post-hole convolute (DPHC) structure was chosen to perform a series of fully 3D PIC simulations using NEPTUNE3D codes, massive data ( 200GB) could be acquired and solved in less than 5 hours. Cold-chamber tests were performed during which only cathode electron emission was considered without temperature rise or ion emission, current loss efficiency was estimated by comparisons between output magnetic field profiles with or without electron emission. PIC simulation results showed three stages of current transforming process with election emission in DPHC structure, the maximum ( 20%) current loss was 437kA at 15ns, while only 0.46% 0.48% was lost when driving current reached its peak. DPHC structure proved valuable functions during energy transform process in PTS facility, and NEPTUNE3D provided tools to explore this sophisticated physics. Project supported by the National Natural Science Foundation of China, Grant No. 11571293, 11505172.

  12. 3-D visualization of geologic structures and processes

    NASA Astrophysics Data System (ADS)

    Pflug, R.; Klein, H.; Ramshorn, Ch.; Genter, M.; Stärk, A.

    Interactive 3-D computer graphics techniques are used to visualize geologic structures and simulated geologic processes. Geometric models that serve as input to 3-D viewing programs are generated from contour maps, from serial sections, or directly from simulation program output. Choice of viewing parameters strongly affects the perception of irregular surfaces. An interactive 3-D rendering program and its graphical user interface provide visualization tools for structural geology, seismic interpretation, and visual post-processing of simulations. Dynamic display of transient ground-water simulations and sedimentary process simulations can visualize processes developing through time.

  13. Finding Organized Structures in 3-D LADAR Data

    DTIC Science & Technology

    2004-12-01

    work exists also on how to extract planar and linear objects from scattered 3-D point clouds , see for example [5], [6]. Methods were even proposed to...of structure detection and segmentation from 3-D point clouds collected from a single sensor location or integrated from multiple locations. In [2...primitives to point clouds are difficult to use practically for large data sets containing multiple complex structures, in opposition to multiple planar

  14. Evaluation of 3D Printer Accuracy in Producing Fractal Structure.

    PubMed

    Kikegawa, Kana; Takamatsu, Kyuuichirou; Kawakami, Masaru; Furukawa, Hidemitsu; Mayama, Hiroyuki; Nonomura, Yoshimune

    2017-01-01

    Hierarchical structures, also known as fractal structures, exhibit advantageous material properties, such as water- and oil-repellency as well as other useful optical characteristics, owing to its self-similarity. Various methods have been developed for producing hierarchical geometrical structures. Recently, fractal structures have been manufactured using a 3D printing technique that involves computer-aided design data. In this study, we confirmed the accuracy of geometrical structures when Koch curve-like fractal structures with zero to three generations were printed using a 3D printer. The fractal dimension was analyzed using a box-counting method. This analysis indicated that the fractal dimension of the third generation hierarchical structure was approximately the same as that of the ideal Koch curve. These findings demonstrate that the design and production of fractal structures can be controlled using a 3D printer. Although the interior angle deviated from the ideal value, the side length could be precisely controlled.

  15. Direct-Write 3D Nanoprinting of Plasmonic Structures

    DOE PAGES

    Winkler, Robert; Schmidt, Franz-Philipp; Karl-Franzens Univ.; ...

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, puremore » gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.« less

  16. Direct-Write 3D Nanoprinting of Plasmonic Structures.

    PubMed

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D; Lewis, Brett B; Kothleitner, Gerald; Rack, Philip D; Plank, Harald

    2017-03-08

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. While several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. In this study, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. By that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  17. Direct-Write 3D Nanoprinting of Plasmonic Structures

    SciTech Connect

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D.; Lewis, Brett B.; Kothleitner, Gerald; Rack, Philip D.; Plank, Harald

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  18. 3D-Fun: predicting enzyme function from structure.

    PubMed

    von Grotthuss, Marcin; Plewczynski, Dariusz; Vriend, Gert; Rychlewski, Leszek

    2008-07-01

    The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.

  19. 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

  20. 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.

  1. The 3D velocity structure beneath Iceland: Identifying melt pathways

    NASA Astrophysics Data System (ADS)

    Allen, R.

    2003-04-01

    The integration of various seismic datasets, recorded by the broadband HOTSPOT network deployed across Iceland, provides one of the highest resolution studies of the crust and mantle structure associated with a plume-ridge system. The mantle P- and S-velocity models (ICEMAN), derived from teleseismic body-wave and surface wave analysis, show a vertical, cylindrical low velocity anomaly ˜200 km in diameter extending from ˜400 km, the maximum depth of resolution, up to ˜200 km above which low velocity material is present beneath all of Iceland. The maximum P- and S-velocity anomalies of -2% and -4% respectively are found beneath the northwestern edge of Vatnajokull. The crustal S-velocity model (ICECRTb) is constrained by local surface waves, refraction experiments and receiver functions, and shows significant variation in crustal thickness. The thinnest, ˜15 km, crust is found around coastal regions, the thickest crust is beneath northwestern Vatnajokull where it reaches a thickness of 45 km. Within this thick crustal root is a vertical low velocity anomaly connecting the core of the mantle anomaly to horizontal low velocity regions that extend along the western and eastern volcanic zones but not the northern volcanic zone. These crustal low velocity zones are interpreted as regions through which melt is fed from the mantle to shallow magma chambers beneath the rift zones, where crustal formation occurs. The pipework between the core of the mantle anomaly and the southern rift zones is responsible for ˜30 km thick crust. Its absence to the north results in relatively thin, ˜20 km thick, crust.

  2. Toward mobile 3D visualization for structural biologists.

    PubMed

    Tanramluk, Duangrudee; Akavipat, Ruj; Charoensawan, Varodom

    2013-12-01

    Technological advances in crystallography have led to the ever-rapidly increasing number of biomolecular structures deposited in public repertoires. This undoubtedly shifts the bottleneck of structural biology research from obtaining high-quality structures to data analysis and interpretation. The recently available glasses-free autostereoscopic laptop offers an unprecedented opportunity to visualize and study 3D structures using a much more affordable, and for the first time, portable device. Together with a gamepad re-programmed for 3D structure controlling, we describe how the gaming technologies can deliver the output 3D images for high-quality viewing, comparable to that of a passive stereoscopic system, and can give the user more control and flexibility than the conventional controlling setup using only a mouse and a keyboard.

  3. A 3-D crustal and uppermost mantle model of the western US from receiver functions and surface wave dispersion derived from ambient noise and teleseismic earthquakes

    NASA Astrophysics Data System (ADS)

    Shen, W.; Schulte-Pelkum, V.; Ritzwoller, M. H.

    2011-12-01

    parameterization of both crustal and uppermost mantle structure. After the inversion, a 3-D model for the crust and uppermost mantle to a depth of 150 km is constructed for this region. Compared with using surface wave data alone, uncertainty in crustal thickness is much lower and as a result, the lower crustal velocity is better constrained given a smaller depth-velocity trade-off. The new 3-D model including Moho depth with attendant uncertainties provides the basis for further analysis on radial anisotropy and geodynamics in the western US, and also forms a starting point for other seismological studies such as body wave tomography and receiver function CCP analysis.

  4. 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.

  5. 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.

  6. Proposed traceable structural resolution protocols for 3D imaging systems

    NASA Astrophysics Data System (ADS)

    MacKinnon, David; Beraldin, J.-Angelo; Cournoyer, Luc; Carrier, Benjamin; Blais, François

    2009-08-01

    A protocol for determining structural resolution using a potentially-traceable reference material is proposed. Where possible, terminology was selected to conform to those published in ISO JCGM 200:2008 (VIM) and ASTM E 2544-08 documents. The concepts of resolvability and edge width are introduced to more completely describe the ability of an optical non-contact 3D imaging system to resolve small features. A distinction is made between 3D range cameras, that obtain spatial data from the total field of view at once, and 3D range scanners, that accumulate spatial data for the total field of view over time. The protocol is presented through the evaluation of a 3D laser line range scanner.

  7. 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

  8. CH5M3D: an HTML5 program for creating 3D molecular structures

    PubMed Central

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

  9. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-04-20

    We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique to consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.

  10. 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

  11. Low velocity crustal flow and crust-mantle coupling mechanism in Yunnan, SE Tibet, revealed by 3D S-wave velocity and azimuthal anisotropy

    NASA Astrophysics Data System (ADS)

    Chen, Haopeng; Zhu, Liangbao; Su, Youjin

    2016-08-01

    We used teleseismic data recorded by a permanent seismic network in Yunnan, SE Tibet, and measured the interstation Rayleigh wave phase velocity between 10 and 60 s. A two-step inversion scheme was used to invert for the 3D S-wave velocity and azimuthal anisotropy structure of 10-110 km. The results show that there are two low velocity channels between depths of 20-30 km in Yunnan and that the fast axes are sub-parallel to the strikes of the low velocity channels, which supports the crustal flow model. The azimuthal anisotropy pattern is quite complicated and reveals a complex crust-mantle coupling mechanism in Yunnan. The N-S trending Lüzhijiang Fault separates the Dianzhong Block into two parts. In the western Dianzhong Block, the fast axis of the S-wave changes with depth, which indicates that the crust and the lithospheric mantle are decoupled. In the eastern Dianzhong Block and the western Yangtze Craton, the crust and the lithospheric mantle may be decoupled because of crustal flow, despite a coherent S-wave fast axis at depths of 10-110 km. In addition, the difference between the S-wave fast axis in the lithosphere and the SKS splitting measurement suggests that the lithosphere and the upper mantle are decoupled there. In the Baoshan Block, the stratified anisotropic pattern suggests that the crust and the upper mantle are decoupled.

  12. Automated 3D structure composition for large RNAs

    PubMed Central

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

    2012-01-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

  13. Automated 3D structure composition for large RNAs.

    PubMed

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W

    2012-08-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.

  14. 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.

  15. Coherent structures in 3D viscous time-periodic flow

    NASA Astrophysics Data System (ADS)

    Znaien, J. G.; Speetjens, M. F. M.; Trieling, R. R.; Clercx, H. J. H.

    2010-11-01

    Periodically driven laminar flows occur in many industrial processes from food-mixing devices to micro-mixer in lab-on-a-chip systems. The present study is motivated by better understanding fundamental transport phenomena in three-dimensional viscous time-periodic flows. Both numerical simulation and three-dimensional Particle Tracking Velocimetry measurements are performed to investigate the 3D advection of a passive scalar in a lid-driven cylindrical cavity flow. The flow is forced by a time-periodic in-plane motion of one endwall via a given forcing protocol. We concentrate on the formation and interaction of coherent structures due to fluid inertia, which play an important role in 3D mixing by geometrically determining the tracer transport. The disintegration of these structures by fluid inertia reflects an essentially 3D route to chaos. Data from tracking experiments of small particles will be compared with predictions from numerical simulations on transport of passive tracers.

  16. 3D printing of nano- and micro-structures

    NASA Astrophysics Data System (ADS)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

    Additive manufacturing or 3D printing techniques are being vigorously investigated as a replacement to the traditional and conventional methods in fabrication to bring forth cost and time effective approaches. Introduction of 3D printing has led to printing micro and nanoscale structures including tissues and organelles, bioelectric sensors and devices, artificial bones and transplants, microfluidic devices, batteries and various other biomaterials. Various microfabrication processes have been developed to fabricate micro components and assemblies at lab scale. 3D Fabrication processes that can accommodate the functional and geometrical requirements to realize complicated structures are becoming feasible through advances in additive manufacturing. This advancement could lead to simpler development mechanisms of novel components and devices exhibiting complex features. For instance, development of microstructure electrodes that can penetrate the epidermis of the skin to collect the bio potential signal may prove very effective than the electrodes that measure signal from the skin's surface. The micro and nanostructures will have to possess extraordinary material and mechanical properties for its dexterity in the applications. A substantial amount of research being pursued on stretchable and flexible devices based on PDMA, textiles, and organic electronics. Despite the numerous advantages these substrates and techniques could solely offer, 3D printing enables a multi-dimensional approach towards finer and complex applications. This review emphasizes the use of 3D printing to fabricate micro and nanostructures for that can be applied for human healthcare.

  17. 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

  18. 3D genome structure modeling by Lorentzian objective function.

    PubMed

    Trieu, Tuan; Cheng, Jianlin

    2016-11-29

    The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. Our method was robust to noise and performed well in comparison with a panel of existing methods on a controlled simulated data set. On a real Hi-C data set of the human genome, our method produced chromosome and genome structures that are consistent with 3D FISH data and known knowledge about the human chromosome and genome, such as, chromosome territories and the cluster of small chromosomes in the nucleus center with the exception of the chromosome 18. The tool and experimental data are available at https://missouri.box.com/v/LorDG.

  19. Coarse-grained modeling of RNA 3D structure.

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  20. RNA and protein 3D structure modeling: similarities and differences.

    PubMed

    Rother, Kristian; Rother, Magdalena; Boniecki, Michał; Puton, Tomasz; Bujnicki, Janusz M

    2011-09-01

    In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed "protein-like" modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using "protein-like" methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions.

  1. 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

  2. Crustal metamorphic fluid flux beneath the Dead Sea Basin: constraints from 2-D and 3-D magnetotelluric modelling

    NASA Astrophysics Data System (ADS)

    Meqbel, Naser; Weckmann, Ute; Muñoz, Gerard; Ritter, Oliver

    2016-12-01

    We report on a study to explore the deep electrical conductivity structure of the Dead Sea Basin (DSB) using magnetotelluric (MT) data collected along a transect across the DSB where the left lateral strike-slip Dead Sea transform (DST) fault splits into two fault strands forming one of the largest pull-apart basins of the world. A very pronounced feature of our 2-D inversion model is a deep, subvertical conductive zone beneath the DSB. The conductor extends through the entire crust and is sandwiched between highly resistive structures associated with Precambrian rocks of the basin flanks. The high electrical conductivity could be attributed to fluids released by dehydration of the uppermost mantle beneath the DSB, possibly in combination with fluids released by mid- to low-grade metamorphism in the lower crust and generation of hydrous minerals in the middle crust through retrograde metamorphism. Similar high conductivity zones associated with fluids have been reported from other large fault systems. The presence of fluids and hydrous minerals in the middle and lower crust could explain the required low friction coefficient of the DST along the eastern boundary of the DSB and the high subsidence rate of basin sediments. 3-D inversion models confirm the existence of a subvertical high conductivity structure underneath the DSB but its expression is far less pronounced. Instead, the 3-D inversion model suggests a deepening of the conductive DSB sediments off-profile towards the south, reaching a maximum depth of approximately 12 km, which is consistent with other geophysical observations. At shallower levels, the 3-D inversion model reveals salt diapirism as an upwelling of highly resistive structures, localized underneath the Al-Lisan Peninsula. The 3-D model furthermore contains an E-W elongated conductive structure to the northeast of the DSB. More MT data with better spatial coverage are required, however, to fully constrain the robustness of the above

  3. Strategies to reconstruct 3D Coffea arabica L. plant structure.

    PubMed

    Matsunaga, Fabio Takeshi; Tosti, Jonas Barbosa; Androcioli-Filho, Armando; Brancher, Jacques Duílio; Costes, Evelyne; Rakocevic, Miroslava

    2016-01-01

    Accurate model of structural elements is necessary to model the foliage and fruit distributions in cultivated plants, both of them being key parameters for yield prediction. However, the level of details in architectural data collection could vary, simplifying the data collection when plants get older and because of the high time cost required. In the present study, we aimed at reconstructing and analyzing plant structure, berry distributions and yield in Coffea arabica (Arabica coffee), by using both detailed or partial morphological information and probabilistic functions. Different datasets of coffee plant architectures were available with different levels of detail depending on the tree age. Three scales of decomposition-plant, axes and metamers were used reconstruct the plant architectures. CoffePlant3D, a software which integrates a series of mathematical, computational and statistical methods organized in three newly developed modules, AmostraCafe3D, VirtualCafe3D and Cafe3D, was developed to accurately reconstruct coffee plants in 3D, whatever the level of details available. The number of metamers of the 2nd order axes was shown to be linearly proportional to that of the orthotropic trunk, and the number of berries per metamer was modeled as a Gaussian function within a specific zone along the plagiotropic axes. This ratio of metamer emission rhythm between the orthotropic trunk and plagiotropic axes represents the pillar of botanical events in the C. arabica development and was central in our modeling approach, especially to reconstruct missing data. The methodology proposed for reconstructing coffee plants under the CoffePlant3D was satisfactorily validated across dataset available and could be performed for any other Arabica coffee variety.

  4. 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.

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

    PubMed

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

    2015-07-29

    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.

  6. 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

  7. 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.

  8. High-resolution teleseismic tomography of upper-mantle structure using an a priori three-dimensional crustal model

    NASA Astrophysics Data System (ADS)

    Waldhauser, Felix; Lippitsch, Regina; Kissling, Edi; Ansorge, Jörg

    2002-08-01

    The effect of an a priori known 3-D crustal model in teleseismic tomography of upper-mantle structure is investigated. We developed a 3-D crustal P-wave velocity model for the greater Alpine region, encompassing the central and western Alps and the northern Apennines, to estimate the crustal contribution to teleseismic traveltimes. The model is constructed by comparative use of published information from active and passive seismic surveys. The model components are chosen to represent the present large-scale Alpine crustal structure and for their significant effect on the propagation of seismic wavefields. They are first-order structures such as the crust-mantle boundary, sedimentary basins and the high-velocity Ivrea body. Teleseismic traveltime residuals are calculated for a realistic distribution of azimuths and distances by coupling a finite-difference technique to the IASP91 traveltime tables. Residuals are produced for a synthetic upper-mantle model featuring two slab structures and the 3-D crustal model on top of it. The crustal model produces traveltime residuals in the range between -0.7 and 1.5 s that vary strongly as a function of backazimuth and epicentral distance. We find that the non-linear inversion of the synthetic residuals without correcting for the 3-D crustal structure erroneously maps the crustal anomalies into the upper mantle. Correction of the residuals for crustal structure before inversion properly recovers the synthetic slab structures placed in the upper mantle. We conclude that with the increasing amount of high-quality seismic traveltime data, correction for near-surface structure is essential for increasing resolution in tomographic images of upper-mantle structure.

  9. 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

  10. 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.

  11. 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.

  12. Cancer3D: understanding cancer mutations through protein structures.

    PubMed

    Porta-Pardo, Eduard; Hrabe, Thomas; Godzik, Adam

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14,700 proteins mapped to more than 24,300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution.

  13. Crustal structure of Bristol Bay Region, Alaska

    SciTech Connect

    Cooper, A.K.; McLean, H.; Marlow, M.S.

    1985-04-01

    Bristol Bay lies along the northern side of the Alaska Peninsula and extends nearly 600 km southwest from the Nushagak lowlands on the Alaska mainland to near Unimak Island. The bay is underlain by a sediment-filled crustal downwarp known as the north Aleutian basin (formerly Bristol basin) that dips southeast toward the Alaska Peninsula and is filled with more than 6 km of strata, dominantly of Cenozoic age. The thickest parts of the basin lie just north of the Alaska Peninsula and, near Port Mollar, are in fault contact with older Mesozoic sedimentary rocks. These Mesozoic rocks form the southern structural boundary of the basin and extend as an accurate belt from at least Cook Inlet to Zhemchug Canyon (central Beringian margin). Offshore multichannel seismic-reflection, sonobuoy seismic-refraction, gravity, and magnetic data collected by the USGS in 1976 and 1982 indicate that the bedrock beneath the central and northern parts of the basin comprises layered, high-velocity, and highly magnetic rocks that are locally deformed. The deep bedrock horizons may be Mesozoic(.) sedimentary units that are underlain by igneous or metamorphic rocks and may correlate with similar rocks of mainland western Alaska and the Alaska Peninsula. Regional structural and geophysical trends for these deep horizons change from northeast-southwest to northwest-southeast beneath the inner Bering shelf and may indicate a major crustal suture along the northern basin edge.

  14. The 3D lightweight structural characteristics of the beetle forewing.

    PubMed

    Chen, Jinxiang; Tuo, Wanyong; Guo, Zhensheng; Yan, Lili

    2017-02-01

    The present paper renewedly expounds upon the characteristics of the 3D lightweight structure of beetle forewings and notes that two biomimetic structures (models) that have appeared in recent years do not comply with these characteristics based on a comparison of the structures of the biological prototypes. The first model features transverse tubules based on observations of circular holes in cross-sectional figures of the Cybister forewing. The second is a biomimetic spherical cavity model with hollow trabeculae that reportedly exhibits superior mechanical properties because its structures are most similar to the biological prototype. Finally, a false biomimetic proposition that the mechanical properties of biomimetic structures with "fiber winding" patterns are superior to those of structures constructed of pure "epoxy" is also noted. Hopefully, the present study can serve to improve the state of research on biomimetic applications of beetle forewing structures.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Manufacturing of a 3D complex hyperstable Cesic structure

    NASA Astrophysics Data System (ADS)

    Kroedel, Matthias; Courteau, Pascal; Poupinet, Anne; Sarri, Giuseppe

    2007-09-01

    Global astrometry requires extremely stable materials for instrument structures, such as optical benches. Cesic®, developed by ECM and Thales Alenia Space for mirrors and high stability structures, offers an excellent compromise in terms of structural strength, stability and very high lightweight capability, with a coefficient of thermal expansion that is virtually zero at cryogenic T°. The High-Stability Optical Bench (HSOB) GAIA study, realized by Thales Alenia Space under ESA contract, aimed to design, develop and test a full-scale representative of the HSOB bench, made entirely of Cesic®. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, a Michelson interferometer composed of integrated optics with nm-resolution. The HSOB bench has been submitted to a homogeneous T° step under vacuum to characterize 3-D expansion behavior of its two arms. The quite negligible interarm differential, measured with a nm-range reproducibility, demonstrates that a complete 3-D structure made of Cesic® has the same CTE homogeneity as do characterization samples, fully in line with the stringent GAIA requirements (1ppm at 120K). This demonstrates that Cesic® properties at cryogenic temperatures are fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM's and Thales Alenia Space's ability to design and manufacture monolithic lightweight highly stable optical structures, based on inner-cell triangular design made possible by the unique Cesic® manufacturing process.

  20. 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.

  1. 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.

  2. An endoscopic 3D scanner based on structured light.

    PubMed

    Schmalz, Christoph; Forster, Frank; Schick, Anton; Angelopoulou, Elli

    2012-07-01

    We present a new endoscopic 3D scanning system based on Single Shot Structured Light. The proposed design makes it possible to build an extremely small scanner. The sensor head contains a catadioptric camera and a pattern projection unit. The paper describes the working principle and calibration procedure of the sensor. The prototype sensor head has a diameter of only 3.6mm and a length of 14mm. It is mounted on a flexible shaft. The scanner is designed for tubular cavities and has a cylindrical working volume of about 30mm length and 30mm diameter. It acquires 3D video at 30 frames per second and typically generates approximately 5000 3D points per frame. By design, the resolution varies over the working volume, but is generally better than 200μm. A prototype scanner has been built and is evaluated in experiments with phantoms and biological samples. The recorded average error on a known test object was 92μm.

  3. 3-D Attenuation Structure around the SAFOD site, Parkfield, California

    NASA Astrophysics Data System (ADS)

    Harrington, N. L.; Thurber, C. H.; Zhang, H.; Roecker, S.

    2006-12-01

    We are developing models of the 3-D attenuation structure, both Qp and Qs, for a region about 15 km square centered on SAFOD. We are analyzing local earthquake data collected in 2001 and 2002 from the UW/RPI PASO array, the UC-Berkeley HRSN, and USGS seismic network stations around Parkfield. We determine the P- or S-wave t* values for an individual local earthquake for each of the observing stations by fitting observed spectra using a joint inversion for a common corner frequency, low-frequency amplitude, and t*. Within our initial data set, we examine 575 events recorded at up to 111 stations and obtain over 19000 P- wave t* values. We use these t* values in simul2000 and tomoDD to perform the inversion to obtain a 3-D, frequency-independent Qp model of the attenuation structure, using an existing 3-D Vp model and associated event locations. We will use this same procedure to obtain the Qs structure. In our preliminary Qp structure results, we observe a high Qp feature (about 250) at 0-8 km depth on the southwest side of the fault. We associate this feature with the high density, high velocity Salinian basement rocks. We also see a moderate Qp feature (about 150) in the fault zone that encompasses the hypocenters of our events. On the northeast side of the fault, we observe Qp values generally increasing with depth, from 125 at the surface to 200 at 8 km. We will present our final Qp and Qs models, identify major features within the two, and discuss how these features relate to the findings of other geophysical studies in the area (seismic velocity, electrical resistivity, anisotropy). We will discuss how these features relate to the nature of the crust in that area, including the local geology, presence of fluids, fracturing, etc.

  4. A geophysical model of lower crustal structure of the Palaezoic crustal root (Bohemian Massif): implications for modern collisional orogens

    NASA Astrophysics Data System (ADS)

    Guy, Alexandra; Edel, Jean Bernard; Schulmann, Karel; Tomek, Cestmir; Lexa, Ondrej

    2010-05-01

    A new model of the structure and composition of Variscan crust is proposed based on 3D gravity modelling, geological data, seismic refraction (CEL09) and reflection (9HR) sections. The Bohemian Massif crust is characterized by succession of positive and negative anomalies of about 60 - 80 km wavelength for nearly constant Moho depths. The southwestern part of the Bohemian Massif displays a large negative Bouguer anomaly corresponding to high grade rocks (granulites, migmatites) of the Palaeozoic crustal root represented by the Moldanubian domain. Adjacent Neo-Proterozoic Brunia microcontinent displays important gravity high corresponding to mafic and intermediate medium grade metamorphic and magmatic rocks. However, the strong gradient marking deep crustal boundary between the root domain and the Brunia microcontinent is located 50 to 70 km westwards from the surface boundary between these units suggesting that in this area the high density basement rocks are covered by thin sheet of low density granulites and migmatites. NW from the Moldanubain domain occurs an important gravity high corresponding to the Neo-Proterozoic basement of the Teplá-Barrandian Unit limited in the north by southeast dipping reflectors of the Teplá suture which is characterized by high density eclogites and ultramafics. The footwall of the suture corresponds to low density felsic crust of the Saxothuringian basement. The reflection and refraction seismics and gravity modelling suggest a complex lithological structure of the Moldanubian domain marked by low density 5 - 10 km thick lower crustal layer located above MOHO, 5 - 10 km thick heavy mafic layer, 10 km thick mid-crustal layer of intermediate density and locally developed 2 - 5 km thick low density layer at the surface. The low density lower crust correlates well with low P velocities in the range 6.0-6.4 km-sec in the CEL09 section. This complex geophysical structure and surface geology are interpreted as a result of partial

  5. Gene3D: modelling protein structure, function and evolution.

    PubMed

    Yeats, Corin; Maibaum, Michael; Marsden, Russell; Dibley, Mark; Lee, David; Addou, Sarah; Orengo, Christine A

    2006-01-01

    The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

  6. Water linked 3D coordination polymers: Syntheses, structures and applications

    NASA Astrophysics Data System (ADS)

    Singh, Suryabhan; Bhim, Anupam

    2016-12-01

    Three new coordination polymers (CPs) based on Cd and Pb, [Cd(OBA)(μ-H2O)(H2O)]n1, [Pb(OBA)(μ-H2O)]n2 [where OBA=4,4'-Oxybis(benzoate)] and [Pb(SDBA)(H2O)]n.1/4DMF 3 (SDBA=4,4'-Sulfonyldibenzoate), have been synthesized and characterized. The single crystal structural studies reveal that CPs 1 and 2 have three dimensional structure. A water molecule bridges two metal centres which appears to the responsible for the dimensionality increase from 2D to 3D. Compound 3 has a supramolecular 3D structure involving water molecule and hydrogen bonds. A structural transformation is observed when 3 was heated at 100 °C or kept in methanol, forming [Pb(SDBA)]n4. Compound 4 is used as supporting matrix for palladium nanoparticles, PdNPs@4. The PdNPs@4 exhibits good catalytic activity toward the reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) in the presence of NaBH4 at room temperature. Luminescence studies revealed that all CPs could be an effective sensor for nitroaromatic explosives.

  7. Active Fault Geometry and Crustal Deformation Along the San Andreas Fault System Through San Gorgonio Pass, California: The View in 3D From Seismicity

    NASA Astrophysics Data System (ADS)

    Nicholson, C.; Hauksson, E.; Plesch, A.

    2012-12-01

    Understanding the 3D geometry and deformation style of the San Andreas fault (SAF) is critical to accurate dynamic rupture and ground motion prediction models. We use 3D alignments of hypocenter and focal mechanism nodal planes within a relocated earthquake catalog (1981-2011) [Hauksson et al., 2012] to develop improved 3D fault models for active strands of the SAF and adjacent secondary structures. Through San Gorgonio Pass (SGP), earthquakes define a mechanically layered crust with predominantly high-angle strike-slip faults in the upper ~10 km, while at greater depth, intersecting sets of strike-slip, oblique slip and low-angle thrust faults define a wedge-shaped volume deformation of the lower crust. In some places, this interface between upper and lower crustal deformation may be an active detachment fault, and may have controlled the down-dip extent of recent fault rupture. Alignments of hypocenters and nodal planes define multiple principal slip surfaces through SGP, including a through-going steeply-dipping predominantly strike-slip Banning fault strand at depth that upward truncates a more moderately dipping (40°-50°) blind, oblique North Palm Springs fault. The North Palm Springs fault may be the active down-dip extension of the San Gorgonio Pass thrust offset at depth by the principal, through-going Banning strand. In the northern Coachella Valley, seismicity indicates that the Garnet Hill and Banning fault strands are most likely sub-parallel and steeply dipping (~70°NE) to depths of 8-10 km, where they intersect and merge with a stack of moderately dipping to low-angle oblique thrust faults. Gravity and water well data confirm that these faults are sub-parallel and near vertical in the upper 2-3 km. Although the dense wedge of deep seismicity below SGP and largely south of the SAF contains multiple secondary fault sets of different orientations, the predominant fault set appears to be a series of en echelon NW-striking oblique strike-slip faults

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. Protein 3D structure computed from evolutionary sequence variation.

    PubMed

    Marks, Debora S; Colwell, Lucy J; 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 C(α)-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 structures

  14. 3D Printing of Hierarchical Silk Fibroin Structures.

    PubMed

    Sommer, Marianne R; Schaffner, Manuel; Carnelli, Davide; Studart, André R

    2016-12-21

    Like many other natural materials, silk is hierarchically structured from the amino acid level up to the cocoon or spider web macroscopic structures. Despite being used industrially in a number of applications, hierarchically structured silk fibroin objects with a similar degree of architectural control as in natural structures have not been produced yet due to limitations in fabrication processes. In a combined top-down and bottom-up approach, we exploit the freedom in macroscopic design offered by 3D printing and the template-guided assembly of ink building blocks at the meso- and nanolevel to fabricate hierarchical silk porous materials with unprecedented structural control. Pores with tunable sizes in the range 40-350 μm are generated by adding sacrificial organic microparticles as templates to a silk fibroin-based ink. Commercially available wax particles or monodisperse polycaprolactone made by microfluidics can be used as microparticle templates. Since closed pores are generated after template removal, an ultrasonication treatment can optionally be used to achieve open porosity. Such pore templating particles can be further modified with nanoparticles to create a hierarchical template that results in porous structures with a defined nanotopography on the pore walls. The hierarchically porous silk structures obtained with this processing technique can potentially be utilized in various application fields from structural materials to thermal insulation to tissue engineering scaffolds.

  15. Diagnosis and control of 3D elastic mechanical structures

    NASA Astrophysics Data System (ADS)

    Krajcin, Idriz; Soeffker, Dirk

    2005-05-01

    In this paper, a model-based approach for fault detection and vibration control of flexible structures is proposed and applied to 3D-structures. Faults like cracks or impacts acting on a flexible structure are considered as unknown inputs acting on the structure. The Proportional-Integral-Observer (PI-Observer) is used to estimate the system states as well as unknown inputs acting on a system. Also the effects of structural changes are understood as external effects (related to the unchanged structure) and are considered as fictitious external forces or moments. The paper deals with the design of the PI-Observer for practical applications when measurement noise and model uncertainties are present and shows its performance in experimental results. As examples, impacts acting upon a one side clamped elastic beam and on a thin plate structure are estimated using displacement or strain measurements. To control the vibration of the flexible plate, two piezoelectric patches bonded on the structure are used as actuators. The control algorithm introduced in this contribution contains a state feedback control and additionally a disturbance rejection. The disturbances are estimated using the PI-Observer. Experimental results show the performance and the robustness properties of the control strategy for the vibration control of a very thin plate.

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. POISs3: A 3D poisson smoother of structured grids

    NASA Astrophysics Data System (ADS)

    Lehtimaeki, R.

    Flow solvers based on solving Navier-Stokes or Euler equations generally need a computational grid to represent the domain of the flow. A structured computational grid can be efficiently produced by algebraic methods like transfinite interpolation. Unfortunately, algebraic methods propagate all kinds of unsmoothness of the boundary into the field. Unsmoothness of the grid, in turn, can result in inaccuracy in the flow solver. In the present work a 3D elliptic grid smoother was developed. The smoother is based on solving three Poisson equations, one for each curvilinear direction. The Poisson equations formed in the physical region are first transformed to the computational (rectilinear) region. The resulting equations form a system of three coupled elliptic quasi-linear partial differential equations in the computational domain. A short review of the Poisson method is presented. The regularity of a grid cell is studied and a skewness value is developed.

  1. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-15

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  2. 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.

  3. Multifunctional 3D printing of heterogeneous hydrogel structures

    NASA Astrophysics Data System (ADS)

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  4. Multifunctional 3D printing of heterogeneous hydrogel structures

    PubMed Central

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-01-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing. PMID:27630079

  5. Image crustal structure of eastern Oklahoma City with TOMODD

    NASA Astrophysics Data System (ADS)

    Chen, C.; Holland, A. A.; Keller, R. G.

    2012-12-01

    There has been a dramatic increase in earthquake activity in Oklahoma since 2009. This dramatic increase was also matched by a marked increase in the number of operating seismic stations within the region. The additional stations include the Earthscope Transportable Arrays and temporary stations provided by the U. S. Geological Survey. The additional seismic stations and earthquakes provide the ability to do local travel time tomography of the crust within the region. For this study we are focusing on the area near the Jones earthquake swarm, that occurred just east of Oklahoma City, and the M5.6, November 2011 Prague earthquake. Major structures are already known in the area, but little is known about crustal structure below the top of the Precambrian basement. We used regionally available and temporary seismic stations along with more than 2000 earthquakes within the region to develop a 3D tomographic model of the crust using TOMODD. The major structures within the area are the Nemaha Ridge, Wilzetta Fault, and Seminole Uplift, and they and other structures as well are expressed within the tomographic model. We are working on determining the resolution and interpretation of the tomographic images.

  6. 3D Wilson cycle: structural inheritance and subduction polarity reversals

    NASA Astrophysics Data System (ADS)

    Beaussier, Stephane; Gerya, Taras; Burg, Jean-Pierre

    2016-04-01

    Many orogenies display along-strike variations in their orogenic wedge geometry. For instance, the Alps is an example of lateral changes in the subducting lithosphere polarity. High resolution tomography has shown that the southeast dipping European lithosphere is separated from the northeast dipping Adriatic lithosphere by a narrow transition zone at about the "Judicarian" line (Kissling et al. 2006). The formation of such 3D variations remains conjectural. We investigate the conditions that can spontaneously induce such lithospheric structures, and intend to identify the main parameters controlling their formation and geometry. Using the 3D thermo-mechanical code, I3ELVIS (Gerya and Yuen 2007) we modelled a Wilson cycle starting from a continental lithosphere in an extensional setting resulting in continental breakup and oceanic spreading. At a later stage, divergence is gradually reversed to convergence, which induce subduction of the oceanic lithosphere formed during oceanic spreading. In this model, all lateral and longitudinal structures of the lithospheres are generated self-consistently, and are consequences of the initial continental structure, tectono-magmatic inheritance, and material rheology. Our numerical simulations point out the control of rheological parameters defining the brittle/plastic yielding conditions for the lithosphere. Formation of several opposing domains of opposing subduction polarity is facilitated by wide and weak oceanic lithospheres. Furthermore, contrasts of strength between the continental and oceanic lithosphere, as well as the angle between the plate suture and the shortening direction have a second order effect on the lateral geometry of the subduction zone. In our numerical experiments systematic lateral changes in the subduction lithosphere polarity during subduction initiation form spontaneously suggesting intrinsic physical origin of this phenomenon. Further studies are necessary to understand why this feature, observed

  7. 3D printing technology using high viscous materials - Synthesis of functional materials and fabrication of 3D metal structure

    NASA Astrophysics Data System (ADS)

    Hong, Seongik

    In the 3D printing technology, the research for using various materials has been performing. In this research work, 3D printable high viscous materials are suggested as one of the solutions for problems in the traditional 3D printing technology. First, Cu-Ag coreshell was synthesized as a functional material. In terms of the reaction rate, reaction rate limiting step was defined as a fundamental research, and then prepared Cu-Ag coreshell was printed and analyzed. Second, the high viscous Cu paste was prepared and then metal 3D printed structure was fabricated by using new printing method. In the synthesis of Cu-Ag coreshell, different sizes of Cu particle, 2μm and 100nm were used, and when 2μm Cu was applied, the reaction rate was limited by film diffusion control. However, when 100nm Cu was applied, reaction rate was controlled by CuO film and the rate of the reaction, which includes removing CuO film in the solution, is limited by chemical reaction control. The shape of Cu-Ag particle is spherical in the 2μm Cu condition and dendrite shape in the 100nm Cu condition respectively. The conductivity of Cu-Ag coreshell paste increased as increasing content of coreshell particle in the paste and sintering temperature. In order to print high viscous metal paste, the high viscous Cu paste was printed by using screw extruder, and the viscosity of Cu paste was measured as a fundamental research. As increasing wt.% of Cu in the paste, the viscosity also increased. In addition, the shrinkage factor was reduced by increasing wt.% of Cu in the paste. An optimized printing condition for the high viscous material was obtained, and by using this condition, 3D metal structure was fabricated. The final product was heat treated and polished. Through these processes, a fine quality of metal 3D structure was printed.

  8. 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.

  9. 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.

  10. Parameterization of 3D brain structures for statistical shape analysis

    NASA Astrophysics Data System (ADS)

    Zhu, Litao; Jiang, Tianzi

    2004-05-01

    Statistical Shape Analysis (SSA) is a powerful tool for noninvasive studies of pathophysiology and diagnosis of brain diseases. It also provides a shape constraint for the segmentation of brain structures. There are two key problems in SSA: the representation of shapes and their alignments. The widely used parameterized representations are obtained by preserving angles or areas and the alignments of shapes are achieved by rotating parameter net. However, representations preserving angles or areas do not really guarantee the anatomical correspondence of brain structures. In this paper, we incorporate shape-based landmarks into parameterization of banana-like 3D brain structures to address this problem. Firstly, we get the triangulated surface of the object and extract two landmarks from the mesh, i.e. the ends of the banana-like object. Then the surface is parameterized by creating a continuous and bijective mapping from the surface to a spherical surface based on a heat conduction model. The correspondence of shapes is achieved by mapping the two landmarks to the north and south poles of the sphere and using an extracted origin orientation to select the dateline during parameterization. We apply our approach to the parameterization of lateral ventricle and a multi-resolution shape representation is obtained by using the Discrete Fourier Transform.

  11. 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).

  12. 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.

  13. 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.

  14. 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

  15. 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).

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

    PubMed

    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.

  17. The 3D Attenuation Structure of Deception Island (Antarctica)

    NASA Astrophysics Data System (ADS)

    Prudencio, J.; De Siena, L.; Ibáñez, J. M.; Del Pezzo, E.; García-Yeguas, A.; Díaz-Moreno, A.

    2015-05-01

    The seismic and volcanological structure of Deception Island (Antarctica) is an intense focus topic in Volcano Geophysics. The interpretations given by scientists on the origin, nature, and location of the structures buried under the island strongly diverge. We present a high-resolution 3D P-wave attenuation tomography model obtained by using the coda normalization method on 20,293 high-quality waveforms produced by active sources. The checkerboard and synthetic anomaly tests guarantee the reproduction of the input anomalies under the island down to a depth of 4 km. The results, once compared with our current knowledge on the geological, geochemical, and geophysical structure of the region, depict Deception as a piecemeal caldera structure coming out of the Bransfield Trough. High-attenuation anomalies contouring the northeastern emerged caldera rim correlate with the locations of sediments. In our interpretation, the main attenuation contrast, which appears under the collapsed southeastern caldera rim, is related to the deeper feeding systems. A unique P-wave high-attenuation spherical-like anomaly in the inner bay extends between depths of 1 and 3 km. The northern contour of the anomaly coincides with the calderic rim both at 1 and 2 km, while smaller anomalies connect it with deeper structures below 3 km, dipping toward the Bransfield Trough. In our interpretation, the large upper anomaly is caused by a high-temperature shallow (1-3 km deep) geothermal system, located beneath the sediment-filled bay in the collapsed blocks and heated by smaller, deeper contributions of molten materials (magma) rising from southeast.

  18. 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

  19. Pack Aluminization Synthesis of Superalloy 3D Woven and 3D Braided Structures

    NASA Astrophysics Data System (ADS)

    Erdeniz, Dinc; Levinson, Amanda J.; Sharp, Keith W.; Rowenhorst, David J.; Fonda, Richard W.; Dunand, David C.

    2015-01-01

    Micro-architectured, precipitation-strengthened structures were created in a new process combining weaving, gas-phase alloying, diffusion, and precipitation. First, high-ductility Ni-20 wt pct Cr wires with 202 μm diameter were braided, or non-crimp orthogonal woven, into three-dimensional structures. Second, these structures were vapor-phase alloyed with Al at 1273 K (1000 °C) by pack cementation, creating uniform NiAl coatings on the wires when using a retort. Also, solid-state bonding was achieved at wire intersections, where two wires were sufficiently close to each other, as determined via optical and X-ray tomographic microscopy. Third, the NiAl-coated wires were fully homogenized and aged to form γ' precipitates distributed in a γ matrix phase, the same microstructure providing strength in nickel-based superalloys. The resulting structures—consisting of wires (i) woven in a controlled three-dimensional architecture, (ii) bonded at contact points and (iii) strengthened by γ' precipitates—are expected to show high strength at ambient and elevated temperatures, low density, and high permeability which is useful for active cooling.

  20. 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.

  1. 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.

  2. 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

  3. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

    PubMed Central

    Wang, Jian; Zhao, Yunjie; Zhu, Chunyan; Xiao, Yi

    2015-01-01

    Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models. PMID:25712091

  4. 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.

  5. 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

  6. Crustal Structure Studies Utilizing Earthquake Sequences

    DTIC Science & Technology

    1989-08-01

    differences were expected. In general the models for the areas north of Fairbanks are reasonably similar which is consistent with the fact that relocations...plate may be generating the stresses causing the intraplate seismicity of Interior and Arctic Alaska as well as producing complex crustal velocities in...gives us an unreversed profile along the Yukon river, but also gives us a fan-like distribution of paths across the Yukon Flats for a more general

  7. Computerized 3-D reconstruction of complicated anatomical structure

    NASA Astrophysics Data System (ADS)

    Andreasen, Arne; Drewes, Asbjorn M.; Assentoft, Joergen E.

    1992-06-01

    In the study of the rabbit hippocampal region, images of 430 serial sections were aligned by a `parameter-shift' algorithm. The resulting 3-D matrix represents a fixed and stained but `whole' rabbit brain. From this virtual object the slice procedure, displacement, and re- alignment could be computer simulated and the artifacts associated with these procedures estimated.

  8. 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.

  9. Imaging crustal structure beneath the southern Appalachians with wavefield migration

    NASA Astrophysics Data System (ADS)

    Hopper, E.; Fischer, K. M.; Rondenay, S.; Hawman, R. B.; Wagner, L. S.

    2016-12-01

    To constrain crustal structures in the southern Appalachians and the suture zone with the Gondwanan-affinity Suwannee terrane, we applied the 2-D generalized Radon transform wavefield migration method to the scattered incident P wavefield recorded by the EarthScope Southeastern Suture of the Appalachian Margin Experiment and adjacent Transportable Array stations. We resolve the root of thickened crust beneath the high topography of the Blue Ridge Mountains and estimate its density contrast with the mantle to be only 104 ± 20 kg/m3. A weak velocity contrast across the crustal root Moho is observed and may be related to an ongoing crustal delamination event, possibly contributing to local tectonic rejuvenation. Beneath the Suwannee terrane, we confirm prior observations of a gently south-southeastward dipping crustal suture, indicating the terminal collision of Laurentia and Gondwana involved several hundred kilometers of overthrusting.

  10. 3D gravity modelling reveals off-axis crustal thickness variations along the western Gakkel Ridge (Arctic Ocean)

    NASA Astrophysics Data System (ADS)

    Schmidt-Aursch, Mechita C.; Jokat, Wilfried

    2016-11-01

    Near-orthogonal ultra-slow (13.3 mm yr- 1 to 6.5 mm yr- 1) sea floor spreading in the absence of large transform faults make the Arctic Gakkel Ridge ideally suited for the study of magmatic processes. To enable this, we generated a three-dimensional gravity model of crustal thickness over the ridge and parts of the adjacent Nansen and Amundsen basins west of 65° E. The model shows that oceanic crust accreted prior to chrons C5/C6 is generally very thin (1-3 km). Magnetic anomalies over this thin crust are highly variable both parallel and perpendicular to the ridge axis. This is the result of amagmatic or weakly volcanic spreading that started with the opening of the basins 56 Ma ago. The separation of Greenland from Svalbard at chron C5/C6 led to the inflow of North Atlantic mantle into the western Eurasia Basin leading to a change in the mantle convection system and the establishment of a magmatic dichotomy along the Gakkel Ridge. Robust magmatism was established in the Western Volcanic Zone (6° 30‧ W-3° 30‧ E), leading to creation of a 6.6 km thick igneous crust, characterized by a strong positive axial magnetic anomaly, numerous volcanic cones, and widespread thick mid-ocean ridge basalts. The transition to the neighbouring Sparsely Magmatic (3° 30‧ E-29° E) and Eastern Volcanic (29° E-85° E) zones is sharp. Peridotites cover the central valley and the inner rift flanks, the central magnetic anomaly vanishes and crustal thickness decreases to 1-4 km. Transverse basement ridges, extending for as much as 100 km into the adjacent basins, intersect the central valley. Although partly of tectonic origin, the transverse ridges are also an expression of long-living magmatic centres, as revealed by increased magnetic anomaly intensities and local thickening of the crust to values as great as 5.9 km.

  11. 3D Discrete Element Simulation of Large-scale Faulting and Crustal Thickening in the India-Asia Collision Zone

    NASA Astrophysics Data System (ADS)

    Jiao, L.; Tapponnier, P.; Donze, F. V.; Scholtes, L.; Gaudemer, Y.; Huang, Z.

    2015-12-01

    Understanding the discontinuous nucleation, growth, and interaction of large faults within continental collision zones remains a challenge. Previous analog experiments simulating the India-Asia collision successfully modeled the development and kinematics of large strike-slip faults within the Eurasian plate. However, these 2D experiments were dynamically unscaled with gravity and did not allow the development of topographic relief. We use the YADE discrete element (DEM) code to alleviate these problems, producing a suite of 3D models. These 3D DEM models also involve the extrusion and rotation of coherent blocks by generating two large strike-slip faults. The location, size and offsets of these faults are consistent with those of the Red River and Altyn Tagh mega-faults. In addition, concurrently with strike-slip movement, the large scale deformation includes the successive formation, from South to North, of thrust faults that bound a growing plateau which may be considered analogous to the Tibet-Qinghai plateau. While based on very simplified boundary conditions and mechanical properties, such modeling results are therefore consistent with the topographic, tectonic and geological evolution of Eastern Asia in the last ~50 million years.

  12. 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.

  13. Crustal structure of the Mariana Trough

    SciTech Connect

    Ambos, E.L.; Hussong, D.M.

    1982-05-10

    Three seismic refraction profiles were shot in the Mariana Trough in the vicinity of the proposed axial rift spreading center. One long east-west trending line was shot across the axial high region, the elevated portion of the trough associated with the rift zone. The two other lines were shot in a rough north-south orientation subparallel to the trend of the axial rift, on crusts 1 and 5--6 m.y. old. Comparison of the results of the ray-tracing analysis for these two profiles indicated that thinning of layer 2A (velocity of 3.3 km/s) and development of a distinct layer 2B (velocity of 5.3 km/s and development of a distinct layer 2B (velocity of 5.3 km/s) and layer 3A (velocity of 6.7 km/s) takes place with increasing crustal age, implying a process of crustal evolution. The presence of large-scale crustal faults was noted in several instances. In addition, a consistent but low upper mantle seismic velocity of 7.7 km/s was measured for all three lines. These characteristics correlate with those previously observed for other areas of young oceanic crust. When compared with major active spreading centers such as the Mid-Atlantic Ridge and East Pacific Rise, the Mariana Trough appears similar to the former in most respects. Both the Mid-Atlantic Ridge and Mariana Trough are slow spreading (1-2 cm/yr half rate) and are characterized by rough topography, an axial rift, and a thick layer/sup 2/. Like the Mid-Atlantic Ridge, the Mariana Trough also has no low-velocity zone in the crust that could be interpreted as a magma chamber at the spreading center.

  14. 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.

  15. Thinned crustal structure and tectonic boundary of the Nansha Block, southern South China Sea

    NASA Astrophysics Data System (ADS)

    Dong, Miao; Wu, Shi-Guo; Zhang, Jian

    2016-12-01

    The southern South China Sea margin consists of the thinned crustal Nansha Block and a compressional collision zone. The Nansha Block's deep structure and tectonic evolution contains critical information about the South China Sea's rifting. Multiple geophysical data sets, including regional magnetic, gravity and reflection seismic data, reveal the deep structure and rifting processes. Curie point depth (CPD), estimated from magnetic anomalies using a windowed wavenumber-domain algorithm, enables us to image thermal structures. To derive a 3D Moho topography and crustal thickness model, we apply Oldenburg algorithm to the gravity anomaly, which was extracted from the observed free air gravity anomaly data after removing the gravity effect of density variations of sediments, and temperature and pressure variations of the lithospheric mantle. We found that the Moho depth (20 km) is shallower than the CPD (24 km) in the Northwest Borneo Trough, possibly caused by thinned crust, low heat flow and a low vertical geothermal gradient. The Nansha Block's northern boundary is a narrow continent-ocean transition zone constrained by magnetic anomalies, reflection seismic data, gravity anomalies and an interpretation of Moho depth (about 13 km). The block extends southward beneath a gravity-driven deformed sediment wedge caused by uplift on land after a collision, with a contribution from deep crustal flow. Its southwestern boundary is close to the Lupar Line defined by a significant negative reduction to the pole (RTP) of magnetic anomaly and short-length-scale variation in crustal thickness, increasing from 18 to 26 km.

  16. 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.

  17. Development of the Improving Process for the 3D Printed Structure

    NASA Astrophysics Data System (ADS)

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

  18. Development of the Improving Process for the 3D Printed Structure

    PubMed Central

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics. PMID:28054558

  19. Development of the Improving Process for the 3D Printed Structure.

    PubMed

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-05

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

  20. Building a 3D Virtual Liver: Methods for Simulating Blood Flow and Hepatic Clearance on 3D Structures

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

    In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver. PMID:27649537

  1. 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.

  2. Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations

    PubMed Central

    Gherardini, Pier Federico; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2010-01-01

    Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms) that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D. PMID:20700534

  3. Synthesis, structure and properties of a 3D acentric coordination polymer with noninterpenetrated (10,3)-d topology

    NASA Astrophysics Data System (ADS)

    Lun, Huijie; Li, Xuefei; Wang, Xiao; Li, Haiyan; Li, Yamin; Bai, Yan

    2017-01-01

    A new coordination polymer, {[Mn(HPIDC)(H2O)]·2H2O}n (1) (H3PIDC = 2-(pyridin-4-yl)-1H-imidazole-4,5-dicarboxylic acid), has been obtained by hydrothermal method and structurally characterized by X-ray single crystal diffraction, elemental analysis and thermogravimetric analysis (TGA). X-ray single crystal diffraction reveals that compound 1 crystallizing in acentric Pna21 space group, exhibits an ultimate racemic three-dimension framework with rare noninterpenetrated (10,3)-d (or utp) topology due to the alternate array of left- and right-handed helixes. Moreover, compound 1 also features ferroelectric, nonlinear optical (NLO) and antiferromagnetic behaviors.

  4. Genome3D: exploiting structure to help users understand their sequences

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cozzetto, Domenico; Dana, José M.; Filippis, Ioannis; Gough, Julian; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mistry, Jaina; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Oates, Matt E.; Punta, Marco; Rackham, Owen J.L.; Stahlhacke, Jonathan; Sternberg, Michael J.E.; Velankar, Sameer; Orengo, Christine

    2015-01-01

    Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models. PMID:25348407

  5. 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.

  6. Histo-anatomic 3D printing of dental structures.

    PubMed

    Schweiger, J; Beuer, F; Stimmelmayr, M; Edelhoff, D; Magne, P; Güth, J F

    2016-11-04

    The creation of dental restorations with natural appearance and biomechanics represents a major challenge for the restorative team. The manufacturing-process of high-aesthetic restorations from tooth-coloured restorative materials is currently dominated by manual manufacturing procedures and the outcome is highly dependent on the knowledge and skills of the performing dental technician. On the other hand, due to the simplicity of the manufacturing process, CAD/CAM restorations from different material classes gain more and more acceptance in the daily routine. Multi-layered restorations show significant aesthetic advantages versus monolithic ones, but are difficult to fabricate using digital technologies. The key element for the successful automated digital fabrication of aesthetic anterior restorations seems to be the form of the individual dentine core as defined by dentine enamel junction (DEJ) covered by a more transparent layer of material imitating the enamel layer to create the outer enamel surface (OES). This article describes the possibilities and technologies available for so-called '4D-printing'. It introduces the digital manufacturing process of multilayered anterior teeth using 3D multipart printing, taking the example of manufacturing replicas of extracted intact natural teeth.

  7. The Deep Crustal Seismic Structure of Colima Volcano, Mexico

    NASA Astrophysics Data System (ADS)

    Gardine, M.; West, M. E.; Dominguez, T.

    2009-12-01

    We present results of 3-D velocity modeling at Colima Volcano, located in the western section of the Trans-Mexican Volcanic Belt and one of North America’s most active volcano centers. From January 2006 - February 2008, twenty broadband seismometers were deployed in a wide-aperture array around the volcano as part of the IRIS/PASSCAL supported Colima Volcano Deep Seismic Experiment (CODEX). Data from this deployment, integrated with data from the Mapping of the Rivera Subduction Zone (MARS) project, have been used to characterize the seismicity along this section of the subduction zone as well as in the immediate vicinity of the volcano. We used subduction-zone earthquakes (depths > 40 km) as well as select regional crustal earthquakes to create a 1-D velocity model of the region. Using this model, slower apparent velocities are systematically seen at most stations close to the volcano. Variations in travel time residuals seen across the CODEX network were used to show initial evidence of a lower-velocity zone in the deep crust with a possible southwest-northeast trend near the volcano with depths of 20-40 km. Seismic tomography with the use of 3-D ray tracing helps to refine and better constrain the details of the low-velocity zone. It appears to be largely concentrated to the south-east of the volcano and extends approximately 30 km west-to-east. Other shallow crustal anomalies in the results match up well with surface geologic features. Additional anomalies in the crust, with a particular emphasis on velocity variations within the deep (>20 km) crust, are being investigated to achieve a better understanding of deep crustal processes underneath a prodigious subduction-zone volcano.

  8. Semiautomatic approaches to account for 3-D distortion of the electric field from local, near-surface structures in 3-D resistivity inversions of 3-D regional magnetotelluric data

    USGS Publications Warehouse

    Rodriguez, Brian D.

    2017-03-31

    This report summarizes the results of three-dimensional (3-D) resistivity inversion simulations that were performed to account for local 3-D distortion of the electric field in the presence of 3-D regional structure, without any a priori information on the actual 3-D distribution of the known subsurface geology. The methodology used a 3-D geologic model to create a 3-D resistivity forward (“known”) model that depicted the subsurface resistivity structure expected for the input geologic configuration. The calculated magnetotelluric response of the modeled resistivity structure was assumed to represent observed magnetotelluric data and was subsequently used as input into a 3-D resistivity inverse model that used an iterative 3-D algorithm to estimate 3-D distortions without any a priori geologic information. A publicly available inversion code, WSINV3DMT, was used for all of the simulated inversions, initially using the default parameters, and subsequently using adjusted inversion parameters. A semiautomatic approach of accounting for the static shift using various selections of the highest frequencies and initial models was also tested. The resulting 3-D resistivity inversion simulation was compared to the “known” model and the results evaluated. The inversion approach that produced the lowest misfit to the various local 3-D distortions was an inversion that employed an initial model volume resistivity that was nearest to the maximum resistivities in the near-surface layer.

  9. Crustal Deformation Analysis Using a 3D FE High-fidelity Model with a Fast Computation Method and Its Application to Inversion Analysis of Fault Slip in the 2011 Tohoku Earthquake

    NASA Astrophysics Data System (ADS)

    Agata, R.; Ichimura, T.; Hori, T.; Hirahara, K.; Hori, M.

    2012-12-01

    Crustal deformation analysis is important in order to understand the interplate coupling and coseismic fault slips. To perform it more accurately, we need a high-fidelity crustal structure model. However, in spite of accumulated crustal data, models with simplified flat shapes or relatively low resolution have been used, because the computation cost using high-fidelity models with a large degree-of-freedom (DOF) could be significantly high. Especially, estimation of the interplate coupling and coseismic fault slip requires the calculation of Green's function (the response displacement due to unit fault slip). To execute this computation in a realistic time, we need to reduce the computation cost. The objectives of our research is following: (1)To develop a method to generate 3D Finite Element (FE) models which represent heterogeneous crustal layers with the complex shape of crustal structure; (2)To develop a fast FE analysis method to perform crustal deformation analysis many times using single computation node, supposing the use of a small-scale computation environment. We developed an automatic FE model generation method using background grids with high quality meshes in a large area by extending the method of (Ichimura et al, 2009). We used Finite Element Method (FEM) because it has an advantage in representing the shape. Hybrid meshes consisting of tetrahedral and voxel elements are generated; the former is used when the interface surfaces and the grids intersect so that the shape of the crust is represented well, while the latter is used in the homogeneous areas. Also, we developed a method for crustal deformation analysis due to fault slip, which solves the FEM equation Ku=f assuming that the crust is an elastic body. To compute it fast, firstly we solved the problem by CG method with a simple preconditioning, parallelizing it by OpenMP. However, this computation took a long time, so we improved the method by introducing Multigrid Method (Saam, 2003) to the

  10. Air-structured optical fiber drawn from a 3D-printed preform.

    PubMed

    Cook, Kevin; Canning, John; Leon-Saval, Sergio; Reid, Zane; Hossain, Md Arafat; Comatti, Jade-Edouard; Luo, Yanhua; Peng, Gang-Ding

    2015-09-01

    A structured optical fiber is drawn from a 3D-printed structured preform. Preforms containing a single ring of holes around the core are fabricated using filament made from a modified butadiene polymer. More broadly, 3D printers capable of processing soft glasses, silica, and other materials are likely to come on line in the not-so-distant future. 3D printing of optical preforms signals a new milestone in optical fiber manufacture.

  11. 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

  12. Using "click-e-bricks" to make 3D elastomeric structures.

    PubMed

    Morin, Stephen A; Shevchenko, Yanina; Lessing, Joshua; Kwok, Sen Wai; Shepherd, Robert F; Stokes, Adam A; Whitesides, George M

    2014-09-10

    Soft, 3D elastomeric structures and composite structures are easy to fabricate using click-e-bricks, and the internal architecture of these structures together with the capabilities built into the bricks themselves provide mechanical, optical, electrical, and fluidic functions.

  13. 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

  14. 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.

  15. 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.

  16. Active Tectonics in the Central Chilean Andes: 3D Tomography Based on the Aftershock Sequence of the 28 August 2004 Shallow Crustal Earthquake

    NASA Astrophysics Data System (ADS)

    Comte, D.; Farias, M.; Charrier, R.; Gonzalez, A.

    2008-12-01

    Most of the seismological research in the Andes has been mainly oriented to the detection and understanding of the seismicity associated with megathrust earthquakes that characterize the subduction environment that governs the Andean tectonics. However, deployments of temporary networks have allowed the detection of intense crustal seismicity beneath the Chilean forearc-arc region. The temporary seismic network deployed along the Las Leñas and Pangal river valleys (34°25'S), between January and May 2004 permitted to better constrain the abundant shallow intra-continental seismicity previously detected in that region. Although most of the seismicity is randomly distributed in the region, several microearthquakes occur along the trace of the major El Fierro fault-system. This system is well recognized between 33°30' and 35°15'S and is located at or close to the eastern contact between Mesozoic and Cenozoic deposits in the Principal Cordillera and, locally, below active volcanoes, being considered to have participated in the extension and tectonic inversion of a widely extended (>600 km long) Cenozoic basin along the Principal Cordillera. Further south, at 35°S, a Mw=6.5 strike-slip shallow earthquake occurred on August 28, 2004, near of the headwater of the Teno river, close to the Planchon volcano. A 3D detailed Vp and Vs velocities determination was obtained along the 2004 earthquake aftershock area. The aftershocks are distributed along one branch of the El Fierro fault system, with a NNE-SSW direction and depths lower than 15 km. The rupture zone coincides with a sharp contrast in Vp and Vs, also in coincidence with the presence of hydrothermal fluids, gypsum diapers and the volcanic arc, suggesting rheological contrast controlling deformation. At the surface, this zone present an intense contractive deformation produced during the Neogene, which differs from what can be observed in other regions. Present day deformation related to seismicity has no

  17. 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…

  18. 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.

  19. Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

    PubMed Central

    Buchan, Daniel W.A.; Shepherd, Adrian J.; Lee, David; Pearl, Frances M.G.; Rison, Stuart C.G.; Thornton, Janet M.; Orengo, Christine A.

    2002-01-01

    We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies. PMID:11875040

  20. 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.

  1. 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.

  2. 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

  3. The 3D structures of VDAC represent a native conformation

    PubMed Central

    Hiller, Sebastian; Abramson, Jeff; Mannella, Carmen; Wagner, Gerhard; Zeth, Kornelius

    2010-01-01

    The most abundant protein of the mitochondrial outer membrane is the voltage-dependent anion channel (VDAC), which facilitates the exchange of ions and molecules between mitochondria and cytosol and is regulated by interactions with other proteins and small molecules. VDAC has been extensively studied for more than three decades, and last year three independent investigations revealed a structure of VDAC-1 exhibiting 19 transmembrane β-strands, constituting a unique structural class of β-barrel membrane proteins. Here, we provide a historical perspective on VDAC research and give an overview of the experimental design used to obtain these structures. Furthermore, we validate the protein refolding approach and summarize biochemical and biophysical evidence that links the 19-stranded structure to the native form of VDAC. PMID:20708406

  4. 3D Numerical Experiments of Lithospheric Transtension Reveal Complex Crustal-Scale Flow and Strain Partitioning in Transdomes

    NASA Astrophysics Data System (ADS)

    Rey, P. F.; Mondy, L. S.; Duclaux, G.; Teyssier, C. P.; Whitney, D. L.

    2015-12-01

    We have used Underworld to perform a series of numerical experiments involving a 256 x 256 x 128 km domain, at a grid resolution of 1.33 km. The kinematic boundary conditions simulate a lithospheric-scale pull-apart setting. We compare the structural and thermal evolution of a model involving a crust of thickness 40 km (TMoho=540ºC) with a model with a crust of thickness 60 km (TMoho=830ºC). We show that in the thick, hot crust model the flow in the pull-apart region is strongly partitioned between the strong upper crust and the weak lower crust. The weak, deep crust flows toward the pull-apart region to isostatically compensate the stretching and thinning of the upper crust. In contrast, the velocity field in the upper crust remains parallel to the imposed direction of extension. In the pull-apart region a transdome, made of two parallel foliation folds (or sub-domes), forms. In the dome, fabrics evolve from strong vertical flattening in between the two sub-domes, to shallow dipping constriction roughly parallel to the direction of extension in the upper part of the transdome.

  5. MUFOLD: A new solution for protein 3D structure prediction.

    PubMed

    Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong

    2010-04-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Calpha or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 A, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8.

  6. Structured light imaging system for structural and optical characterization of 3D tissue-simulating phantoms

    NASA Astrophysics Data System (ADS)

    Liu, Songde; Smith, Zach; Xu, Ronald X.

    2016-10-01

    There is a pressing need for a phantom standard to calibrate medical optical devices. However, 3D printing of tissue-simulating phantom standard is challenged by lacking of appropriate methods to characterize and reproduce surface topography and optical properties accurately. We have developed a structured light imaging system to characterize surface topography and optical properties (absorption coefficient and reduced scattering coefficient) of 3D tissue-simulating phantoms. The system consisted of a hyperspectral light source, a digital light projector (DLP), a CMOS camera, two polarizers, a rotational stage, a translation stage, a motion controller, and a personal computer. Tissue-simulating phantoms with different structural and optical properties were characterized by the proposed imaging system and validated by a standard integrating sphere system. The experimental results showed that the proposed system was able to achieve pixel-level optical properties with a percentage error of less than 11% for absorption coefficient and less than 7% for reduced scattering coefficient for phantoms without surface curvature. In the meanwhile, 3D topographic profile of the phantom can be effectively reconstructed with an accuracy of less than 1% deviation error. Our study demonstrated that the proposed structured light imaging system has the potential to characterize structural profile and optical properties of 3D tissue-simulating phantoms.

  7. Crustal structure across southern Mexico inferred from gravity data

    NASA Astrophysics Data System (ADS)

    Campos-Enríquez, J. O.; Sánchez-Zamora, O.

    2000-11-01

    We present a gravity model of the crustal structure in southern Mexico based on interpretation of a detailed marine gravity profile perpendicularly across the Middle America Trench offshore from Acapulco, and a regional gravity transect extending into continental Mexico across the Sierra Madre del Sur, the central sector of the Trans-Mexican Volcanic Belt, the Sierra Madre Oriental, the Coastal Plain, and into the Gulf of Mexico. The elastic thickness of the Cocos lithospheric plate was found to be 30 km. In agreement with a previous seismic refraction study, no major differences in crustal structure were observed on both sides of the O'Gorman Fracture Zone. The gravity high seaward of the trench is interpreted as due to the incipient flexure and crustal thinning. The gravity low at the axis of the trench is explained by the increase in water depth and the existence of low-density accreted or continental-derived sediments (2.25 and 2.40 g/cm 3). A gravity high of 50 mGal extending about 100 km landward is interpreted as caused by local shoaling of the Moho. The crust attains a thickness of 42 km under the Trans-Mexican Volcanic Belt but thins beneath the Coastal Plain and the continental slope of the Gulf of Mexico. Gravity highs around the Sierra de Tamaulipas are interpreted in terms of relief of the lower-upper crustal interface, implying a shallow basement.

  8. Subtractive 3D Printing of Optically Active Diamond Structures

    NASA Astrophysics Data System (ADS)

    Martin, Aiden A.; Toth, Milos; Aharonovich, Igor

    2014-05-01

    Controlled fabrication of semiconductor nanostructures is an essential step in engineering of high performance photonic and optoelectronic devices. Diamond in particular has recently attracted considerable attention as a promising platform for quantum technologies, photonics and high resolution sensing applications. Here we demonstrate the fabrication of optically active, functional diamond structures using gas-mediated electron beam induced etching (EBIE). The technique achieves dry chemical etching at room temperature through the dissociation of surface-adsorbed H2O molecules by energetic electrons in a water vapor environment. Parallel processing is possible by electron flood exposure and the use of an etch mask, while high resolution, mask-free, iterative editing is demonstrated by direct write etching of inclined facets of diamond microparticles. The realized structures demonstrate the potential of EBIE for the fabrication of optically active structures in diamond.

  9. Study on embedding fiber Bragg grating sensor into the 3D printing structure for health monitoring

    NASA Astrophysics Data System (ADS)

    Li, Ruiya; Tan, Yuegang; Zhou, Zude; Fang, Liang; Chen, Yiyang

    2016-10-01

    3D printing technology is a rapidly developing manufacturing technology, which is known as a core technology in the third industrial revolution. With the continuous improvement of the application of 3D printing products, the health monitoring of the 3D printing structure is particularly important. Fiber Bragg grating (FBG) sensing technology is a new type of optical sensing technology with unique advantages comparing to traditional sensing technology, and it has great application prospects in structural health monitoring. In this paper, the FBG sensors embedded in the internal structure of the 3D printing were used to monitor the static and dynamic strain variation of 3D printing structure during loading process. The theoretical result and experimental result has good consistency and the characteristic frequency detected by FBG sensor is consistent with the testing results of traditional accelerator in the dynamic experiment. The results of this paper preliminary validate that FBG embedded in the 3D printing structure can effectively detecting the static and dynamic stain change of the 3D printing structure, which provide some guidance for the health monitoring of 3D printing structure.

  10. Delineation of nuclear structures in 3D multicellular systems

    SciTech Connect

    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.

  11. Imaging solar coronal magnetic structures in 3D

    NASA Astrophysics Data System (ADS)

    Cartledge, N. P.

    The study of solar coronal structures and, in particular prominences, is a key part of understanding the highly complex physical mechanisms occurring in the Sun's atmosphere. Solar prominences are important in their own right and some of the most puzzling questions in solar theory have arisen through their study. For example, how do they form and how is their mass continuously replenished? How can the magnetic field provide their continuous support against gravity over time periods of several months? How can such cool, dense material exist in thermal equilibrium in the surrounding coronal environment? Why do they erupt? A study of their structure and that of the surrounding medium is important in determining the nature of the coronal plasma and magnetic field. Also, prominences are closely associated with other key phenomena such as coronal mass ejections and eruptive solar flares which occur as a prominence loses equilibrium and rises from the solar surface. Our current understanding of these fascinating structures is extremely limited and we know very little about their basic global structure. In fact, recent prominence observations have caused our basic paradigms to be challenged (Priest, 1996) and so we must set up new models in order to gain even a fundamental understanding. Prominences are highly nonlinear, three-dimensional structures. Large feet (or barbs) reach out from the main body of a prominence and reach down to the photosphere where the dense material continuously drains away. These provide a real clue to the three-dimensional nature of the coronal field and its relation to the photospheric field. It is important, therefore, to make stereographic observations of prominences in order to gain a basic understanding of their essentially three-dimensional nature and attempt to formulate new paradigms for their structure and evolution. There is no doubt that the study of prominences in three dimensions is a crucial exercise if we are to develop a better

  12. 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.

  13. Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures

    DTIC Science & Technology

    2015-11-17

    fabricated using 3D printer . The fill factor decreases radially outwards and the voids are visible in the unit cells as you approach the periphery of the...with thin walls) [29]. Figure 6: Examples of lenses fabricated with AM (a) GRIN lens fabricated using 3D printer . The fill factor decreases...AFRL-RW-EG-TP-2015-002 Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures Jeffery W. Allen Monica S. Allen Brett

  14. 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.

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

    SciTech Connect

    ANDERSON, C. A.

    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 is 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.

  16. 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.

  17. Lithospheric 3D gravity modelling using upper-mantle density constraints: Towards a characterization of the crustal configuration in the North Patagonian Massif area, Argentina

    NASA Astrophysics Data System (ADS)

    Gómez Dacal, María Laura; Tocho, Claudia; Aragón, Eugenio; Sippel, Judith; Scheck-Wenderoth, Magdalena; Ponce, Alexis

    2017-03-01

    The North Patagonian Massif is an Argentinean plateau that has an average height of 1200 m and stands from 500 to 700 m above the neighboring areas. During Paleogene, it suffered a sudden uplift of more than 1200 m without noticeable internal deformation; thus, it could be related to isostatic disequilibrium. To shed light on the geodynamic development of the area it is necessary to characterize the present-day configuration of the crust. In this study, a lithospheric-scale 3D density model was developed by integrating all the available data of the area with the objective of assessing the depth of the crust-mantle discontinuity (Moho). During the construction of the initial density model, we tested different mantle density scenarios obtained using P- and S-wave velocities from tomographic models, converting them into densities and comparing the conversions with densities obtained from xenoliths. Below the North Patagonian Massif plateau, we have derived a Moho depth between 40 and 50 km which is from 2 to 7 km deeper than its surroundings. There is an evident correlation between high topography and deep Moho that would indicate isostatic equilibrium at present. The model results provide a new approach to the Moho depth in an area where there is no seismic constraining information about this discontinuity. In addition, we found a spatial correlation between the variation of the mean crustal density and the location of the Paleozoic terranes that were proposed to constitute the basement of Argentina.

  18. 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

  19. 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.

  20. Small-angle scattering and 3D structure interpretation.

    PubMed

    Trewhella, Jill

    2016-10-01

    This review focuses on advances in the application of solution small-angle scattering (SAS) in structural analysis of biomolecules and the complexes they form. Examples highlighted illustrate the unique contribution of SAS, using both X-rays and neutrons, in hybrid or integrative modelling methods. The increased information content when neutron scattering with contrast variation is used is a particular focus. Finally, progress toward an agreed reporting framework, the development of open data and model archives, and the importance of these initiatives is covered.

  1. 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.

  2. 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

  3. Crustal structure near the Arctic Mid-Ocean ridge

    SciTech Connect

    Jackson, H.R.; Reid, I.; Falconer, R.K.H.

    1982-03-10

    Seismic reflection and crustal refraction studies were carried out at the FRAM I ice station near the Arctic Mid-Ocean Ridge crust. This ridge is spreading at the very slow rate of 55 mm yr/sup -1/. Upper mantle P/sub n/ arrivals with apparent velocities averaging 7.9 km/s are observed at distance ranges less than 15 km, with corresponding intercept times of typically 1:1 s of which 0.5 can be attributed to the travel path through a sedimentary layer. Anisotropy of about 6% appears to be present. These early P/sub n/ arrivals are observed on seven of the eight refraction lines studied, but crustal velocities are not well constrained. Modeling was done by computing travel time curves for a number of possible velocity structures for comparison with the data and suggests a crustal thickness between 2 and 3 km. This thin crust is associated with low-amplitude magnetic anomalies. The remaining refraction line was shot within a region of enhanced magnetic anomaly amplitudes the Yermak H zone, where the data interpretation indicates a crustal thickness of about 8 km. This thicker crust and associated strong magnetic anomalies may be due to the 'Yermak hot spot,' a region of high magmatic activity. The generally thin crust is probably due to low basaltic productivity at the ridge crest, as a result of increased cooling at the very slow spreading rate.

  4. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cuff, Alison; Dana, Jose M.; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Rackham, Owen J. L.; Smith, James; Sternberg, Michael J. E.; Velankar, Sameer; Yeats, Corin; Orengo, Christine

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs). PMID:23203986

  5. 3D nano-structures for laser nano-manipulation

    PubMed Central

    Seniutinas, Gediminas; Gervinskas, Gediminas; Brasselet, Etienne; Juodkazis, Saulius

    2013-01-01

    Summary The resputtering of gold films from nano-holes defined in a sacrificial PMMA mask, which was made by electron beam lithography, was carried out with a dry plasma etching tool in order to form well-like structures with a high aspect ratio (height/width ≈ 3–4) at the rims of the nano-holes. The extraordinary transmission through the patterns of such nano-wells was investigated experimentally and numerically. By doing numerical simulations of 50-nm and 100-nm diameter polystyrene beads in water and air, we show the potential of such patterns for self-induced back-action (SIBA) trapping. The best trapping conditions were found to be a trapping force of 2 pN/W/μm2 (numerical result) exerted on a 50-nm diameter bead in water. The simulations were based on the analytical Lorentz force model. PMID:24062979

  6. 3-D Structure of Sunspots using Imaging Spectroscopy

    NASA Technical Reports Server (NTRS)

    Balasubramaniam, K. S.; Gary, G. Allen; Reardon, K.

    2006-01-01

    We use the Interferometric BIdimensional Spectrometer (IBIS) of the INAF/Arcetri Astrophysical Observatory and installed at the National Solar Observatory (NSO) Dunn Solar Telescope, to understand the structure of sunspots. Using the spectral lines FeI 6301.5 A, FeII 7224.4 A, and CaII 8542.6 A, we examine the spectroscopic variation of sunspot penumbral and umbral structures at the heights of formation of these lines. These high resolution observations were acquired on 2004 July 30-31, of active region NOAA 10654, using the high order NSO adaptive optics system. We map the spatio-temporal variation of Doppler signatures in these spectral lines, from the photosphere to the chromosphere. From a 70-minute temporal average of individual 32-second cadence Doppler observations we find that the averaged velocities decrease with height, about 3.5 times larger in the deeper photosphere (FeII 7224.4 A; height-of-formation approx. 50 km) than in the upper photosphere FeI 6301.5 A; height-of-formation approx. 350 km), There is a remarkable coherence of Doppler signals over the height difference of 300 km. From a high-speed animation of the Doppler sequence we find evidence for what appears to be ejection of high speed gas concentrations from edges of penumbral filaments into the surrounding granular photosphere. The Evershed flow persists a few arcseconds beyond the traditionally demarcated penumbra-granulation boundary. We present these and other results and discuss the implications of these measurements for sunspot models.

  7. Fabrication of 2D and 3D photonic structures using laser lithography

    NASA Astrophysics Data System (ADS)

    Gaso, P.; Jandura, D.; Pudis, D.

    2016-12-01

    In this paper we demonstrate possibilities of three-dimensional (3D) printing technology based on two photon polymerization. We used three-dimensional dip-in direct-laser-writing (DLW) optical lithography to fabricate 2D and 3D optical structures for optoelectronics and for optical sensing applications. DLW lithography allows us use a non conventional way how to couple light into the waveguide structure. We prepared ring resonator and we investigated its transmission spectral characteristic. We present 3D inverse opal structure from its design to printing and scanning electron microscope (SEM) imaging. Finally, SEM images of some prepared photonic crystal structures were performed.

  8. 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).

  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. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J. ); Jones, G.L. )

    1996-01-01

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  11. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J.; Jones, G.L.

    1996-12-31

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  12. 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.

  13. Electrodeposition-based 3D Printing of Metallic Microarchitectures with Controlled Internal Structures.

    PubMed

    Seol, Seung Kwon; Kim, Daeho; Lee, Sanghyeon; Kim, Jung Hyun; Chang, Won Suk; Kim, Ji Tae

    2015-08-26

    3D printing of metallic microarchitectures with controlled internal structures is realized at room temperature in ambient air conditions by the manipulation of metal ion concentration and pulsed electric potentials in the electrolyte meniscus during the meniscus-guided electrodeposition. Precise control of the printing nozzle enables the drawing of complex 3D microarchitectures with well-defined geometries and positions.

  14. 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

  15. Searching protein 3-D structures for optimal structure alignment using intelligent algorithms and data structures.

    PubMed

    Novosád, Tomáš; Snášel, Václav; Abraham, Ajith; Yang, Jack Y

    2010-11-01

    In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the current research collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins--all to all protein similarity. For the calculation of protein similarity, we use term frequency × inverse document frequency ( tf × idf ) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision. We have chosen the structural classification of proteins (SCOP) database for verification of the precision of our algorithm because it is maintained primarily by humans. The next success of this paper would be the ability to determine SCOP categories of proteins not included in the latest version of the SCOP database (v. 1.75) with nearly 100% precision.

  16. 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.

  17. 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

  18. Crustal structure of central Syria: The intracontinental Palmyride mountain belt

    NASA Astrophysics Data System (ADS)

    Al-Saad, Damen; Sawaf, Tarif; Gebran, Ali; Barazangi, Muawia; Best, John A.; Chaimov, Thomas A.

    1992-07-01

    Along a 450-km transect across central Syria seismic reflection data, borehole information, potential field data and surface geologic mapping have been combined to examine the crustal structure of the northern Arabian platform beneath Syria. The transect is surrounded by the major plate boundaries of the Middle East, including the Dead Sea transform fault system along the Levantine margin to the west, the Bitlis suture and East Anatolian fault to the north, and the Zagros collisional belt to the northeast and east. Three main tectonic provinces of the northern Arabian platform in Syria are crossed by this transect from south to north: the Rutbah uplift, the Palmyra fold-thrust belt, and the Aleppo plateau. The Rutbah uplift in southern Syria is a broad, domal basement-cored structure with a thick Phanerozoic (mostly Paleozoic) cover of 6-7 km. Isopachs based on well and seismic reflection data indicate that this region was an early Paleozoic depocenter. The Palmyra fold-thrust belt, the northeastern arm of the Syrian Arc, is a northeast-southwest-trending intracontinental mountain belt that acts as a mobile tectonic zone between the relatively stable Rutbah uplift to the south and the less stable Aleppo plateau to the north. Short-wavelength en-echelon folds characterized by relatively steep, faulted southeast flanks dominate in the southwest, most strongly deformed segment of the belt, while a complex system of deeply rooted faults and broad folds characterize the northeastern region, described in this study. The Aleppo plateau lies immediately north of the Palmyride belt, with a combined Paleozoic and Mesozoic sedimentary section that averages 4-5 km in thickness. Although this region appears relatively undeformed on seismic reflection data when compared to Palmyride deformation, a system of near-vertical, probable strike-slip faults crosscut the region in a dominantly northeasterly direction. Gravity and magnetic modeling constrains the deep crustal structure

  19. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere.

  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. 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.

  2. 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.

  3. Crustal Thickness and Lower Crustal Velocity Structure Beneath the Endeavour Segment of the Juan de Fuca Ridge

    NASA Astrophysics Data System (ADS)

    Hill, R.; Soule, D. C.; Wilcock, W. S. D.; Toomey, D. R.; Hooft, E. E. E.; Weekly, R. T.

    2014-12-01

    In 2009, a multi-scale seismic tomography experiment was conducted on the Endeavour segment of the Juan de Fuca Ridge aboard the R/V Marcus G. Langseth. Ocean bottom seismometers were deployed at 64 sites and recorded 5567 shots of a 36-element, 6600 in.3 airgun array. The experiment extended 100 km along-axis and 60 km cross-axis. Two crustal tomographic analyses have previously been completed using data from the experiment. First, 93,000 manually picked crustal refraction arrivals (Pg) were used to develop a three-dimensional model of crustal velocity and thickness in the upper crust (Weekly et al. 2014). Second, this model was used as the starting model in an analysis that incorporated ~19,000 Moho reflection arrivals (PmP) for non-ridge crossing paths to image lower crustal velocity structure and crustal thickness off-axis. A key feature of this model is a ~0.5-1 km increase in crustal thickness beneath a bathymetric plateau that extends to either side of the central portion of the Endeavour segment. We present a tomographic inversions that incorporates ridge-crossing paths to examine spatial variations in lower crustal velocity and crustal thickness beneath the ridge axis. The preliminary results from an inversion that incorporates ~8700 manually picked ridge-crossing PmP arrival times reveals a ~10-km-wide low velocity zone extending throughout the lower crust with a velocity anomaly of -0.3 to -0.5 km/s at ≥4 km depth. This low velocity zone extends both to the north and south of the axial magma chamber reflector imaged previously beneath the central Endeavour. The inversion also shows significant variations in apparent crustal thickness along axis but additional analysis is required to understand whether these variations are well resolved.

  4. Crustal velocity structure of western Dharwar Craton, South India

    NASA Astrophysics Data System (ADS)

    Sarkar, D.; Chandrakala, K.; Padmavathi Devi, P.; Sridhar, A. R.; Sain, K.; Reddy, P. R.

    2001-03-01

    A deep seismic sounding (DSS) experiment was carried out across the Indian shield in 1972-1975. Kaila et al. (Kaila, K.L., Roy Chowdhury, K., Reddy, P.R., Krishna, V.G., Hari Narain, Subbotin, S.I., Sollogub, V.B., Chekunov, A.V., Kharetchko, G.E., Lazarenko, M.A., Ilchenko T.V., 1979. Crustal structure along Kavali-Udipi profile in the Indian peninsular shield from deep seismic sounding. J. Geol. Soc. of Ind., 20, 307-333) presented a crustal depth section based on the interpretation of the analog seismic data. In this paper, we re-examine the crustal structure of the Western Dharwar Craton (WDC) by reprocessing the data of three major shot points. Kinematic 1-D inversion, followed by 2-D forward modeling of the first arrival refraction and a few persistent wide-angle reflection phases, was carried out to build, a first order two-dimensional velocity model of this segment of the profile. This model brings out a simple crustal velocity structure consisting of an upper and lower crust. The upper crust (velocity 6.0-6.2 km/s) is on average 23 km thick, which is underlain by a lower crust of velocity 6.8-7.0 km/s. The average Moho depth in this part is about 37-40 km, with higher-than-normal P n velocity of 8.4 km/s. A relatively deep Moho in this part of the Archean peninsular shield is associated with relatively low velocities in the lower crust, perhaps indicating absence of underplating in this region. Present results bring out the fact that the crust of WDC is not so typical as many other Archean crusts, in terms of both thickness and velocities.

  5. 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.

  6. Fluorescence in situ hybridization applications for super-resolution 3D structured illumination microscopy.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Cremer, Marion; Schermelleh, Lothar

    2013-01-01

    Fluorescence in situ hybridization on three-dimensionally preserved cells (3D-FISH) is an efficient tool to analyze the subcellular localization and spatial arrangement of targeted DNA sequences and RNA transcripts at the single cell level. 3D reconstructions from serial optical sections obtained by confocal laser scanning microscopy (CLSM) have long been considered the gold standard for 3D-FISH analyses. Recent super-resolution techniques circumvent the diffraction-limit of optical resolution and have defined a new state-of-the-art in bioimaging. Three-dimensional structured illumination microscopy (3D-SIM) represents one of these technologies. Notably, 3D-SIM renders an eightfold improved volumetric resolution over conventional imaging, and allows the simultaneous visualization of differently labeled target structures. These features make this approach highly attractive for the analysis of spatial relations and substructures of nuclear targets that escape detection by conventional light microscopy. Here, we focus on the application of 3D-SIM for the visualization of subnuclear 3D-FISH preparations. In comparison with conventional fluorescence microscopy, the quality of 3D-SIM data is dependent to a much greater extent on the optimal sample preparation, labeling and acquisition conditions. We describe typical problems encountered with super-resolution imaging of in situ hybridizations in mammalian tissue culture cells and provide optimized DNA-/(RNA)-FISH protocols including combinations with immunofluorescence staining (Immuno-FISH) and DNA replication labeling using click chemistry.

  7. 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.

  8. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

    PubMed Central

    Li, Haotian; Huang, Yangyu

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets. PMID:28358834

  9. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.

    PubMed

    Li, Haotian; Huang, Yangyu; Xiao, Yi

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets.

  10. A 3D acquisition system combination of structured-light scanning and shape from silhouette

    NASA Astrophysics Data System (ADS)

    Sun, Changku; Tao, Li; Wang, Peng; He, Li

    2006-05-01

    A robust and accurate three dimensional (3D) acquisition system is presented, which is a combination of structured-light scanning and shape from silhouette. Using common world coordinate system, two groups of point data can be integrated into the final complete 3D model without any integration and registration algorithm. The mathematics model of structured-light scanning is described in detail, and the shape from silhouette algorithm is introduced as well. The complete 3D model of a cup with a handle is obtained successfully by the proposed technique. At last the measurement on a ball bearing is performed, with the measurement precision better than 0.15 mm.

  11. 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

  12. 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

  13. The Crustal Structure and Seismicity of Eastern Venezuela

    NASA Astrophysics Data System (ADS)

    Schmitz, M.; Martins, A.; Sobiesiak, M.; Alvarado, L.; Vasquez, R.

    2001-12-01

    from FU-Berlin and IRIS/PASSCAL Instrument Centre. key words: Seismic refraction, seismicity, crustal structure, Venezuela, Cariaco earthquake.

  14. 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.

  15. 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

  16. Deformable registration of 3D vessel structures to a single projection image

    NASA Astrophysics Data System (ADS)

    Zikic, Darko; Groher, Martin; Khamene, Ali; Navab, Nassir

    2008-03-01

    Alignment of angiographic preoperative 3D scans to intraoperative 2D projections is an important issue for 3D depth perception and navigation during interventions. Currently, in a setting where only one 2D projection is available, methods employing a rigid transformation model present the state of the art for this problem. In this work, we introduce a method capable of deformably registering 3D vessel structures to a respective single projection of the scene. Our approach addresses the inherent ill-posedness of the problem by incorporating a priori knowledge about the vessel structures into the formulation. We minimize the distance between the 2D points and corresponding projected 3D points together with regularization terms encoding the properties of length preservation of vessel structures and smoothness of deformation. We demonstrate the performance and accuracy of the proposed method by quantitative tests on synthetic examples as well as real angiographic scenes.

  17. 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.

  18. 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

  19. 3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

    PubMed

    Brigo, Laura; Urciuolo, Anna; Giulitti, Stefano; Giustina, Gioia Della; Tromayer, Maximilian; Liska, Robert; Elvassore, Nicola; Brusatin, Giovanna

    2017-03-25

    Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5 µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures.

  20. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

    PubMed Central

    Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian

    2017-01-01

    Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation

  1. Edge structure preserving 3D image denoising by local surface approximation.

    PubMed

    Qiu, Peihua; Mukherjee, Partha Sarathi

    2012-08-01

    In various applications, including magnetic resonance imaging (MRI) and functional MRI (fMRI), 3D images are becoming increasingly popular. To improve the reliability of subsequent image analyses, 3D image denoising is often a necessary preprocessing step, which is the focus of the current paper. In the literature, most existing image denoising procedures are for 2D images. Their direct extensions to 3D cases generally cannot handle 3D images efficiently because the structure of a typical 3D image is substantially more complicated than that of a typical 2D image. For instance, edge locations are surfaces in 3D cases which would be much more challenging to handle compared to edge curves in 2D cases. We propose a novel 3D image denoising procedure in this paper, based on local approximation of the edge surfaces using a set of surface templates. An important property of this method is that it can preserve edges and major edge structures (e.g., intersections of two edge surfaces and pointed corners). Numerical studies show that it works well in various applications.

  2. Crustal structure variation along the Lesser Antilles Arc

    NASA Astrophysics Data System (ADS)

    Schlaphorst, David; Kendall, Mike; Blundy, Jon; Melekhova, Elena; Baptie, Brian; Latchman, Joan; Bouin, Marie-Paule; Tait, Steve

    2014-05-01

    Subduction zones are the major location for the formation of continental crust. Therefore, an investigation of the crustal and mantle structure variation of these areas helps understanding the process of continental crust growth. Here we focus on a seismological investigation of the Lesser Antilles Arc. This island arc system is built by the relatively slow subduction (~ 2cm/yr) of the North and South American plates beneath the Caribbean plate. From the island of Grenada in the South to the Virgin Islands in the North significant variations in sediment load, petrology and volcanism are observed along the arc. The abundance of broadband seismic stations on the Lesser Antilles islands in combination with the abundance of cumulated samples allows for a link between the seismic methods with a detailed petrological analysis. We use data from three-component broadband stations located on the individual islands along the arc. We investigate crustal structure using receiver functions to determine Moho depth and V P/V S ratio. The ratio gives an idea about the material of the subsurface as well as its water and its melt contents. We use the extended-time multitaper frequency domain cross-correlation receiver-function (ETMTRF) by Helffrich (2006) to compute the receiver functions. This method has the advantage of resistance to noise and gives stable solutions for the data, despite its large amount of oceanic noise. Our results show clear along-arc crustal properties. There are regions where the Moho is not very sharp due to a low velocity contrast. The real data results are then compared to synthetic receiver functions based on plausible models. We compute a range of synthetic crustal models and receiver functions based on petrologic constraints from cumulates. The seismic velocities are obtained from experimental data using different temperatures and pressures to simulate different depths. The initial water content was also varied to model dry and wet slab conditions. Our

  3. 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

  4. 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.

  5. The crustal structure of the Alpha Ridge, Arctic Ocean (Invited)

    NASA Astrophysics Data System (ADS)

    Funck, T.; Jackson, H. R.; Shimeld, J.

    2010-12-01

    In March and April 2008, refraction and reflection seismic data were acquired over Alpha Ridge in the Arctic Ocean as part of the ARTA project. The refraction seismic data set comprises two lines. The main line extends from the mouth of Nansen Sound between Axel Heiberg Island and Ellesmere Island, across the shelf and onto the Alpha Ridge; the total length is 350 km. Data along this line were acquired with an average receiver spacing of 1.3 km. The seismic energy was created by explosive charges; the spacing between shots was 22 km. A 175-km-long cross line was located on Alpha Ridge with a receiver and shot spacing of 1.5 km and 21 km, respectively. Water depth and gravity were measured at all receiver locations. Reflection seismic data were acquired from a drifting ice camp close to the cross line, utilizing a 10 cu. in. sleeve gun and three hydrophones. The length of the drift path was 27 km. Velocity models for both refraction seismic lines were developed by forward and inverse techniques (RAYINVR). In addition, a tomographic inversion (JIVE3D) was carried out along the main line. On the main line, up to 30-km-thick continental crust is encountered in the south, which is divided into three layers with velocities ranging from 5.5 to 6.6 km/s. The Moho shallows northward to 23 km and an up to 8-km-thick sedimentary basin is observed (1.6 to 4.5 km/s). Below the shelf, the crustal velocities increase to 6.2 to 6.8 km/s and a high-velocity lower crustal layer (7.5 km/s) with a maximum thickness of 9 km appears, which results in a gradual northward deepening of the Moho to 32 km. Together with the high-velocity lower crust, a 2-km-thick layer with velocities of 5.0 km/s is observed, which overlies the crust and is interpreted as volcanic layer. Both layers are interpreted to relate to the formation of the Alpha Ridge. The ridge itself farther to the north is characterized by three crustal layers. A 2-to 5-km-thick upper layer with velocities of 4.7 to 5.4 km/s and

  6. The Crustal and Mantle Velocity Structure in Central Asia from 3D Travel Time Tomography

    DTIC Science & Technology

    2010-09-01

    to the southern margin of Asia during the Paleozoic- Mesozoic closure of the Tethys Ocean (Tapponnier et al., 1981; Burtman and Molnar, 1993; Yin...Proust, and C. Cassaigneau (1981). Mesozoic ophiolites, sutures, and large scale tectonic movements in Afghanistan, Earth Planet. Sci. Lett. 52: 355–371

  7. A 3-D Puzzle Approach to Building Protein-DNA Structures.

    PubMed

    Hinton, Deborah M

    2017-02-02

    Despite recent advances in structural analysis, it is still challenging to obtain a high resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3-D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.

  8. 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.

  9. 3D and 4D atlas system of living human body structure.

    PubMed

    Suzuki, N; Takatsu, A; Hattori, A; Ezumi, T; Oda, S; Yanai, T; Tominaga, H

    1998-01-01

    A reference system for accessing anatomical information from a complete 3D structure of the whole body "living human", including 4D cardiac dynamics, was reconstructed with 3D and 4D data sets obtained from normal volunteers. With this system, we were able to produce a human atlas in which sectional images can be accessed from any part of the human body interactively by real-time image generation.

  10. Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.

    PubMed

    Weisenburger, Siegfried; Boening, Daniel; Schomburg, Benjamin; Giller, Karin; Becker, Stefan; Griesinger, Christian; Sandoghdar, Vahid

    2017-02-01

    We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology.

  11. Linear-time protein 3-D structure searching with insertions and deletions

    PubMed Central

    2010-01-01

    Background Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools for searching for similar structures in biomolecular 3-D structure databases are becoming increasingly important in the structural biology of the post-genomic era. Results We consider an important, fundamental problem of reporting all substructures in a 3-D structure database of chain molecules (such as proteins) which are similar to a given query 3-D structure, with consideration of indels (i.e., insertions and deletions). This problem has been believed to be very difficult but its exact computational complexity has not been known. In this paper, we first prove that the problem in unbounded dimensions is NP-hard. We then propose a new algorithm that dramatically improves the average-case time complexity of the problem in 3-D in case the number of indels k is bounded by a constant. Our algorithm solves the above problem for a query of size m and a database of size N in average-case O(N) time, whereas the time complexity of the previously best algorithm was O(Nmk+1). Conclusions Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant. PMID:20047663

  12. Tailored complex 3D vortex lattice structures by perturbed multiples of three-plane waves.

    PubMed

    Xavier, Jolly; Vyas, Sunil; Senthilkumaran, Paramasivam; Joseph, Joby

    2012-04-20

    As three-plane waves are the minimum number required for the formation of vortex-embedded lattice structures by plane wave interference, we present our experimental investigation on the formation of complex 3D photonic vortex lattice structures by a designed superposition of multiples of phase-engineered three-plane waves. The unfolding of the generated complex photonic lattice structures with higher order helical phase is realized by perturbing the superposition of a relatively phase-encoded, axially equidistant multiple of three noncoplanar plane waves. Through a programmable spatial light modulator assisted single step fabrication approach, the unfolded 3D vortex lattice structures are experimentally realized, well matched to our computer simulations. The formation of higher order intertwined helices embedded in these 3D spiraling vortex lattice structures by the superposition of the multiples of phase-engineered three-plane waves interference is also studied.

  13. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy.

    PubMed

    Punjani, Ali; Brubaker, Marcus A; Fleet, David J

    2017-04-01

    Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

  14. Single cell detection using 3D magnetic rolled-up structures.

    PubMed

    Ger, Tzong-Rong; Huang, Hao-Ting; Huang, Chen-Yu; Lai, Mei-Feng

    2013-11-07

    A 3D rolled-up structure made of a SiO2 layer and a fishbone-like magnetic thin film was proposed here as a biosensor. The magnetoresistance (MR) measurement results of the sensor suggest that the presence of the stray field, which is induced by the magnetic nanoparticles, significantly increased the switching field. Comparing the performance of the 2D sensor and 3D sensor designed in this study, the response in switching field variation was 12.14% in the 2D sensor and 62.55% in the 3D sensor. The response in MR ratio variation was 4.55% in the 2D sensor and 82.32% in the 3D sensor. In addition, the design of the 3D sensor structure also helped to attract and trap a single magnetic cell due to its stronger stray field compared with the 2D structure. The 3D magnetic biosensor designed here can provide important information for future biochip research and applications.

  15. 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

  16. Efficient global wave propagation adapted to 3-D structural complexity: a pseudospectral/spectral-element approach

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-12-01

    We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34 s down to 11 s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.

  17. 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

  18. 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

  19. Regional Geophysical Surveys and Crustal Structure of the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Rodríguez-Chavez, F.; Fucugauchi, J. U.

    2007-05-01

    Results of processing and modeling of anomaly data from regional geophysical surveys in the southern sector of the Gulf of Mexico are presented. The Gulf of Mexico has been intensively studied for several years, mainly because of the economic potential of the oil and gas resources. The basin may have formed by sea-floor spreading, rifting and lateral translation/rotation of continental slivers ssociated with major break-up and drifting apart of North and South America continental plates in the mid Mesozoic. Major structural features and crustal structure, including the continent-ocean transition and Gulf coastal passive margin are relatively poorly understood. Aerogeophysical gravity and magnetic surveys have been conducted and data are processed and modeled to investigate on the Gulf crustal structure. Spectral statistical estimates of regional basement depths derived from aeromagnetics give mean depths of 8000 m. Estimates derived from gravity anomalies are in the order of 10000 m. Depths derived from 2D and 3D seismic reflection surveys conducted for oil exploration purposes in selected areas indicate average depths to basement from 6000 m to values grater than those derived from potential field data.

  20. Crustal structure of the high Andes in the North Pampean flat slab segment from magnetic and gravity data

    NASA Astrophysics Data System (ADS)

    Sánchez, Marcos A.; Winocur, Diego; Álvarez, Orlando; Folguera, Andrés; Martinez, Myriam P.

    2017-01-01

    The Main Andes at the northern Chilean-Pampean flat slab segment were formed by the inversion of late Oligocene to early Miocene extensional depocenters in Neogene times. Their structure, size and depth are loosely constrained by field data since these sequences have amalgamated forming an almost continuous blanket with scarce basement outcrops. Satellite and aerial gravity and magnetic data are used in this work to define a 3D model that shows the basement structure at depth and adjust 2D structural sections previously based on field data. The results indicate complex basin geometry with depocenters of variable size and depth buried beneath Mesozoic (?)-Paleogene and Neogene sections. Additionally, previously proposed crustal heterogeneities across this orogenic segment are geophysically constrained with a new crustal heterogeneity identified on the basis of a modeled 2D crustal section. We propose hypothetically, that this crustal discontinuity could have played a role in controlling Paleogene extension at the hanging wall of an asymmetric rift basin, explaining the locus and development of the Doña Ana Basin. Finally, this work provides new information about Cenozoic structure and Paleozoic basement architecture, presumably derived from amalgamation history of one of the highest and more inaccessible regions of the Andes.

  1. 3D-printing and mechanics of bio-inspired articulated and multi-material structures.

    PubMed

    Porter, Michael M; Ravikumar, Nakul; Barthelat, Francois; Martini, Roberto

    2016-12-21

    3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic.

  2. 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.

  3. 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.

  4. 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.

  5. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Definition of subsurface stratigraphy, structure and rock properties from 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Hart, Bruce S.

    1999-10-01

    This paper summarizes how three-dimensional (3-D) seismic technology is being used, primarily in the petroleum industry, to define subsurface structure, stratigraphy and rock properties. A 3-D seismic data volume: (a) provides a more accurate image of the subsurface than can be obtained with 2-D seismic methods; (b) is continuous, and so has a much greater spatial sampling than is obtained with 2-D seismic or other subsurface data (e.g., wells); and (c) can be viewed and interpreted interactively from a variety of perspectives, thus enhancing the interpreter's ability to generate an accurate description of subsurface features of interest. Seismic interpretation was once the almost exclusive realm of geophysicists, however, most 3-D seismic interpretation today is conducted by multidisciplinary teams that integrate geophysical, geological, petrophysical and engineering data and concepts into the 3-D seismic interpretation. These factors, plus proper survey design, help to increase the chances of success of a 3-D seismic interpretation project. Although there are cases where the technology is not appropriate or cannot be applied (for economic reasons or otherwise), the general success of 3-D seismic has led it to become a mainstay of the petroleum industry. The approach and technology, first developed in that industry, have potential applications in other applied and fundamental earth science disciplines, including mining, environmental geology, structural geology and stratigraphy.

  11. 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.

  12. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    PubMed

    McGuire, Ross; Verhoeven, Stefan; Vass, Márton; Vriend, Gerrit; de Esch, Iwan J P; Lusher, Scott J; Leurs, Rob; Ridder, Lars; Kooistra, Albert J; Ritschel, Tina; de Graaf, Chris

    2017-02-27

    3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

  13. 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.

  14. Novel scanning electron microscopy methods for analyzing the 3D structure of the Golgi apparatus.

    PubMed

    Koga, Daisuke; Ushiki, Tatsuo; Watanabe, Tsuyoshi

    2017-01-01

    The structure of the Golgi apparatus has been extensively examined by light and electron microscopy, but details of its three-dimensional (3D) structure have remained unclear because of the technical limitations of conventional microscopy techniques. To overcome this problem, we have developed several novel scanning electron microscopy (SEM) methods for observing the 3D structure of subcellular organelles including the Golgi apparatus: (1) an osmium maceration method that facilitates SEM observation of membranous organelles, including the Golgi apparatus, by selectively removing soluble cytoplasmic proteins, (2) an osmium impregnation/maceration method that combines an osmium impregnation method with the osmium maceration method to determine the polarity of the Golgi apparatus by SEM, (3) a correlative light and SEM method that combines a cryosectioning technique with the osmium maceration method to enable correlation of the immunocytochemical distribution of molecules with the 3D ultrastructure of the Golgi apparatus, and (4) array tomography based on the systematic collection and integration of SEM images of serial ultrathin sections on glass slides for revealing the 3D ultrastructure of the entire Golgi apparatus. Together, the novel SEM techniques listed above can reveal the complete 3D structure of the Golgi apparatus in different cell types.

  15. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    PubMed Central

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine (http://3d-e-chem.github.io/3D-e-Chem-VM/) that integrates cheminformatics and bioinformatics tools for the analysis of protein–ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein–ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb). PMID:28125221

  16. 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

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

    PubMed

    Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

    2015-04-28

    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.

  18. Crustal structure variations along the Lesser Antilles Arc

    NASA Astrophysics Data System (ADS)

    Schlaphorst, D.; Kendall, J. M.; Melekhova, E.; Blundy, J.; Baptie, B.; Latchman, J. L.

    2013-12-01

    Continental crust is predominantly formed along subduction zones. Therefore, an investigation of the crustal and mantle structure variation of these areas is crucial for understanding the growth of continental crust. This work deals with the seismological characteristics along the Lesser Antilles Arc, an island arc system built by the relatively slow subduction (~2cm/yr) of the North and South American plates beneath the Caribbean plate. The amount of subducted sediments changes significantly from sediment-rich subduction in the South to sediment-poor subduction in the North. The abundance of broadband seismic stations on the Lesser Antilles islands enables a range of seismic methods to be used to study arc processes. Furthermore, the abundance of cumulate samples allows for a detailed petrological analysis, which can be related to the seismological patterns. We use data from three component broadband stations located on the individual islands along the arc. From the island of Grenada in the South to the Virgin Islands in the North significant variations in sediment load, petrology and volcanism are observed along the arc. In this work, we investigate crustal structure using receiver functions to determine Moho depth and Vp/Vs ratio. The ratio gives an idea about the material of the subsurface as well as its water and its melt contents. The receiver functions are computed using the extended-time multitaper frequency domain cross-correlation receiver-function (ETMTRF) by Helffrich (2006). This method has the advantage of resistance to noise, which is helpful since most of the data around the arc will have been collected by stations close to the ocean, thus containing a large amount of noise. Our results show clear variations in these measurements. There are also regions where the Moho is not very sharp due to a low velocity contrast. The real data results were then compared to synthetic receiver functions from subsurface models. We compute a range of synthetic

  19. Preliminary Results of Crustal Structure beneath the Wabash Valley Seismic Zone Using Teleseismic Receiver Functions and Ambient Noise Tomography

    NASA Astrophysics Data System (ADS)

    Zhu, L.; Aziz Zanjani, A.; Hu, S.; Liu, Y.; Herrmann, R. B.; Conder, J. A.

    2015-12-01

    As part of a on-going EarthScope FlexArray project, we deployed 45 broadband seismographs in a 300-km-long linear profile across the Wabash Valley Seismic Zone (WVSZ). Here we present preliminary results of crustal structure beneath WVSZ based on teleseismic receiver functions and ambient noise tomography. We combined waveform data of the temporary stations in 2014 with those of permanent seismic stations and the transportable array stations in our study area since 2011. We found 656 teleseismic events with clear P-wave signals and obtained 2657 good-quality receiver functions of 84 stations using a time-domain iterative deconvolution method. We estimated crustal thickness and Vp/Vs ratio beneath each station using the H-κ stacking method. A high-resolution crustal structural image along the linear profile was obtained using the Common-Conversion-Point (CCP) stacking method. We also measured Rayleigh-wave phase and group velocities from 5 to 50 s by cross-correlating ambient noises between stations and did joint-inversion of receiver functions and surface wave dispersions for S-velocity structures beneath selected stations. The results show that the average crustal thickness in the region is 47 km with a gentle increase of crustal thickness from southeast to northwest. A mid-crustal interface is identified in the CCP image that also deepens from 15 km in the southeastern end to >20 km in the northwest. The CCP image shows that the low-velocity sedimentary layer along the profile is broad and is thickest (~10 km) near the center of the Wabash Valley. Beneath the center of the Valley there is a 40-km-wide positive velocity discontinuity at a depth of 40 km in the lower crust that might be the top of a rift pillow in this failed continental rift. Further results using 3D joint inversion and CCP migration will be presented at the meeting.

  20. 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.

  1. Structure-From-Motion in 3D Space Using 2D Lidars

    PubMed Central

    Choi, Dong-Geol; Bok, Yunsu; Kim, Jun-Sik; Shim, Inwook; Kweon, In So

    2017-01-01

    This paper presents a novel structure-from-motion methodology using 2D lidars (Light Detection And Ranging). In 3D space, 2D lidars do not provide sufficient information for pose estimation. For this reason, additional sensors have been used along with the lidar measurement. In this paper, we use a sensor system that consists of only 2D lidars, without any additional sensors. We propose a new method of estimating both the 6D pose of the system and the surrounding 3D structures. We compute the pose of the system using line segments of scan data and their corresponding planes. After discarding the outliers, both the pose and the 3D structures are refined via nonlinear optimization. Experiments with both synthetic and real data show the accuracy and robustness of the proposed method. PMID:28165372

  2. Deep Crustal Structure of S-Atlantic Margins

    NASA Astrophysics Data System (ADS)

    Becker, K.; Schnabel, M.; Franke, D.; Heyde, I.; Schreckenberger, B.; Koopmann, H.; Krawczyk, C. M.; Trumbull, R. B.

    2013-12-01

    We investigate the crustal structure along the southern South Atlantic margins with a focus on the high velocity lower crustal bodies (HVLC). This is a distinct zone at the base of the crust, where seismic P-wave velocities exceed 7.0 km/s and locally reach values up to 7.7 km/s. The study is based on a selected set of refraction seismic lines on conjugate margin segments of Uruguay-Argentina and Namibia-South Africa, acquired during marine geophysical cruises in 2004 and 1998. We performed new P-wave tomography complemented with gravity modeling along two crustal transects, and combine these with previous seismic and gravity models. The results are used to examine the interplay of rifting and magmatism during the evolution of the South Atlantic, what activated the spreading phase and how this is reflected in the distribution of high velocity lower crust. On all sections we observe HVLC, even on a magma poor southernmost section at the western margin. The HVLC varies strongly in shape and size along the margin. From South to North the area of the HVLC on 2D velocity sections increases on both margins. However, the HVLC bodies along the South American margin are much smaller than on the South African margin, possibly indicating asymmetric break up. A striking feature is the distinct seaward shift of the HVLC relative to the seaward dipping reflectors (SDRs). While in the south, the HVLC is situated below the SDRs, towards the north the HVLC formed seaward of the SDRs. From this seaward migration we infer that the formation of HVLC in the magma-rich northern sections may have formed at least partly after rifting and break up.

  3. 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.

  4. 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.

  5. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    PubMed

    Kim, Minseong; Kim, GeunHyung

    2015-11-01

    Micro/nanofibrous structures have been applied widely in various tissue-engineering applications because the topological structures are similar to the extracellular matrix (ECM), which encourages a high degree of cell adhesion and growth. However, it has been difficult to produce a three-dimensional (3D) fibrous structure using controllable macro-pores. Recently, cellulose has been considered a high-potential natural-origin biomaterial, but its use in 3D biomedical structures has been limited due to its narrow processing window. Here, we suggest a new 3D cellulose scaffold consisting of multi-layered struts made of submicron-sized entangled fibers that were fabricated using an electrohydrodynamic direct jet (EHDJ) process that is spin-printing. By optimizing processing conditions (electric field strength, cellulose feeding rate, and distance between nozzle and target), we can achieve a multi-layered cellulose structure consisting of the cylindrically entangled cellulose fibers. To compare the properties of the fabricated 3D cellulose structure, we used a PCL fibrous scaffold, which has a similar fibrous morphology and pore geometry, as a control. The physical and in vitro biocompatibilities of both fibrous scaffolds were assessed using human dermal fibroblasts, and the cellulose structure showed higher cell adhesion and metabolic activities compared with the control. These results suggest the EHDJ process to be an effective fabricating tool for tissue engineering and the cellulose scaffold has high potential as a tissue regenerative material.

  6. Enhanced genome annotation using structural profiles in the program 3D-PSSM.

    PubMed

    Kelley, L A; MacCallum, R M; Sternberg, M J

    2000-06-02

    A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18 %. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95 % confidence. 3D-PSSM is available to the community as a web server: http://www.bmm.icnet.uk/servers/3dpssm

  7. Structure light telecentric stereoscopic vision 3D measurement system based on Scheimpflug condition

    NASA Astrophysics Data System (ADS)

    Mei, Qing; Gao, Jian; Lin, Hui; Chen, Yun; Yunbo, He; Wang, Wei; Zhang, Guanjin; Chen, Xin

    2016-11-01

    We designed a new three-dimensional (3D) measurement system for micro components: a structure light telecentric stereoscopic vision 3D measurement system based on the Scheimpflug condition. This system creatively combines the telecentric imaging model and the Scheimpflug condition on the basis of structure light stereoscopic vision, having benefits of a wide measurement range, high accuracy, fast speed, and low price. The system measurement range is 20 mm×13 mm×6 mm, the lateral resolution is 20 μm, and the practical vertical resolution reaches 2.6 μm, which is close to the theoretical value of 2 μm and well satisfies the 3D measurement needs of micro components such as semiconductor devices, photoelectron elements, and micro-electromechanical systems. In this paper, we first introduce the principle and structure of the system and then present the system calibration and 3D reconstruction. We then present an experiment that was performed for the 3D reconstruction of the surface topography of a wafer, followed by a discussion. Finally, the conclusions are presented.

  8. Towards an efficient compression of 3D coordinates of macromolecular structures

    PubMed Central

    Valasatava, Yana; Bradley, Anthony R.; Rose, Alexander S.; Duarte, Jose M.; Prlić, Andreas

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format. PMID:28362865

  9. Towards an efficient compression of 3D coordinates of macromolecular structures.

    PubMed

    Valasatava, Yana; Bradley, Anthony R; Rose, Alexander S; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

  10. 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.

  11. Simulation approach of atomic layer deposition in large 3D structures

    NASA Astrophysics Data System (ADS)

    Schwille, Matthias C.; Barth, Jonas; Schössler, Timo; Schön, Florian; Bartha, Johann W.; Oettel, Martin

    2017-04-01

    We present a new simulation method predicting thicknesses of thin films obtained by atomic layer deposition in high aspect ratio 3D geometries as they appear in MEMS manufacturing. The method features a Monte-Carlo computation of film deposition in free molecular flow, as well as in the Knudsen and diffusive gas regime, applicable for large structures. We compare our approach to analytic and simulation results from the literature. The capability of the method is demonstrated by a comparison to experimental film thicknesses in a large 3D structure. Finally, the feasability to extract process parameters, i.e. sticking coefficients is shown.

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

    PubMed

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

    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 3Å. 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.

  13. 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

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

    PubMed

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

    2016-07-08

    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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Protein-protein interaction networks studies and importance of 3D structure knowledge.

    PubMed

    Lu, Hui-Chun; Fornili, Arianna; Fraternali, Franca

    2013-12-01

    Protein-protein interaction networks (PPINs) are a powerful tool to study biological processes in living cells. In this review, we present the progress of PPIN studies from abstract to more detailed representations. We will focus on 3D interactome networks, which offer detailed information at the atomic level. This information can be exploited in understanding not only the underlying cellular mechanisms, but also how human variants and disease-causing mutations affect protein functions and complexes' stability. Recent studies have used structural information on PPINs to also understand the molecular mechanisms of binding partner selection. We will address the challenges in generating 3D PPINs due to the restricted number of solved protein structures. Finally, some of the current use of 3D PPINs will be discussed, highlighting their contribution to the studies in genotype-phenotype relationships and in the optimization of targeted studies to design novel chemical compounds for medical treatments.

  4. 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.

  5. Voxel-coding method for quantification of vascular structure from 3D images

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Shahrokni, Ali; Zoroofi, Reza A.

    2001-05-01

    This paper presents an image processing method for information extraction from 3D images of vasculature. It automates the study of vascular structures by extracting quantitative information such as skeleton, length, diameter, and vessel-to- tissue ratio for different vessels as well as their branches. Furthermore, it generates 3D visualization of vessels based on desired anatomical characteristics such as vessel diameter or 3D connectivity. Steps of the proposed approach are as follows. (1) Preprocessing, in which intensity adjustment, optimal thresholding, and median filtering are done. (2) 3D thinning, in which medial axis and skeleton of the vessels are found. (3) Branch labeling, in which different branches are identified and each voxel is assigned to the corresponding branch. (4) Quantitation, in which length of each branch is estimated, based on the number of voxels assigned to it, and its diameter is calculated using the medial axis direction. (5) Visualization, in which vascular structure is shown in 3D, using color coding and surface rendering methods. We have tested and evaluated the proposed algorithms using simulated images of multi-branch vessels and real confocal microscopic images of the vessels in rat brains. Experimental results illustrate performance of the methods and usefulness of the results for medical image analysis applications.

  6. 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.

  7. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; ...

    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

  8. 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.

  9. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

    PubMed Central

    Shi, Ya-Zhou; Jin, Lei; Wang, Feng-Hua; Zhu, Xiao-Long; Tan, Zhi-Jie

    2015-01-01

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions. PMID:26682822

  10. Crustal structure along the active Costa Rican volcanic arc

    NASA Astrophysics Data System (ADS)

    Lizarralde, D.; Holbrook, W. S.; van Avendonk, H. J.; Mora Fernandez, M.; Alvarado, G. E.; Harder, S. H.

    2010-12-01

    We present results from an explosion-source seismic refraction transect along the entire active Costa Rican volcanic arc. The seismic data were acquired in 2005 as part of the TICO-CAVA experiment with the goals of delineating the basic crustal architecture of this relatively young volcanic arc, understanding magmatic emplacement processes, and estimating the bulk composition and growth rates of arc crust. The seismic transect extends ~280 km along the axis of the arc and consists of 16 shots (200 - 1200 kg) recorded by 710 seismometers. The active Costa Rican arc consists of two segments with distinct morphologies, the Guanacaste Cordillera (GC) in the north and Central Cordillera (CC) in the south. This segmentation is linked to the subducting Cocos ridge, which occurs beneath the CC and has a northern boundary roughly coincident with the arc segment boundary. Volcanoes of the GC rise from a plateau of ~500 m elevation to maximum heights of ~1500 m, while the CC volcanoes rise from ~1500 m to heights of 3500 m. The crustal structure beneath these segments is distinctly different. The entire arc is covered by a ~5-km-thick carapace with velocities of 4.5-5.8 km/s that probably represent volcaniclastics, flows and small plutons. Beneath the GC, a 1- to 2-km-thick “grainitic” layer (6.0-6.1 km/s) lies beneath the carapace. Velocities below this granitic layer suggest a somewhat more mafic composition, but they increase slowly with depth from 6.2-6.3 km/s between 6-15 km depth. Total crustal thickness beneath the GC is ~40 km, but analysis of crustal thickness is ongoing. The crust beneath Guanacaste thus has a velocity structure very similar to average continental crust, though with slightly slower velocities, perhaps due to high temperatures beneath the arc. As the arc has only been active in this location for <5 m.y., this suggests that either the earlier Neogene arc to the west substantially modified the oceanic-plateau crustal foundation here or that the

  11. 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

  12. Crustal Structure of the Northern Zagros Zone from Seismic Observations

    NASA Astrophysics Data System (ADS)

    Sibol, M.; Gritto, R.; Siegel, J. E.; Ghalib, H. A.; Chen, Y.; Herrmann, R. B.; Aleqab, G. I.; Tkalcic, H.; Quigley, K. C.

    2008-12-01

    The current study is concerned with estimating the local and regional crustal structure of north and northeastern Iraq, including the northern extension of the Zagros collision zone. The goal of our work is to derive local and regional seismic velocity structures using receiver function- and surface wave dispersion analyses and to use these velocity models to obtain accurate hypocenter locations and event focal mechanisms. Global seismic network coverage in this region is poor and extrapolated velocity models found in the literature lack sufficient accuracy to permit events to be located with significant precision. Ten three- component broadband stations composing the North Iraq Seismographic Network (NISN) were installed in late 2005. At present, over 650 GB of seismic waveform data have been analyzed. Our analysis of waveform data indicates clear propagation paths from the south or west across the Arabian shield as well as from the north into NISN. Phases including Pn, Pg, Sn, Lg, as well as LR are clearly observed on these seismograms. In contrast, blockage or attenuation of S-wave energy is observed for propagation paths across the Zagros- Bitlis zone from the east, as well as along the axis of the Zagros from the south-east. Supporting these findings are the results of surface wave analysis. Waves generated by events located to the south of NISN propagating across the Arabian shield produce dispersion curves with energy distributed over a broad frequency band including the development of higher modes. In contrast, waves from events to the south-east which propagate along the axis of the Zagros mountains generate dispersion curves that diverge over a broad frequency range, indicating multi-pathing caused by the complex structure of the Zagros zone. These results are corroborated by receiver function analyses which indicate a dipping Moho beneath the Zagros mountains. While the Moho below the foothills is estimated at 40-50 km depth, it dips to 45-55 km depth

  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. Graphene originated 3D structures grown on the assembled nickel particles

    NASA Astrophysics Data System (ADS)

    Paronyan, Tereza; Harutyunyan, Avetik; Honda Research Institute USA Inc. Team

    2013-03-01

    Recently, the fabrication of various morphologies of graphene originated structures became very important due to the perspective of wide range of new applications. Particularly, free standing 3D structured graphene foams could be imperative in energy related areas . Here, we present the new approach of the CVD growth of 3D graphene network by using primarily sintered Ni particle's (~40 μm size) assembles as a template-catalyst via decomposition of low rate of CH4 at 1100° C based on synthesis method described earlier. SEM and Raman spectra analysis revealed the formation of graphene structure containing a single up to few layers grown on the sintered metal particles served as a catalyst-template. After etching the metal frame without using any support polymer, 3D free-standing graphene microporous structure was formed demonstrating high BET surface area. Two probe measurements of frame resistance were ~2-8 Ω. Our approach allows controllable tune the pore size and thereby the surface area of 3D graphene network through the variation of the template-catalyst particles size.

  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. 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.

  17. 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.

  18. 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.

  19. Studies of the 3D Structure of the Nucleon at Jlab

    SciTech Connect

    Avakian, Harut

    2016-07-01

    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.

  20. 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.

  1. 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.

  2. 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

    2016-08-09

    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.

  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. Recursive estimation of 3D motion and surface structure from local affine flow parameters.

    PubMed

    Calway, Andrew

    2005-04-01

    A recursive structure from motion algorithm based on optical flow measurements taken from an image sequence is described. It provides estimates of surface normals in addition to 3D motion and depth. The measurements are affine motion parameters which approximate the local flow fields associated with near-planar surface patches in the scene. These are integrated over time to give estimates of the 3D parameters using an extended Kalman filter. This also estimates the camera focal length and, so, the 3D estimates are metric. The use of parametric measurements means that the algorithm is computationally less demanding than previous optical flow approaches and the recursive filter builds in a degree of noise robustness. Results of experiments on synthetic and real image sequences demonstrate that the algorithm performs well.

  5. 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

  6. 3D electrical structure of porphyry copper deposit: A case study of Shaxi copper deposit

    NASA Astrophysics Data System (ADS)

    Chen, Xiang-Bin; Lü, Qing-Tian; Yan, Jia-Yong

    2012-06-01

    Located in Lu-Zong ore concentration area, middle-lower Yangtze metallogenic belt, ShaXi porphyry copper deposit is a typical hydrothermal deposit. To investigate the distribution of deep ore bodies and spatial characteristics of host structures, an AMT survey was conducted in mining area. Eighteen pseudo-2D resistivity sections were constructed through careful processing and inversion. These sections clearly show resistivity difference between the Silurian sandstones formation and quartz diorite porphyry and this porphyry copper formation was controlled by the highly resistive anticlines. Using 3D block Kriging interpolation method and 3D visualization techniques, we constructed a detailed 3D resistivity model of quartz diorite porphyry which shows the shape and spatial distribution of deep ore bodies. This case study can serve as a good example for future ore prospecting in and around this mining area.

  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. 3D printed low-loss THz waveguide based on Kagome photonic crystal structure.

    PubMed

    Yang, Jing; Zhao, Jiayu; Gong, Cheng; Tian, Haolin; Sun, Lu; Chen, Ping; Lin, Lie; Liu, Weiwei

    2016-10-03

    A low-loss hollow core terahertz waveguide based on Kagome photonic crystal structure has been designed and fabricated by 3D printing. The 3D printed waveguide has been characterized by using THz time-domain spectroscopy. The results demonstrate that the obtained waveguide features average power propagation loss of 0.02 cm-1 for 0.2-1.0 THz (the minimum is about 0.002 cm-1 at 0.75 THz). More interesting, it could be simply mechanically spliced without any additional alignment, while maintaining the excellent performance. The 3D printing technique will be a promising solution to fabricate Kagome THz waveguide with well controllable characteristics and low cost.

  9. Human Sinoatrial Node Structure: 3D Microanatomy of Sinoatrial Conduction Pathways

    PubMed Central

    Csepe, Thomas A.; Zhao, Jichao; Hansen, Brian J.; Li, Ning; Sul, Lidiya V.; Lim, Praise; Wang, Yufeng; Simonetti, Orlando P.; Kilic, Ahmet; Mohler, Peter J.; Janssen, Paul ML.; Fedorov, Vadim V.

    2016-01-01

    Introduction Despite a century of extensive study on the human sinoatrial node (SAN), the structure-to-function features of specialized SAN conduction pathways (SACP) are still unknown and debated. We report a new method for direct analysis of the SAN microstructure in optically-mapped human hearts with and without clinical history of SAN dysfunction. Methods Two explanted donor human hearts were coronary-perfused and optically-mapped. Structural analyses of histological sections parallel to epicardium (~13-21μm intervals) were integrated with optical maps to create 3D computational reconstructions of the SAN complex. High-resolution fiber fields were obtained using 3D Eigen-analysis of the structure tensor, and used to analyze SACP microstructure with a fiber-tracking approach. Results Optical mapping revealed normal SAN activation of the atria through a lateral SACP proximal to the crista terminalis in Heart #1 but persistent SAN exit block in diseased Heart #2. 3D structural analysis displayed a functionally-observed SAN border composed of fibrosis, fat, and/or discontinuous fibers between SAN and atria, which was only crossed by several branching myofiber tracts in SACP regions. Computational 3D fiber-tracking revealed that myofiber tracts of SACPs created continuous connections between SAN #1 and atria, but in SAN #2, SACP region myofiber tracts were discontinuous due to fibrosis and fat. Conclusions We developed a new integrative functional, structural and computational approach that allowed for the resolution of the specialized 3D microstructure of human SACPs for the first time. Application of this integrated approach will shed new light on the role of the specialized SAN microanatomy in maintaining sinus rhythm. PMID:26743207

  10. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

    PubMed

    Lee, Karen J I; Calder, Grant M; Hindle, Christopher R; Newman, Jacob L; Robinson, Simon N; Avondo, Jerome J H Y; Coen, Enrico S

    2016-12-26

    Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

  11. 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.

  12. Modeling and characterization of 2-D and 3-D textile structural composites

    SciTech Connect

    Yang, J.M.

    1986-01-01

    This dissertation studies the analytical modeling and experimental characterization of various two-dimensional and three-dimensional textile structure composites. In the analytical approach, various theoretical models were established to predict the stiffness, strength, nonlinear deformation, and failure behavior of triaxial woven-fabric composites, 3-D braided composites, and multilayer multidirectional warp knit fabric composites in polymer and metal matrices. The structure performance maps of various textile structural composites were also established, based upon these analytical methods. In the experimental approach, extensive mechanical testing and microstructural characterization were performed to investigate the thermomechanical properties and failure behavior of 3-D braided FP/Al composites. Results of this research will serve as the basis for assessing the potential of textile composites for structural applications.

  13. 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

  14. Cryo-EM structure of a 3D DNA-origami object

    PubMed Central

    Bai, Xiao-chen; Martin, Thomas G.; Scheres, Sjors H. W.; Dietz, Hendrik

    2012-01-01

    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. PMID:23169645

  15. Parametric estimation of 3D tubular structures for diffuse optical tomography.

    PubMed

    Larusson, Fridrik; Anderson, Pamela G; Rosenberg, Elizabeth; Kilmer, Misha E; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L

    2013-02-01

    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.

  16. 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.

  17. ConvNet-Based Localization of Anatomical Structures in 3D Medical Images.

    PubMed

    de Vos, Bob; Wolterink, Jelmer; de Jong, Pim; Leiner, Tim; Viergever, Max; Isgum, Ivana

    2017-02-23

    Localization of anatomical structures is a prerequisite for many tasks in medical image analysis. We propose a method for automatic localization of one or more anatomical structures in 3D medical images through detection of their presence in 2D image slices using a convolutional neural network (ConvNet). A single ConvNet is trained to detect presence of the anatomical structure of interest in axial, coronal, and sagittal slices extracted from a 3D image. To allow the ConvNet to analyze slices of different sizes, spatial pyramid pooling is applied. After detection, 3D bounding boxes are created by combining the output of the ConvNet in all slices. In the experiments 200 chest CT, 100 cardiac CT angiography (CTA), and 100 abdomen CT scans were used. The heart, ascending aorta, aortic arch, and descending aorta were localized in chest CT scans, the left cardiac ventricle in cardiac CTA scans, and the liver in abdomen CT scans. Localization was evaluated using the distances between automatically and manually defined reference bounding box centroids and walls. The best results were achieved in localization of structures with clearly defined boundaries (e.g. aortic arch) and the worst when the structure boundary was not clearly visible (e.g. liver). The method was more robust and accurate in localization multiple structures.

  18. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    NASA Astrophysics Data System (ADS)

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; zur Loye, Hans-Conrad

    2012-11-01

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi2O2(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P21 (a=9.6479(9) Å, b=4.2349(4) Å, c=11.9615(11) Å, β=109.587(1)°), which contains Bi2O2 chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi4Na4(1R3S-cam)8(EtOH)3.1(H2O)3.4 (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P21 (a=19.0855(7) Å, b=13.7706(5) Å, c=19.2429(7) Å, β=90.701(1)°) 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 Bi3+, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer.

  19. Structural and functional imaging of 3D microfluidic mixers using optical coherence tomography.

    PubMed

    Xi, Chuanwu; Marks, Daniel L; Parikh, Devang S; Raskin, Lutgarde; Boppart, Stephen A

    2004-05-18

    To achieve high mixing efficiency in microfluidic devices, complex designs are often required. Microfluidic devices have been evaluated with light and confocal microscopy, but fluid-flow characteristics at different depths are difficult to separate from the en face images produced. By using optical coherence tomography (OCT), an imaging modality capable of imaging 3D microstructures at micrometer-scale resolutions over millimeter-size scales, we obtained 3D dynamic functional and structural data for three representative microfluidic mixers: a Y channel mixer, a 3D serpentine mixer, and a vortex mixer. In the serpentine mixer, OCT image analysis revealed that the mixing efficiency was linearly dependent on the Reynolds number, whereas it appeared to have exponential dependence when imaged with light microscopy. The visual overlap of fluid flows in light-microscopy images leads to an overestimation of the mixing efficiency, an effect that was eliminated with OCT imaging. Doppler OCT measurements determined velocity profiles at various points in the serpentine mixer. Mixing patterns in the vortex mixer were compared with light-microscopy and OCT image analysis. These results demonstrate that OCT can significantly improve the characterization of 3D microfluidic device structure and function.

  20. 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.

  1. 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.

  2. 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.

  3. Pipeline inwall 3D measurement system based on the cross structured light

    NASA Astrophysics Data System (ADS)

    Shen, Da; Lin, Zhipeng; Xue, Lei; Zheng, Qiang; Wang, Zichi

    2014-01-01

    In order to accurately realize the defect detection of pipeline inwall, this paper proposes a measurement system made up of cross structured light, single CCD camera and a smart car, etc. Based on structured light measurement technology, this paper mainly introduces the structured light measurement system, the imaging mathematical model, and the parameters and method of camera calibration. Using these measuring principles and methods, the camera in remote control car platform achieves continuous shooting of objects and real-time rebound processing as well as utilizing established model to extract 3D point cloud coordinate to reconstruct pipeline defects, so it is possible to achieve 3D automatic measuring, and verifies the correctness and feasibility of this system. It has been found that this system has great measurement accuracy in practice.

  4. 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.

  5. The crystal structure of Aspergillus fumigatus cyclophilin reveals 3D domain swapping of a central element.

    PubMed

    Limacher, Andreas; Kloer, Daniel P; Flückiger, Sabine; Folkers, Gerd; Crameri, Reto; Scapozza, Leonardo

    2006-02-01

    The crystal structure of Aspergillus fumigatus cyclophilin (Asp f 11) was solved by the multiwavelength anomalous dispersion method and was refined to a resolution of 1.85 A with R and R(free) values of 18.9% and 21.4%, respectively. Many cyclophilin structures have been solved to date, all showing the same monomeric conformation. In contrast, the structure of A. fumigatus cyclophilin reveals dimerization by 3D domain swapping and represents one of the first proteins with a swapped central domain. The domain-swapped element consists of two beta strands and a subsequent loop carrying a conserved tryptophan. The tryptophan binds into the active site, inactivating cis-trans isomerization. This might be a means of biological regulation. The two hinge loops leave the protein prone to misfolding. In this context, alternative forms of 3D domain swapping that can lead to N- or C-terminally swapped dimers, oligomers, and aggregates are discussed.

  6. Band like Electronic Structures in Square Hollow Quantum Dots by 3D-MHFKS Calculation

    NASA Astrophysics Data System (ADS)

    Takizawa, Tokihiro; Okada, Hoshihito; Matsuse, Takehiro

    To find novel aspects of the electronic structures in quantum dots (QD) from a view point of spatial broken symmetry, 3-dimensional-mesh Hartree-Fock-Kohn-Sham (3D-MHFKS) calculations1 are applied to the interacting electron system of electron number N in a symmetry broken hollow QD. For the case of a square hollow quantum dot confined in square hard wall (HW) potential (SSHQD), the magnetic (B) field dependence of the obtained single particle energy levels and chemical potentials in B-N diagram are shown to have a band like electronic structures over the wide B-field range up to 20T. To clarify the origin of the band like electronic structures in SSHQD, 3D-MHFKS calculations are also applied for the mixed symmetry QD's with a circular hollow in square HW potential (SCHQD) and with a square hollow in circular HW potential (CSHQD).

  7. Effective 3D protein structure prediction with local adjustment genetic-annealing algorithm.

    PubMed

    Zhang, Xiao-Long; Lin, Xiao-Li

    2010-09-01

    The protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing the energy function. The protein folding structure prediction is computationally challenging and has been shown to be NP-hard problem when the 3D off-lattice AB model is employed. In this paper, the local adjustment genetic-annealing (LAGA) algorithm was used to search the ground state of 3D offlattice AB model for protein folding structure. The algorithm included an improved crossover strategy and an improved mutation strategy, where a local adjustment strategy was also used to enhance the searching ability. The experiments were carried out with the Fibonacci sequences. The experimental results demonstrate that the LAGA algorithm appears to have better performance and accuracy compared to the previous methods.

  8. Fabrication of 3D embedded hollow structures inside polymer dielectric PMMA with femtosecond laser

    NASA Astrophysics Data System (ADS)

    Zheng, Chong; Chen, Tao; Hu, Anming; Liu, Shibing; Li, Junwei

    2016-11-01

    Recent progresses in femtosecond laser (fs) manufacturing have already proved that fs laser is a powerful tool in three dimensional internal structure fabrications. However, most studies are mainly focused on realize such structures in inorganic transparent dielectric, such as photosensitive glass and fused silica, etc. In this study, we present two methods to fabricate embedded internal 3D structures in a polymer dielectric material polymethyl methacrylate (PMMA). Both continuous hollow structure such as microfluidic channels and discrete hollow structures such as single microcavities are successfully fabricated with the help of femtosecond lasers. Among them, complicated 3D microchannel with a total length longer than 10mm and diameters around 80μm to 200μm are fabricated with a low repetition rate Ti: sapphire femtosecond laser by direct laser writing at a speed ranging from 25μm/s to 2000μm/s microcavities which function as concave microball lenses (CMBLs) and can be applied in super-wide-angle imaging are fabricated with a high repetition rate femtosecond fiber laser due to the distinct heat accumulation effect after 5s irradiation with the tightly focused fs laser beam. These new approaches proved that femtosecond laser direct writing technology has great application potential in 3D integrated devices manufacturing in the future.

  9. Fragment-based strategy for structural optimization in combination with 3D-QSAR.

    PubMed

    Yuan, Haoliang; Tai, Wenting; Hu, Shihe; Liu, Haichun; Zhang, Yanmin; Yao, Sihui; Ran, Ting; Lu, Shuai; Ke, Zhipeng; Xiong, Xiao; Xu, Jinxing; Chen, Yadong; Lu, Tao

    2013-10-01

    Fragment-based drug design has emerged as an important methodology for lead discovery and drug design. Different with other studies focused on fragment library design and active fragment identification, a fragment-based strategy was developed in combination with three-dimensional quantitative structure-activity relationship (3D-QSAR) for structural optimization in this study. Based on a validated scaffold or fragment hit, a series of structural optimization was conducted to convert it to lead compounds, including 3D-QSAR modelling, active site analysis, fragment-based structural optimization and evaluation of new molecules. 3D-QSAR models and active site analysis provided sufficient information for confirming the SAR and pharmacophoric features for fragments. This strategy was evaluated through the structural optimization on a c-Met inhibitor scaffold 5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one, which resulted in an c-Met inhibitor with high inhibitory activity. Our study suggested the effectiveness of this fragment-based strategy and the druggability of our newly explored active region. The reliability of this strategy indicated it could also be applied to facilitate lead optimization of other targets.

  10. Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins.

    PubMed

    Uversky, Vladimir N

    2015-03-01

    Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins or regions that do not have unique 3D structures under functional conditions. Therefore, from the viewpoint of their lack of stable 3D structure, IDPs/IDPRs are inherently unstable. As much as structure and function of normal ordered globular proteins are determined by their amino acid sequences, the lack of unique 3D structure in IDPs/IDPRs and their disorder-based functionality are also encoded in the amino acid sequences. Because of their specific sequence features and distinctive conformational behavior, these intrinsically unstable proteins or regions have several applications in biotechnology. This review introduces some of the most characteristic features of IDPs/IDPRs (such as peculiarities of amino acid sequences of these proteins and regions, their major structural features, and peculiar responses to changes in their environment) and describes how these features can be used in the biotechnology, for example for the proteome-wide analysis of the abundance of extended IDPs, for recombinant protein isolation and purification, as polypeptide nanoparticles for drug delivery, as solubilization tools, and as thermally sensitive carriers of active peptides and proteins.

  11. Fragment-based strategy for structural optimization in combination with 3D-QSAR

    NASA Astrophysics Data System (ADS)

    Yuan, Haoliang; Tai, Wenting; Hu, Shihe; Liu, Haichun; Zhang, Yanmin; Yao, Sihui; Ran, Ting; Lu, Shuai; Ke, Zhipeng; Xiong, Xiao; Xu, Jinxing; Chen, Yadong; Lu, Tao

    2013-10-01

    Fragment-based drug design has emerged as an important methodology for lead discovery and drug design. Different with other studies focused on fragment library design and active fragment identification, a fragment-based strategy was developed in combination with three-dimensional quantitative structure-activity relationship (3D-QSAR) for structural optimization in this study. Based on a validated scaffold or fragment hit, a series of structural optimization was conducted to convert it to lead compounds, including 3D-QSAR modelling, active site analysis, fragment-based structural optimization and evaluation of new molecules. 3D-QSAR models and active site analysis provided sufficient information for confirming the SAR and pharmacophoric features for fragments. This strategy was evaluated through the structural optimization on a c-Met inhibitor scaffold 5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one, which resulted in an c-Met inhibitor with high inhibitory activity. Our study suggested the effectiveness of this fragment-based strategy and the druggability of our newly explored active region. The reliability of this strategy indicated it could also be applied to facilitate lead optimization of other targets.

  12. 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.

  13. 3D Printed Modeling of the Mitral Valve for Catheter-Based Structural Interventions.

    PubMed

    Vukicevic, Marija; Puperi, Daniel S; Jane Grande-Allen, K; Little, Stephen H

    2017-02-01

    As catheter-based structural heart interventions become increasingly complex, the ability to effectively model patient-specific valve geometry as well as the potential interaction of an implanted device within that geometry will become increasingly important. Our aim with this investigation was to combine the technologies of high-spatial resolution cardiac imaging, image processing software, and fused multi-material 3D printing, to demonstrate that patient-specific models of the mitral valve apparatus could be created to facilitate functional evaluation of novel trans-catheter mitral valve repair strategies. Clinical 3D transesophageal echocardiography and computed tomography images were acquired for three patients being evaluated for a catheter-based mitral valve repair. Target anatomies were identified, segmented and reconstructed into 3D patient-specific digital models. For each patient, the mitral valve apparatus was digitally reconstructed from a single or fused imaging data set. Using multi-material 3D printing methods, patient-specific anatomic replicas of the mitral valve were created. 3D print materials were selected based on the mechanical testing of elastomeric TangoPlus materials (Stratasys, Eden Prairie, Minnesota, USA) and were compared to freshly harvested porcine leaflet tissue. The effective bending modulus of healthy porcine MV tissue was significantly less than the bending modulus of TangoPlus (p < 0.01). All TangoPlus varieties were less stiff than the maximum tensile elastic modulus of mitral valve tissue (3697.2 ± 385.8 kPa anterior leaflet; 2582.1 ± 374.2 kPa posterior leaflet) (p < 0.01). However, the slopes of the stress-strain toe regions of the mitral valve tissues (532.8 ± 281.9 kPa anterior leaflet; 389.0 ± 156.9 kPa posterior leaflet) were not different than those of the Shore 27, Shore 35, and Shore 27 with Shore 35 blend TangoPlus material (p > 0.95). We have demonstrated that patient-specific mitral valve models can be

  14. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

    PubMed

    Miao, Zhichao; Adamiak, Ryszard W; Antczak, Maciej; Batey, Robert T; Becka, Alexander J; Biesiada, Marcin; Boniecki, Michał J; Bujnicki, Janusz; Chen, Shi-Jie; Cheng, Clarence Yu; Chou, Fang-Chieh; Ferré-D'Amaré, Adrian R; Das, Rhiju; Dawson, Wayne K; Feng, Ding; Dokholyan, Nikolay V; Dunin-Horkawicz, Stanisław; Geniesse, Caleb; Kappel, Kalli; Kladwang, Wipapat; Krokhotin, Andrey; Łach, Grzegorz E; Major, François; Mann, Thomas H; Magnus, Marcin; Pachulska-Wieczorek, Katarzyna; Patel, Dinshaw J; Piccirilli, Joseph A; Popenda, Mariusz; Purzycka, Katarzyna J; Ren, Aiming; Rice, Greggory M; Santalucia, John; Sarzynska, Joanna; Szachniuk, Marta; Tandon, Arpit; Trausch, Jeremiah J; Tian, Siqi; Wang, Jian; Weeks, Kevin M; Williams, Benfeard; Xiao, Yi; Xu, Xiaojun; Zhang, Dong; Zok, Tomasz; Westhof, Eric

    2017-01-30

    RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All the puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal notable need for algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

  15. 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

  16. 3D structure tensor analysis of light microscopy data for validating diffusion MRI

    PubMed Central

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A.; Kohama, Steven G.; Jespersen, Sune Nørhøj; Kroenke, Christopher D.

    2015-01-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image “stacks” acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations

  17. Functional classification of protein 3D structures from predicted local interaction sites.

    PubMed

    Parasuram, Ramya; Lee, Joslynn S; Yin, Pengcheng; Somarowthu, Srinivas; Ondrechen, Mary Jo

    2010-12-01

    A new approach to the functional classification of protein 3D structures is described with application to some examples from structural genomics. This approach is based on functional site prediction with THEMATICS and POOL. THEMATICS employs calculated electrostatic potentials of the query structure. POOL is a machine learning method that utilizes THEMATICS features and has been shown to predict accurate, precise, highly localized interaction sites. Extension to the functional classification of structural genomics proteins is now described. Predicted functionally important residues are structurally aligned with those of proteins with previously characterized biochemical functions. A 3D structure match at the predicted local functional site then serves as a more reliable predictor of biochemical function than an overall structure match. Annotation is confirmed for a structural genomics protein with the ribulose phosphate binding barrel (RPBB) fold. A putative glucoamylase from Bacteroides fragilis (PDB ID 3eu8) is shown to be in fact probably not a glucoamylase. Finally a structural genomics protein from Streptomyces coelicolor annotated as an enoyl-CoA hydratase (PDB ID 3g64) is shown to be misannotated. Its predicted active site does not match the well-characterized enoyl-CoA hydratases of similar structure but rather bears closer resemblance to those of a dehalogenase with similar fold.

  18. 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.

  19. Comparison of low cost 3D structured light scanners for face modeling.

    PubMed

    Bakirman, Tolga; Gumusay, Mustafa Umit; Reis, Hatice Catal; Selbesoglu, Mahmut Oguz; Yosmaoglu, Serra; Yaras, Mehmet Cem; Seker, Dursun Zafer; Bayram, Bulent

    2017-02-01

    This study aims to compare three different structured light scanner systems to generate accurate 3D human face models. Among these systems, the most dense and expensive one was denoted as the reference and the other two that were low cost and low resolution were compared according to the reference system. One female face and one male face were scanned with three light scanner systems. Point-cloud filtering, mesh generation, and hole-filling steps were carried out using a trial version of commercial software; moreover, the data evaluation process was realized using CloudCompare open-source software. Various filtering and mesh smoothing levels were applied on reference data to compare with other low-cost systems. Thus, the optimum reduction level of reference data was evaluated to continue further processes. The outcome of the presented study shows that low-cost structured light scanners have a great potential for 3D object modeling, including the human face. A considerable cheap structured light system has been used due to its capacity to obtain spatial and morphological information in the case study of 3D human face modeling. This study also discusses the benefits and accuracy of low-cost structured light systems.

  20. 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

    2015-05-28

    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.

  1. Rapid Fabrication of Cell-Laden Alginate Hydrogel 3D Structures by Micro Dip-Coating

    PubMed Central

    Ghanizadeh Tabriz, Atabak; Mills, Christopher G.; Mullins, John J.; Davies, Jamie A.; Shu, Wenmiao

    2017-01-01

    Development of a simple, straightforward 3D fabrication method to culture cells in 3D, without relying on any complex fabrication methods, remains a challenge. In this paper, we describe a new technique that allows fabrication of scalable 3D cell-laden hydrogel structures easily, without complex machinery: the technique can be done using only apparatus already available in a typical cell biology laboratory. The fabrication method involves micro dip-coating of cell-laden hydrogels covering the surface of a metal bar, into the cross-linking reagents calcium chloride or barium chloride to form hollow tubular structures. This method can be used to form single layers with thickness ranging from 126 to 220 µm or multilayered tubular structures. This fabrication method uses alginate hydrogel as the primary biomaterial and a secondary biomaterial can be added depending on the desired application. We demonstrate the feasibility of this method, with survival rate over 75% immediately after fabrication and normal responsiveness of cells within these tubular structures using mouse dermal embryonic fibroblast cells and human embryonic kidney 293 cells containing a tetracycline-responsive, red fluorescent protein (tHEK cells). PMID:28286747

  2. 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

  3. LigandBox: A database for 3D structures of chemical compounds.

    PubMed

    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.

  4. 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.

  5. Propagation of Coronal Mass Ejections in 3D and the Structure of the Inner Heliosphere

    NASA Astrophysics Data System (ADS)

    Gallagher, P. T.; Byrne, J. P.; Maloney, S. A.; McAteer, J.

    2011-12-01

    Solar coronal mass ejections (CMEs) are the most significant drivers of adverse space weather on Earth, but the physics governing their propagation through the heliosphere is not well understood. Although stereoscopic imaging of CMEs with NASA's Solar Terrestrial Relations Observatory (STEREO) has provided some insight into their three-dimensional (3D) propagation, the mechanisms governing their evolution remain unclear because of difficulties in reconstructing their true 3D structure. In this talk I will describe the use of an elliptical tie-pointing technique to reconstruct a CME front in 3D, enabling us to quantify its deflected trajectory from high latitudes along the ecliptic, and measure its increasing angular width and propagation. At large distances from the Sun (>7 R_sun), I will describe how its motion is determined by drag effects in the solar wind, using ENLIL simulations of the inner heliosphere. By combining a 3D reconstruction with modelling of the solar wind, we predict an arrival time within 30 mins of the in-situ detection of the CME at ACE

  6. 3D analysis of vortical structures in an abdominal aortic aneurysm by stereoscopic PIV

    NASA Astrophysics Data System (ADS)

    Deplano, Valérie; Guivier-Curien, Carine; Bertrand, Eric

    2016-11-01

    The present work presents an experimental in vitro three-dimensional analysis of the flow dynamics in an abdominal aortic aneurysm (AAA) through stereoscopic particle image velocimetry (SPIV) measurements. The experimental set-up mimics the pathophysiological context involving a shear thinning blood analogue fluid, compliant AAA and aorto-iliac bifurcation walls and controlled inlet and outlet flow rate and pressure waveforms as well as working fluid temperature. SPIV was carefully calibrated and conducted to assess the three velocity components in the AAA volume. For the first time in the literature, the 3D vortex ring genesis, propagation, and vanishing in the AAA bulge are experimentally described and quantified. In comparison with classical 2-component PIV measurements (2C PIV), the third component of the velocity vector was shown to be of importance in such a geometry, especially, during the deceleration phase of the flow rate. The 3D velocity magnitude reached up more than 20 % of the 2D one showing that 2C PIV are definitively not accurate enough to provide a complete description of flow behaviour in an AAA. In addition to potential clinical implications of a full 3D vortex ring description in AAA evolution, the 3D in vitro experimental quantification of the flow dynamics carried out in the present study offers an interesting tool for the validation of fluid-structure interaction numerical studies dealing with AAA.

  7. 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

  8. Ambient Noise Tomography of Canada: Crustal Structures, Lithosphere Temperatures and Topography

    NASA Astrophysics Data System (ADS)

    Currie, C. A.; Kao, H.; Behr, Y.; Hyndman, R. D.; Townend, J.

    2012-12-01

    The continental lithosphere of Canada contains a record of tectonic events that have shaped this region over the last 4 Ga, from the ancient orogens that formed the cratonic core to ongoing deformation of the more juvenile accreted terranes of the Canadian Cordillera. This study presents the first continental-scale study of the shear wave velocity structure of Canada using ambient noise tomography, which allows better resolution than previous tomography models based on earthquake waveforms. The analysis includes data recorded from 2003 to 2009 at 788 seismic stations covering Canada and adjacent regions. Vertical-component recordings are used to map Rayleigh wave velocities at different periods and thereby construct a pseudo-3D shear wave velocity (Vs) model extending to ~100 km depth. The Vs model exhibits pronounced spatial variations. Within the Canadian Cordillera, a velocity discontinuity is observed at ~10 km depth that may mark a mid-crustal detachment separating largely felsic upper crustal rocks from more mafic rocks. In the stable craton region, velocity variations appear to correspond with terrane boundaries mapped in surface geology. Crustal thickness varies between 30 and 50 km, with the thinnest crust below the Canadian Cordillera and thicker crust underlying the southwest part of the Western Canada Sedimentary Basin, the northern United States between 90W and 115W, and Lake Erie. In many areas, the Moho is a well-defined velocity discontinuity of a few km, but in some places (e.g., the western edge of the Western Canada Sedimentary Basin), the velocities exhibit a vertical gradation over ~10 km, suggesting that there may be a zone of mixing between crustal and mantle rocks or areas where the lowermost crust is partially eclogitized. In the mantle, the largest velocity contrast is between the low velocity Canadian Cordillera and the high velocity craton. Within the craton, there are well-resolved regional variations that appear to correspond with

  9. Determination and validation of mTOR kinase-domain 3D structure by homology modeling.

    PubMed

    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.

  10. 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.

  11. Analysis of the 3D Structure and Velocity of a CME on 2 January 2008

    NASA Astrophysics Data System (ADS)

    López, F. M.; Cremades, H.

    We perform an analysis of the 3D structure and velocity of a CME (coronal mass ejection) ejected on 2 January 2008. The event was imaged by both STEREO A and B spacecraft (mutual separation of ˜44°), providing polarized images of the event from two different points of view. To obtain information on the 3D structure of the CME from polarized images, a polarization technique (Moran & Davila, Science 305, 66, 2003) is applied. Aided by this method, we have constructed topographical maps which show the height of the various event features from the plane of the sky (i.e. toward or away from the observer) and have dinamically analyzed and compared the real and projected on the plane of the sky velocities.

  12. 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.

  13. 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.

  14. Analysis and 3D visualization of structures of animal brains obtained from histological sections

    NASA Astrophysics Data System (ADS)

    Forero-Vargas, Manuel G.; Fuentes, Veronica; Lopez, D.; Moscoso, A.; Merchan, Miguel A.

    2002-11-01

    This paper presents a new application for the analysis of histological sections and their 3D visualization. The process is performed in few steps. First, a manual process is necessary to determine the regions of interest, including image digitalization, drawing of borders and alignment between all images. Then, a reconstruction process is made. After sampling the contour, the structure of interest is displayed. The application is experimentally validated and some results on histological sections of a rodent's brain (hamster and rat) are shown.

  15. The crustal structure of Egypt and the northern Red Sea region

    NASA Astrophysics Data System (ADS)

    Hosny, Ahmed; Nyblade, Andrew

    2016-09-01

    P-wave receiver functions from 26 stations in the Egyptian National Seismic Network (ENSN) have been modeled using the H-k stacking method and in a joint inversion method with Rayleigh wave group velocities to investigate crustal structure across Egypt and the northern Red Sea region. The new estimates of crustal structure, when combined with previous results, show that along the rifted margins of the Red Sea, Gulf of Suez and Gulf of Aqaba crustal thickness ranges from 25 to 30 km, the average crustal Vp/Vs ratio is 1.77, and the average crustal shear-wave velocity is 3.6 km/s. Beneath northern and central Egypt, including the Sinai Peninsula, crustal thickness ranges from 32 to 38 km, the average crustal Vp/Vs ratio is 1.79, and the average crustal shear-wave velocity is 3.5 km/s. Beneath southern Egypt, crustal thickness ranges from 35 to 40 km, the average crustal Vp/Vs ratio is 1.76, and the average crustal shear-wave velocity is 3.7 km/s. In southern Egypt, the crust is also characterized by a 10-20 km thick mafic lower crust. These findings indicate that crust along the rifted margins of the northern Red Sea, and Gulfs of Suez and Aqaba have been thinned by about 5 to 10 km. The thick mafic lower crust in southern Egypt can be attributed to suturing during the Neoproterozoic collision of east Gondwana against the Sahara metacraton. Overall, the structure of the crust in Egypt away from the northern Red Sea region is similar to the structure of Precambrian crust in many other parts of Africa.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Crustal structures from the Wuyi-Yunkai orogen to the Taiwan orogen: The onshore-offshore wide-angle seismic experiments of the TAIGER and ATSEE projects

    NASA Astrophysics Data System (ADS)

    Kuo, Yao-Wen; Wang, Chien-Ying; Kuo-Chen, Hao; Jin, Xin; Cai, Hui-Teng; Lin, Jing-Yi; Wu, Francis T.; Yen, Horng-Yuan; Huang, Bor-Shouh; Liang, Wen-Tzong; Okaya, David; Brown, Larry

    2016-12-01

    Knowledge of the crustal structure is important for understanding the tectonic framework and geological evolution of southeastern China and adjacent areas. In this study, we integrated the datasets from the TAIGER (TAiwan Integrated GEodynamic Research) and ATSEE (Across Taiwan Strait Explosion Experiment) projects to resolve onshore-offshore deep crustal seismic profiles from the Wuyi-Yunkai orogen to the Taiwan orogen in southeastern China. Three seismic profiles were resolved, and the longest profile was 850 km. Unlike 2D and 3D first arrival travel-time tomography from previous studies, we used both refracted and reflected phases (Pg, Pn, PcP, and PmP) to model the crustal structures and the crustal reflectors. In total, data from 40 shots, 2 earthquakes, and approximately 1,950 stations were used; 15,612 arrivals were selected among three transects. Using these data, we determined the complex crustal evolution since the Paleozoic era , involving the closed Paleozoic rift basin in central Fujian, the Cenozoic extension due to the South China Sea opening beneath the coastline of southern Fujian, and the on-going collision of the Taiwan orogen. The shape of the Moho, which also reflects the crustal evolution, can be summarized as follows: 30 km deep to the west of Fujian, deepening toward central Fujian ( 35 km), becoming shallower toward the Taiwan Strait ( 28 km), deepening again toward the mountain belt of Taiwan ( 42 km), and becoming shallower toward the Pacific Ocean ( 10 km).

  1. [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].

    PubMed

    Korkosh, V S; Zhorov, B S; Tikhonov, D B

    2016-01-01

    An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

  2. 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.

  3. 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.

  4. 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.; 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.

  5. 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.

  6. 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).

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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

    2015-09-08

    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.

  12. 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.

  13. 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

  14. 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.

  15. Development of biologically active compounds by combining 3D QSAR and structure-based design methods

    NASA Astrophysics Data System (ADS)

    Sippl, Wolfgang

    2002-11-01

    One of the major challenges in computational approaches to drug design is the accurate prediction of the binding affinity of novel biomolecules. In the present study an automated procedure which combines docking and 3D-QSAR methods was applied to several drug targets. The developed receptor-based 3D-QSAR methodology was tested on several sets of ligands for which the three-dimensional structure of the target protein has been solved - namely estrogen receptor, acetylcholine esterase and protein-tyrosine-phosphatase 1B. The molecular alignments of the studied ligands were determined using the docking program AutoDock and were compared with the X-ray structures of the corresponding protein-ligand complexes. The automatically generated protein-based ligand alignment obtained was subsequently taken as basis for a comparative field analysis applying the GRID/GOLPE approach. Using GRID interaction fields and applying variable selection procedures, highly predictive models were obtained. It is expected that concepts from receptor-based 3D QSAR will be valuable tools for the analysis of high-throughput screening as well as virtual screening data

  16. 3D Density Structure and LOS Observations of a Model CME

    NASA Astrophysics Data System (ADS)

    Manchester, W. B.; Lugaz, N.; Gombosi, T.; de Zeeuw, D.; Sokolov, I.; Toth, G.

    2004-12-01

    We present synthetic Thomson-scattered white-light images of a simulated coronal mass ejection (CME). The simulations are based on a 3-D MHD model of a CME propagating through a bimodal solar wind characteristic of solar minimum. The CME is driven by a 3-D Gibson-Low flux rope inserted in the helmet streamer of the steady-state corona. Synthetic coronograph images are produced that follow the evolution of the CME to 1 AU from several points of view. The white light images provide a basis for comparison with wide angle coronographs, like those of SMEI or STEREO. We find that a large amount of plasma is swept up from the solar wind by the CME-driven shock wave, which dominates the density structure far from the Sun. We also find that the shape of this compressed plasma is highly distorted by the variation in speed of the ambient solar wind. Comparisons of 2-D integrated images to the 3-D density structure show that the viewing angle severely effects the line-of-sight appearance of the CME, as well as the estimated mass of the CME from such 2D images.

  17. 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.

  18. 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

  19. 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.

  20. Structured light 3D tracking system for measuring motions in PET brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Jørgensen, Morten R.; Paulsen, Rasmus R.; Højgaard, Liselotte; Roed, Bjarne; Larsen, Rasmus

    2010-02-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a DLP projector and a CCD camera is set up on a model of the High Resolution Research Tomograph (HRRT). Methods to reconstruct 3D point clouds of simple surfaces based on phase-shifting interferometry (PSI) are demonstrated. The projector and camera are calibrated using a simple stereo vision procedure where the projector is treated as a camera. Additionally, the surface reconstructions are corrected for the non-linear projector output prior to image capture. The results are convincing and a first step toward a fully automated tracking system for measuring head motions in PET imaging.

  1. Imaging and 3D reconstruction of cerebrovascular structures in embryonic zebrafish.

    PubMed

    Ethell, Douglas W; Cameron, D Joshua

    2014-04-22

    Zebrafish are a powerful tool to study developmental biology and pathology in vivo. The small size and relative transparency of zebrafish embryos make them particularly useful for the visual examination of processes such as heart and vascular development. In several recent studies transgenic zebrafish that express EGFP in vascular endothelial cells were used to image and analyze complex vascular networks in the brain and retina, using confocal microscopy. Descriptions are provided to prepare, treat and image zebrafish embryos that express enhanced green fluorescent protein (EGFP), and then generate comprehensive 3D renderings of the cerebrovascular system. Protocols include the treatment of embryos, confocal imaging, and fixation protocols that preserve EGFP fluorescence. Further, useful tips on obtaining high-quality images of cerebrovascular structures, such as removal the eye without damaging nearby neural tissue are provided. Potential pitfalls with confocal imaging are discussed, along with the steps necessary to generate 3D reconstructions from confocal image stacks using freely available open source software.

  2. 3-D multiobservable probabilistic inversion for the compositional and thermal structure of the lithosphere and upper mantle: III. Thermochemical tomography in the Western-Central U.S.

    NASA Astrophysics Data System (ADS)

    Afonso, Juan Carlos; Rawlinson, Nicholas; Yang, Yingjie; Schutt, Derek L.; Jones, Alan G.; Fullea, Javier; Griffin, William L.

    2016-10-01

    We apply a novel 3-D multiobservable probabilistic tomography method that we have recently developed and benchmarked, to directly image the thermochemical structure of the Colorado Plateau and surrounding areas by jointly inverting P wave and S wave teleseismic arrival times, Rayleigh wave dispersion data, Bouguer anomalies, satellite-derived gravity gradients, geoid height, absolute (local and dynamic) elevation, and surface heat flow data. The temperature and compositional structures recovered by our inversion reveal a high level of correlation between recent basaltic magmatism and zones of high temperature and low Mg# (i.e., refertilized mantle) in the lithosphere, consistent with independent geochemical data. However, the lithospheric mantle is overall characterized by a highly heterogeneous thermochemical structure, with only some features correlating well with either Proterozoic and/or Cenozoic crustal structures. This suggests that most of the present-day deep lithospheric architecture reflects the superposition of numerous geodynamic events of different scale and nature to those that created major crustal structures. This is consistent with the complex lithosphere-asthenosphere system that we image, which exhibits a variety of multiscale feedback mechanisms (e.g., small-scale convection, magmatic intrusion, delamination, etc.) driving surface processes. Our results also suggest that most of the present-day elevation in the Colorado Plateau and surrounding regions is the result of thermochemical buoyancy sources within the lithosphere, with dynamic effects (from sublithospheric mantle flow) contributing only locally up to ˜15-35%.

  3. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Astrophysics Data System (ADS)

    Nandhakumar, N.; Smith, Philip W.

    1993-12-01

    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.

  4. 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.

  5. 1d, 2d, and 3d periodic structures: Electromagnetic characterization, design, and measurement

    NASA Astrophysics Data System (ADS)

    Brockett, Timothy John

    Periodic structures have many useful applications in electromagnetics including phased arrays, frequency selective surfaces, and absorbing interfaces. Their unique properties can be used to provide increased performance in antenna gain, electromagnetic propagation, and electromagnetic absorption. In antenna arrays, repeating elements create a larger eective aperture, increasing the gain of the antenna and the ability to scan the direction of the main beam. Three-dimensional periodic structures, such as an array of shaped pillars such as columns, cones, or prisms have the potential of improving electromagnetic absorption, improving performance in applications such as solar cell eciency and absorbing interfaces. Furthermore, research into periodic structures is a continuing endeavor where novel approaches and analysis in appropriate applications can be sought. This dissertation will address the analysis, diagnostics, and enhancement of 1D, 2D, and 3D periodic structures for antenna array applications and solar cell technology. In particular, a unique approach to array design will be introduced to prevent the appearance of undesirable grating lobes in large antenna arrays that employ subarrays. This approach, named the distortion diagnostic procedure, can apply directly to 1D and 2D periodic structures in the form of planar antenna arrays. Interesting corollaries included here are developments in millimeter-wave antenna measurements including spiral planar scanning, phaseless measurements, and addressing antennas that feature an internal source. Finally, analysis and enhancement of 3D periodic structures in nanostructure photovoltaic arrays and absorbing interfaces will be examined for their behavior and basic operation in regards to improved absorption of electromagnetic waves.

  6. 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.

  7. 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

  8. Protein contact maps: A binary depiction of protein 3D structures

    NASA Astrophysics Data System (ADS)

    Emerson, Isaac Arnold; Amala, Arumugam

    2017-01-01

    In recent years, there has been a considerable interest in examining the structure and dynamics of complex networks. Proteins in 3D space may also be considered as complex systems emerged through the interactions of their constituent amino acids. This representation provides a powerful framework to uncover the general organized principle of protein contact network. Here we reviewed protein contact map in terms of protein structure prediction and analyses. In addition, we had also discussed the various computational techniques for the prediction of protein contact maps and the tools to visualize contact maps.

  9. 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

  10. A 3D model describing the initial structure of an artificial hydrological catchment

    NASA Astrophysics Data System (ADS)

    Maurer, T.; Schneider, A.; Buczko, U.; Gerke, H. H.

    2009-04-01

    The initial development stages of artificially constructed hydrologic catchments are characterized by the absence of vegetation, soil organic matter and soil horizons. This results in increased surface runoff and favors erosion processes that dominate the initial phase. Hydraulic conditions on artificial catchments thus are governed by rapidly changing surface structures as well as by the primary internal structural framework. Contemporary hydrological modeling does not consider any dynamic change of relevant structural features but rather assumes a stable, invariant landscape. The objective of this study was the digital visualization and quantitative description of the initial state and its early structural dynamics, exemplified for the small artificial hydrological catchment "Huehnerwasser" near Cottbus, Germany. Photogrammetric surveys of surface and internal structural units (clay basis liner) during the construction phase provided spatially and temporally resolved data for digital elevation models (DEM). Interpolated physical and chemical soil properties obtained at a borehole grid (e.g., texture) are used for the visualization of spatial distribution of relevant (hydraulic) parameters. The data are merged in a database and visualized in the 3D-GIS application GoCAD. The specific technological construction processes determines the internal structure of the artificial catchment. Resulting differences in bulk density and texture are supposed to have considerable impact on hydraulic properties. A structure generator program was implemented to reproduce the initial structure of the sediment layer as closely as possible. Results of the digital structure generation are checked with non-invasive geophysical measurements, on-site bore holes data and off-site 2D vertical spoil exploration. The accuracy of structure generator results will be compared with predictions of different interpolation methods. Thus, the structure model will serve as a basis for deriving the 3D

  11. Towards Automated Seismic Moment Tensor Inversion in Australia Using 3D Structural Model

    NASA Astrophysics Data System (ADS)

    Hingee, M.; Tkalcic, H.; Fichtner, A.; Sambridge, M.; Kennett, B. L.; Gorbatov, A.

    2009-12-01

    There is significant seismic activity in the region around Australia, largely due to the plate boundaries to the north and to the east of the mainland. This seismicity poses serious seismic and tsunamigenic hazard in a wider region, and risk to coastal areas of Australia, and is monitored by Geoscience Australia (GA) using a network of permanent broadband seismometers within Australia. Earthquake and tsunami warning systems were established by the Australian Government and have been using the waveforms from the GA seismological network. The permanent instruments are augmented by non-GA seismic stations based both within and outside of Australia. In particular, seismic moment tensor (MT) solutions for events around Australia as well as local distances are useful for both warning systems and geophysical studies in general. These monitoring systems, however, currently use only one dimensional, spherically-symmetric models of the Earth for source parameter determination. Recently, a novel 3D model of Australia and the surrounding area has been developed from spectral element simulations [1], taking into account not only velocity heterogeneities, but also radial anisotropy and seismic attenuation. This development, inter alia, introduces the potential of providing significant improvements in MT solution accuracy. Allowing reliable MT solutions with reduced dependence on non-GA stations is a secondary advantage. We studied the feasibility of using 1D versus 3D structural models. The accuracy of the 3D model has been investigated, confirming that these models are in most cases superior to the 1D models. A full MT inversion method using a point source approximation was developed as the first step, keeping in mind that for more complex source time functions, a finite source inversion will be needed. Synthetic experiments have been performed with random noise added to the signal to test the code in the both 1D and 3D setting, using a precomputed library of structural Greens

  12. 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

  13. Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

    PubMed

    Hossain, Md Anowar; Roslan, Hairul Azman

    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.

  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. Uncovering the structural basis of protein interactions with efficient clustering of 3-D interaction interfaces.

    PubMed

    Aung, Z; Tan, S-H; Ng, S-K; Tan, K-L

    2007-01-01

    The biological mechanisms with which proteins interact with one another are best revealed by studying the structural interfaces between interacting proteins. Protein-protein interfaces can be extracted from 3-D structural data of protein complexes and then clustered to derive biological insights. However, conventional protein interface clustering methods lack computational scalability and statistical support. In this work, we present a new method named "PPiClust" to systematically encode, cluster and analyze similar 3-D interface patterns in protein complexes efficiently. Experimental results showed that our method is effective in discovering visually consistent and statistically significant clusters of interfaces, and at the same time sufficiently time-efficient to be performed on a single computer. The interface clusters are also useful for uncovering the structural basis of protein interactions. Analysis of the resulting interface clusters revealed groups of structurally diverse proteins having similar interface patterns. We also found, in some of the interface clusters, the presence of well-known linear binding motifs which were non-contiguous in the primary sequences. These results suggest that PPiClust can discover not only statistically significant but also biologically significant protein interface clusters from protein complex structural data.

  16. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular